Probabilistic Interpretations for MYCIN’s Certainty Factors
UAI-P-1985-PG-9-20 | November 2016
In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA
Publications
Publications by Year
-
Impact of Pre-Adapted HIV Transmission
Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
Nature Medicine | May 2016, Vol 22: pp. 606-613
Bonnie Mathieson Young Investigator Award
Linear mixed model for heritability estimation that explicitly addresses environmental variation
David Heckerman, Deepti Gurdasani, Carl Kadie, Cristina Pomilla, Tommy Carstensen, Hilary Martin, Kenneth Ekoru, Rebecca N. Nsubuga, Gerald Ssenyomo, Anatoli Kamali, Pontiano Kaleebu, Christian Widmer, Manjinder S. Sandhu
Proceedings of the National Academy of Sciences | April 2016
-
Computational and Statistical Issues in Personalized Medicine
Christoph Lippert, David Heckerman
XRDS: Crossroads, The ACM Magazine for Students - Computational Biology | July 2015, Vol 24(4): pp. 24-27
Anti-Hepatitis C Virus T-Cell Immunity in the Context of Multiple Exposures to the Virus
Katja Pfafferott, Pooja Deshpande, Elizabeth McKinnon, Shahzma Merani, Andrew Lucas, David Heckerman, Simon Mallal, Mina John, Silvana Gaudieri, Michaela Lucas
June 2015
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
Garbiel R. A. Margarido, David Heckerman
PLoS Comput Biol | April 2015
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of virology | April 2015, Vol 89: pp. 4015-4019
Accurate Liability Estimation Improves Power in Ascertained Case-Control Studies
Omer Weissbrod, Christoph Lippert, Dan Geiger, David Heckerman
Nature Methods | February 2015, Vol 12: pp. 332-334
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of Virology | January 2015
-
Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
October 2014
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Bioinformatics | September 2014, pp. btu504
Addendum on the scoring of Gaussian directed acyclic graphical models
Jack Kuipers, Giusi Moffa, David Heckerman
Annal Statistics | August 2014, Vol 42: pp. 1689-1691
HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes
Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker
Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948
Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
Science | July 2014, Vol 345(6193)
Publication Publication Publication Publication Publication Project
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas S. Richardson
Kybernetika | July 2014
Eliciting cytotoxic T-lymphocyte responses from synthetic vectors containing one or two epitopes in a C57BL/6 mouse model using peptide-containing biodegradable microspheres and adjuvants
R. M. Rubsamen, C. V. Herst, P. M. Lloyd, David Heckerman
June 2014
Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
Quantifying the Uncertainty in Heritability
Nicholas Furlotte, David Heckerman, Christoph Lippert
MSR-TR-2014-161 | March 2014
-
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
eLife | October 2013
Epigenome-wide association studies without the need for cell-type composition
James Zhou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
Nature Methods | August 2013
Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication
Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm
Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365
The benefits of selecting phenotype-specific variants for applications of mixed models in genomics
Christoph Lippert, Gerald Quon, Eun Yong Kang, Carl Kadie, Jennifer Listgarten, David Heckerman
MSR-TR-2013-138 | May 2013
Influence of HLA-C Expression Level on HIV Control
Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington
Science | April 2013, Vol 340(6128): pp. 87-91
FaST-LMM-Select for addressing confounding from spatial structure and rare variants
Jennifer Listgarten, Christoph Lippert, David Heckerman
MSR-TR-2013-137 | April 2013
Second International Enterprise Distributed Object Computing Workshop (EDOC )
HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes
Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John
AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905
Causal Independence for Knowledge Acquisition and Inference
MSR-TR-93-10 | March 2013
HIV-1 p24gag Derived Conserved Element DNA Vaccine Increases the Breadth of Immune Response in Mice
Viraj Kulkarni, Margherita Rosati, Antonio Valentin, Brunda Ganneru, Ashish K. Singh, Jian Yan, Morgane Rolland, Candido Alicea, Rachel Kelly Beach, Gen-Mu Zhang, Sylvie Le Gall, Kate E. Broderick, Niranjan Y. Sardesai, David Heckerman, Beatriz Mothe, Christian Brander, David B. Weiner, James I. Mullins, George N. Pavlakis, Barbara K. Felber
PLoS ONE | March 2013, pp. e60245
Asymptotic Model Selection for Directed Networks with Hidden Variables
Dan Geiger, David Heckerman, Chris Meek
MSR-TR-96-07 | February 2013
An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data
Christoph Lippert, Jennifer Listgarten, Bob Davidson, Jeff Baxter, Hoifung Poon, Carl Kadie, David Heckerman
Scientific Reports | January 2013, Vol 3
High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control
Zaza M. Ndhlovu, Lori B. Chibnik, Jacqueline Proudfoot, Seanna Vine, Ashley McMullen, Kevin Cesa, Filippos Porichis, R. Brad Jones, Donna Marie Alvino, Meghan G. Hart, Eleni Stampouloglou, Alicja Piechocka-Trocha, Carl Kadie, Florencia Pereyra, David Heckerman, Philip L. De Jager, Bruce D. Walker, Daniel E. Kaufmann
Blood Journal | January 2013, Vol 121(5)
An Experimental Comparison of Several Clustering and Initialization Methods
Marina Meila, David Heckerman
MSR-TR-98-06 | January 2013
Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins
Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen
January 2013
A powerful and efficient set test for genetic markers that handles confounders
Jennifer Listgarten, Christoph Lippert, Carl Kadie, David Heckerman
Bioinformatics | January 2013
-
Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme
Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216
Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope
Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder
Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654
Extraneous markers used for genetic similarity leads to loss of power in GWAS and heritability determination
Christoph Lippert, Gerald Quon, Jennifer Listgarten, David Heckerman
MSR-TR-2012-120 | December 2012
Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan
Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura
Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476
Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis
Jessica L. Prince, Daniel T. Claiborne, Jonathan M. Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A. Prentice, Ling Yue, Sundaram A. Vishwanathan, William Kilembe, Paul Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter
PLoS Pathogens | November 2012, pp. e1003041
Co-operative additive effects between HLA alleles in control of HIV-1
Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
PLoS ONE | October 2012, pp. e47799
Improved Learning in U.S. History and Decision Competence with Decision-Focused Curriculum
David Jacobson, Andrew Parker, Chris Spetzler, Wandi Bruine de Bruin, Keith Hollenbeck, David Heckerman, Baruch Fischhoff
PLoS ONE | September 2012
Patterns of methylation heritability in a genome-wide analysis of four brain regions
Gerald Quon, Christoph Lippert, David Heckerman, Jennifer Listgarten
Nucleic Acids Research | August 2012
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans
Paul J. McLaren, Stephan Ripke, Kimberly Pelak, Amy C. Weintrob, Nikolaos A. Patsopoulos, Xiaoming Jia, Rachel L. Erlich, Niall J. Lennon, Carl Kadie, David Heckerman, Namrata Gupta, David W. Haas, Steven G. Deeks, Florencia Pereyra, Bruce D. Walker, Paul I. W. de Bakker
Human Molecular Genetics | June 2012, Vol 21(19): pp. 4334-4347
Improved linear mixed models for genome-wide association studies
Jennifer Listgarten, Christoph Lippert, Carl Kadie, Robert I. Davidson, Eleazar Eskin, David Heckerman
Nature Methods | May 2012, Vol 9: pp. 3–4
Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243
Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity
Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme
Journal of Virology | April 2012
Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
February 2012
High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection
Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John
Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234
CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Jennifer Zamarreno, Mattia Schiaulini, Cristina Miranda, Marta Ruiz-Riol, Christoph T. Berger, M. Jose Herrero, Eduard Palou, Montse Plana, Morgane Rolland, Ashok Khatri, David Heckerman, Florencia Pereyra, Bruce D. Walker, David Weiner, Roger Paredes, Bonaventura Clotet, Barbara K. Felber, George N. Pavlakis, James I. Mullins, Chirstian Brander
PLoS ONE | January 2012, pp. e29717
-
HIV-specific CD4 T cell responses to different viral proteins have discordant associations with viral load and clinical outcome
Srinika Ranasinghe, Michael Flanders, Sam Cutler, Damien Z. Soghoian, Musie Ghebremicahel, Isaiah Davis, Madelene Lindqvist, Florencia Pereyra, Bruce D. Walker, David Heckerman, Hendrik Streeck
Journal of Virology | October 2011
FaST linear mixed models for genome-wide association studies
Christoph Lippert, Jennifer Listgarten, Ying Liu, Carl Kadie, Bob Davidson, David Heckerman
Nature Methods | October 2011, Vol 8: pp. 833-835
A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD
Alan E. Renton, Elisa Majounie, Adrian Waite, Javier Simon-Sanchez, Sara Rollinson, J. Raphael Gibbs, Jennifer C Scymick, Hannu Laaksovirta, John. C. van Swieten, Liisa Myllykangas, Hannu Kalimo, Anders Paetau, Yevgeniya Abramzon, Anne M. Remes, Alice Kaganovich, Sonja W. Scholz, Jamie Duckworth, Jinhui Ding, Daniel W. Harmer, Dena G. Hernandez, Janel O. Johnson, Kin Mok, Mina Ryten, Danyah Trabzuni, Rita J. Guerreiro, Richard W. Orrell, James Neal, Alex Murray, Justin Pearson, Iris E. Jansen, David Sondervan, Harro Seelaar, Derek Blake, Kate Young, Nicola Halliwell, Janis Bennion Callister, Greg Toulson, Anna Richardson, Alex Gerhard, Julie Snowden, David Mann, David Neary, Michael A. Nalls, Terhi Peuralinna, Lilja Jansson, Veli-Matti Isovaiita, Anna-Lotta Kaivorinne, Maarit Holtta-Vuori, Elina Ikonen, Raimo Sulkava, MIchael Benatar, Joanne Wuu, Adriano Chio, Garbiella Restagno, Giuseppe Borghero, Mario Sabatelli, The ITALSGEN Consortium, David Heckerman, Ekaterina ROgaeva, Lorne Zinman, Jeffrey D. Rothstein, MIchael Sendtner, Carsten Drepper, Evan E. Eichler, Can Alkan, Ziedulla Abdullaev, Svetlana D. Pack, Amalia Dutra, Evengenia Pak, John Hardy, Andrew SIngleton, Nigel M. Williams, Peter Heutink, Stuart Pickering-Brown, Huw R. Morris, Pentti J. Tienari, Bryan J. Traynor
Neuron | September 2011, Vol 72(2): pp. 257-268
Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes
Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John
The Journal of Immunology | September 2011
Definition of the viral targets of protective HIV-1-specific T cell responses
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Marcus Daniels, Cristina Miranda, Jennifer Zamarreno, Vanessa Bach, Rosario Zuniga, Susana Perez-Alvarez, Chirstoph T. Berger, Maria C. Puertas, Javier Martinez-Picado, Morgane Rolland, Marilu Farfan, James J. Szinger, William H. Hildebrand, Otto O. Yang, Victor Sanchez-Merino, Chanson J. Brumme, Zabrina L. Brumme, David Heckerman, Todd M. Allen, James I. Mullins, Guadalupe Gomez, Philip J. Goulder, Bruce D. Walker, Jose M. Gatell, Bonaventura Clotet, Better T. Korber, Jorge Sanchez, Chirstian Brander
Journal of Translational Medicine | August 2011, Vol 9(208)
HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100
Conditional Random Fields for Fast, Large-Scale Genome-Wide Association Studies
Jim Huang, Chris Meek, Carl Kadie, David Heckerman
PLoS ONE | July 2011
Variable HIV Peptide Stability in Human Cytosol is Critical to Epitope Presentation and Immune Escape
Estibaliz Lazaro, Carl Kadie, Pamela Stamegna, Shao Chong Zhang, Pauline Gourdain, Nicole Y. Lai, Mei Zhang, Sergio A. Martinez, David Heckerman, Sylvie Le Gall
J Clin Invest | June 2011
Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations
Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M. Carlson, Mark A. Brockman, Swati Mishra, Zabrina L. Brumme, Stephen Hickling, Christopher S.W. Tang, Toshiyuki Miura, Chris Seebregts, David Heckerman, Thumbi Ndung'u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater
April 2011
HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703
Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder
The Journal of Immunology | April 2011
Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences
Morgane Rolland, Nicole Frahm, David C. Nickle, Nebojsa Jojic, Wenjie Deng, Todd M. Allen, Christian Brander, David Heckerman, James I. Mullins
PLoS One | March 2011, Vol 28(6): pp. e17969
Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C
Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u
February 2011
Reduced Replication Capacity of NL4-3 Recombinant Viruses Encoding Reverse Transcriptase Integrase Sequences From HIV-1 Elite Controllers
Zabrina L. Brumme, Chun Li, Toshiyuki Miura, Jennifer Sela, Pamela C. Rosato, Chanson J. Brumme, Tristan J. Markle, Eric Martin, Brian L. Block, Alicja Trocha, Carl Kadie, Todd M. Allen, Florencia Pereyra, David Heckerman, Bruce D. Walker, Mark A. Brockman
J Acquir Immune Defic Syndr. | February 2011
-
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Science The International HIV Controllers Study | December 2010, Vol 330(6010): pp. 1551-1557
The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms
Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder
Journal of Virology | November 2010
Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection
Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen
Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949
Chromosome 9p21 in Amyotrophic Lateral Sclerosis in Finland: A Genome-Wide Association Study
Hannu Laaksovirta, Terhi Peuralinna, Jennifer C. Schymick, Sonja W. Scholz, Shaoi-Lin Lai, Liisa Myllykangas, Raimo Sulkava, Lilja Jansson, Dena G. Hernandez, J. Raphael Gibbs, Michael A. Nalls, David Heckerman, Pentti J. Tienari, Bryan J. Traynor
The Lancet Neurology | October 2010, pp. 978-985
Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters
Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u
Journal of Virology | October 2010
Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics
Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins
PLoS ONE | September 2010, pp. e12463
Correction for Hidden Confounders in the Genetic Analysis of Gene Expression
Jennifer Listgarten, Carl Kadie, Eric E. Schadt, David Heckerman
September 2010
Pearl Causality and the Value of Control
Ross Shachter, David Heckerman
Heuristics, Probability and Causality: A Tribute to Judea Pearl | May 2010
Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs
Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal
The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377
Beyond Atopy: Multiple Patterns of Sensitization in Relation to Asthma in a Birth Cohort Study
Angela Simpson, Vincent Y. Tan, John Winn, Markus Svensén, Christopher Bishop, David Heckerman, Iain Buchan, Adnan Custovic
American Journal of Respiratory and Critical Care Medicine | February 2010, Vol 181: pp. 1200-1206
Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection
Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888
CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription
Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert
The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51
Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences
Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander
JEM | January 2010
Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time
Michiko Koga, Ai Kawana-Tachikawa, David Heckerman, Takashi Odawara, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Toshiyuki Miura, Aikichi Iwamoto
Microbiology and Immunology | January 2010, Vol 54(4): pp. 196-205
-
PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612
HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins
Zabrina L. Brumme, Mina John, Jonathan M. Carlson, Chanson J. Brumme, Dennison Chan, Mark A. Brockman, Luke C. Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal
August 2009
Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study
Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran
Retrovirology | August 2009
HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
July 2009
Update on the Pathfinder Project
David Heckerman, Eric Horvitz, Bharat Nathwani
Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care | May 2009
Problem Formulation as the Reduction of a Decision Model
UAI-P-1990-PG-82-89 | May 2009
SRC Technical Note 1998-004 (March 1998). Rejected by Information Processing Letters.
Estimating false discovery rates for contingency tables
Jonathan M. Carlson, David Heckerman, Guy Shani
MSR-TR-2009-53 | May 2009
Adaptation of HIV-1 to Human Leukocyte Antigen Class I
Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Pendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung'u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder
Nature | April 2009, Vol 458: pp. 641-645
Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles
Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins
AIDS Research and Human Retroviruses | March 2009
HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1
Toshiyuki Miura, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Florencia Pereyra, Alicja Trocha, Brian L. Block, Arne Schneidewind, Todd M. Allen, David Heckerman, Bruce D. Walker
Journal of Virology | January 2009, Vol 83(1): pp. 140-149
HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering
Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder
Journal of Virology | January 2009, pp. JVI.02017-08
Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1
Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen
Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855
-
Design, Expression, and Processing of Epitomized Hepatitis C Virus-Encoded CTL Epitopes
Daniel Yerly, David Heckerman, Todd Allen, Todd J. Suscovich, Nebojsa Jojic, Carl Kadie, Werner J. Pichler, Andreas Cerny, Christian Brander
The Journal of Immunology | November 2008, Vol 181: pp. 6361-6370
Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman
PLoS Computational Biology | November 2008, Vol 4: pp. e1000225
In Silico Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman
October 2008
Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point
Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder
Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559
Continuous Time Dynamic Topic Models
Chong Wang, David Blei, David Heckerman
UAI-P-2008-PG-579-586 | July 2008
Tech Report 2003 61
Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
MSR-TR-2008-97 | July 2008
Comparison Of Immunogen Designs That Optimize Peptide Coverage: Reply To Fischer et al.
David C Nickle, Nebojsa Jojic, David Heckerman, Darko Kirovski, Vladimir Jojic, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins
PLoS Computational Biology | March 2008, pp. e25
Efficient Control of Population Structure in Model Organism Association Mapping
Hyun Min Kang, Noah A. Zaitlen, Claire M. Wade, Andrew Kirby, David Heckerman, Mark J. Daly, Eleazar Eskin
Genetics | March 2008, Vol 178(3): pp. 1709-1723
Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure
KC Ngumbela, CL Day, Z Mncube, K Nair, D Ramduth, C Thobakgale, E Moodley, S Reddy, C de Pierres, N Mkhwanazi, K Bishop, M van der Stok, N Ismail, I honeyborne, H Crawford, DG Kavanagh, C Rousseau, D Nickle, J Mullins, David Heckerman, B Korber, H Coovadia, P Kiepiela, PJ Goulder, BD Walker
AIDS Res Hum Retroviruses | January 2008, Vol 24(1): pp. 72-82
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads
Morgane Rolland, David Heckerman, Wenjie Deng, Christine M. Rousseau, Hoosen Coovadia, Karen Bishop, Philip J.R. Goulder, Bruce D. Walker, Chirstian Brander, James I. Mullins
PLoS ONE | January 2008, pp. e1424
Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes
Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker
Journal of Virology | January 2008, pp. JVI.00535-8
HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load
Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins
Journal of Virology | January 2008, Vol 82: pp. 6434-6446
Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
AIDS | January 2008
Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection
Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker
Journal of Virology | January 2008, Vol 82: pp. 9216-9227
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients
Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen
Hepatology | January 2008, Vol 48: pp. 1769-1778
Statistical Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman
MSR-TR-2008-07 | January 2008
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients
Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter
Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017
-
Reflection and Action Under Scarce Resources: Theoretical Principles and Empirical Study
Eric Horvitz, Gregory Cooper, David Heckerman
November 2007
Combinatorics of The Vaccine Design Problem: Definition and An Algorithm
Darko Kirovski, David Heckerman, Nebojsa Jojic
MSR-TR-2007-148 | November 2007
Increased Cytotoxic T-Lymphocyte Epitope Variant Cross-Recognition and Functional Avidity Are Associated with Hepatitis C Virus Clearance
Daniel Yerly, David Heckerman, Todd M. Allen, John V. Chisholm III, Kellie Faircloth, Caitlyn H. Linde, Nicole Frahm, Joerg Timm, Werner J. Pichler, Andreas Cerny, Christian Brander
Journal of Virology | October 2007, Vol 82(6): pp. 3147-3153
A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander, David Heckerman
PLoS Computational Biology | October 2007, Vol 4(10): pp. e188
Extensive HLA class I allele promiscuity among viral CTL epitopes
Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D. Walker, Alessandro Sette, David Heckerman, Bette T. Korber, Christian Brander
European Journal of Immunology | September 2007, Vol 37(9): pp. 2419-2433
Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1
Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan, Jonathan M. Carlson
PLoS Pathogens | July 2007
Leveraging Hierarchical Population Structure in Discrete Association Studies
Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman
PLoS One | July 2007, Vol 2: pp. e591
Determining the Number of Non-Spurious Arcs in a Learned DAG Model: Investigation of a Bayesian and a Frequentist Approach
Jennifer Listgarten, David Heckerman
MSR-TR-2007-60 | May 2007
Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections
Christine M. Rousseau, Gerald H. Learn, Tanmoy Bhattacharya, David C. Nickle, David Heckerman, Senica Chetty, Christian Brander, Philip J. R. Goulder, Bruce D. Walker, Photini Kiepiela, Bette T. Korber, James I. Mullins
Journal of Virology | May 2007
Coping with Viral Diversity in HIV Vaccine Design
David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins
PLoS Computational Biology | April 2007, pp. e75
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations
Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber
Science | January 2007, Vol 315: pp. 1583-1586
-
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load
Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthia Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Pendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H. Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I. Mullins, David Heckerman, Bruce D. Walker, Philip Goulder
Nature Medicine | December 2006
Identifying the effects of human immune pressure on the evolution of HIV.
Jonathan M. Carlson, Carl Kadie, David Heckerman
December 2006
Learning MHC I – Peptide Binding
Nebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Kadie, Ora Schueler-Furman
June 2006, Vol 22(14): pp. e227-e235
A Bayesian Approach to Causal Discovery
David Heckerman, Chris Meek, Gregory Cooper
Computation, Causation, and Discovery | Published by AAAI Press | 2006 | Computation, Causation, and Discovery edition
ISBN: 978-3-540-30609-2
-
Considering Cost Asymmetry in Learning Classifiers
Francis Bach, David Heckerman, Eric Horvitz
Machine Learning Research | October 2005, Vol 7: pp. 1713-1741
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction
David Heckerman, Carl Kadie, Jennifer Listgarten
MSR-TR-2005-127 | September 2005
Using Epitomes To Model Genetic Diversity: Rational Design Of HIV Vaccines
Nebojsa Jojic, Vladimir Jojic, Brendan J. Frey, Chris Meek, David Heckerman
NIPS | May 2005
Stopping Spam
Joshua Goodman, David Heckerman, Robert Rounthwaite
Scientific American | April 2005, Vol 292: pp. 42-49
-
Large-Sample Learning of Bayesian Networks is NP-Hard
Max Chickering, David Heckerman, Chris Meek
Journal of Machine Learning Research | December 2004, Vol 5: pp. 1287-1330
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas Richardson
MSR-TR-2004-94 | September 2004
Joint Discovery Of Haplotype Blocks And Complex Trait Associations From SNP Sequences
Nebojsa Jojic, Vladimir Jojic, David Heckerman
UAI-P-2004-PG-286-292 | July 2004
Symposium on Networked Systems Design and Implemenentation (NSDI)
ARMA Time-Series Modeling with Graphical Models
Bo Thiesson, Max Chickering, David Heckerman, Chris Meek
Proceedings of the Twentieth Conference on Uncertainty in Artificial Intelligence | July 2004
Probabilistic Models for Relational Data
David Heckerman, Chris Meek, Daphne Koller
MSR-TR-2004-30 | March 2004
Probabilistic Entity-Relationship Models, PRMs and Plate Models
David Heckerman, Chris Meek, Daphne Koller
Introduction to Statistical Relational Learning | Published by MIT Press | 2004
-
A Characterization of the Dirichlet Distribution Through Global and Local Independence
Dan Geiger, David Heckerman
MSR-TR-94-16 | November 2003
Annal Statistics
Model-Based Clustering and Visualization of Navigation Patterns on a Web Site
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
Data Mining and Knowledge Discovery | October 2003, Vol 7(4): pp. 399-424
Also in KDD 2000
Efficient Approximations for Learning Phylogenetic HMM Models from Data
Vladimir Jojic, Nebojsa Jojic, Chris Meek, Daniel Geiger, Adam Siepel, David Haussler, David Heckerman
MSR-TR-2003-62 | October 2003
-
An MDP-Based Recommender System
Guy Shani, Ronen I. Brafman, David Heckerman
UAI-P-2002-PG-453-460 | August 2002
Proceedings of Twentieth Conference on Uncertainty in Artificial Intelligence, Banff, Canada, UAI Press
Autoregressive Tree Models For Time-Series Analysis
Chris Meek, Max Chickering, David Heckerman
Proceedings of the Second International SIAM Conference on Data Mining | August 2002
CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence
Carl Kadie, Chris Meek, David Heckerman
MSR-TR-2002-46 | August 2002
Proceedings of Twenty Fourth Conference on Uncertainty in Artificial Intelligence, Helsinki, Finland, UAI Press
Staged Mixture Modeling and Boosting
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence | August 2002
-
Learning Mixtures Of Smooth, Nonuniform Deformation Models For Probabilistic Image Matching
Nebojsa Jojic, Brendan J. Frey, Patrice Simard, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, Key West, FL | May 2001
The Learning-Curve Sampling Method Applied to Model-Based Clustering
Chris Meek, Bo Thiesson, David Heckerman
Journal of Machine Learning Research | February 2001, Vol 2: pp. 397-418
Also appears as Technical Report MSR-TR-01-34, Microsoft Research, February, 2001.
Accelerating EM For Large Databases
Bo Thiesson, Chris Meek, David Heckerman
Machine Learning | January 2001, Vol 45: pp. 279-299
Also appears as Technical Report MSR-TR-99-31, Microsoft Research, May, 1999 (Revised February, 2001).
Learning Bayesian Networks From Dependency Networks: A Preliminary Study
Geoff Hulten, Max Chickering, David Heckerman
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, ® Key West, FL | January 2001
Parameter Priors for Directed Acyclic Graphical Models and the Characterization of Several Probability Distributions
Dan Geiger, David Heckerman
MSR-TR-98-67 | January 2001
The Learning-Curve Method Applied To Clustering
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, ® Key West, Florida | January 2001
An Evaluation of the Diagnostic Accuracy of Pathfinder
David Heckerman, Bharat N. Nathwani
Comput Biomed Res | November 2001, Vol 25(1): pp. 56-74
-
Dependency Networks for Inference, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
MSR-TR-2000-16 | October 2000
Proceedings of the International Conference on Dependable Systems and Networks
Targeted Advertising with Inventory Management
Max Chickering, David Heckerman
MSR-TR-2000-49 | October 2000
ACM Special Interest Group on E-Commerce (EC00), ® Minneapolis, MN
Goal-Oriented Clustering
Max Chickering, David Heckerman, Chris Meek, John Platt, Bo Thiesson
MSR-TR-2000-82 | May 2000
Visualization of Navigation Patterns on a Web Site Using Model Based Clustering
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
MSR-TR-2000-18 | March 2000
A Decision-Theoretic Approach to Targeted Advertising
Max Chickering, David Heckerman
MSR-TR-2000-17 | February 2000
Proceedings of the International Conference on Functional Programming
Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
Proceedings of Sixteenth Conference on Uncertainty in Artificial Intelligence, ® Stanford, CA | January 2000
-
Fast Learning from Sparse Data
Max Chickering, David Heckerman
MSR-TR-2000-15 | August 1999
Proceedings of the Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON
Computationally Efficient Methods for Selecting Among Mixtures of Graphical Models
Max Chickering, David Heckerman, Chris Meek
Bayesian Statistics 6 | Published by Oxford University Press | 1999 | Bayesian Statistics 6 edition
Computationally Efficient Methods For Selecting Among Mixtures Of Graphical Models, With Discussion
Bo Thiesson, Chris Meek, David Maxwell Chickering, David Heckerman
Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting | Published by Oxford University Press | 1999 | Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting edition
Editors: Bernardo, J., Berger, J., Dawid, A., and Smith, A.
The Compilation of Decision Models
David Heckerman, John Breese, Eric Horvitz
March 1999
-
Stratified Exponential Families: Graphical Models and Model Selection
Dan Geiger, David Heckerman, Henry King, Chris Meek
MSR-TR-98-31 | July 1998
A Bayesian Approach to Filtering Junk E-Mail
David Heckerman, Eric Horvitz, Mehran Sahami, Susan Dumais
AAAI Workshop on Learning for Text Categorization | July 1998
Inferring Informational Goals from Free-Text Queries: A Bayesian Approach
MSR-TR-1998-5 | July 1998
Proceedings of the Fourth Conference on Uncertainty in Artificial Intelligence (UAI1988)
The Lumiere Project: Bayesian User Modeling for Inferring the Goals and Needs of Software Users
Eric Horvitz, Jack Breese, David Heckerman, David Hovel, Koos Rommelse
Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence, Madison, WI, July 1998, Morgan Kaufmann: San Francisco. | July 1998
Empirical Analysis of Predictive Algorithms for Collaborative Filtering
John S. Breese, David Heckerman, Carl Kadie
MSR-TR-98-12 | May 1998
Inductive Learning Algorithms and Representations for Text Categorization
Susan Dumais, John Platt, David Heckerman, Mehran Sahami
7th International Conference on Information and Knowledge Management | January 1998
-
Learning Mixtures of DAG Models
Bo Thiesson, Chris Meek, Max Chickering, David Heckerman
MSR-TR-97-30 | December 1997
Revised May 1998
Models and Selection Criteria for Regression and Classification
David Heckerman, Chris Meek
MSR-TR-97-08 | August 1997
Symposium on Discrete Algorithms
A Bayesian Approach To Learning Bayesian Networks With Local Structure
Max Chickering, David Heckerman, Chris Meek
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, ® Providence, RI | August 1997
Structure and Parameter Learning for Causal Independence and Causal Interaction Models
Chris Meek, David Heckerman
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, Providence, RI | August 1997
Embedded Bayesian Network Classifiers
David Heckerman, Chris Meek
MSR-TR-97-06 | March 1997
-
A Comparison of Scientific and Engineering Criteria for Bayesian Model Selection
David Heckerman, Max Chickering
MSR-TR-96-12 | June 1996
Tools and Algorithms for the Construction and Analysis of Systems (TACAS '07)
Decision-Theoretic Case-Based Reasoning
John S. Breese, David Heckerman
MSR-TR-95-03 | May 1996
IEEE Transactions on Systems, Man, and Cybernetics
Decision-Theoretic Troubleshooting: A Framework for Repair and Experiment
John S. Breese, David Heckerman
MSR-TR-96-06 | March 1996
Probabilistic Independence Networks for Hidden Markov Probability Models
Padhraic Smyth, David Heckerman, Michael I. Jordan
MSR-TR-96-03 | January 1996
-
A Characterization of the Bivariate Normal-Wishart Distribution
Dan Geiger, David Heckerman
MSR-TR-95-53 | November 1995
Learning Bayesian Networks: A Unification for Discrete and Gaussian Domains
David Heckerman, Dan Geiger
UAI-P-1995-PG-274-284 | August 1995
Robotics Science and System Workshop on Task and Motion Planning
A Characterization of the Dirichlet Distribution with Application to Learning Bayesian Networks
Dan Geiger, David Heckerman
UAI-P-1995-PG-196-207 | August 1995
Real-Time Graphics Architectures, Algorithms, and Programming Systems: Project Technical Report
On Finding A Cycle Basis With A Shortest Maximal Cycle
Max Chickering, Dan Geiger, David Heckerman
Information Processing Letters | August 1995, Vol 54: pp. 55-58
A Bayesian Approach to Learning Causal Networks
MSR-TR-95-04 | August 1995
Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence (UAI1995)
A Definition and Graphical Representation for Causality
Proceedings of Eleventh Conference on Uncertainty in Artificial Intelligence, Montreal, Quebec | May 1995
Decision-Theoretic Troubleshooting
David Heckerman, John S. Breese, Koos Rommelse
CACM | May 1995
A Tutorial on Learning With Bayesian Networks
MSR-TR-95-06 | March 1995
Real-World Applications of Bayesian Networks
David Heckerman, Abe Mamdani, Michael P. Wellman
Communications of the ACM | March 1995, Vol 38(3): pp. 24-26
Learning Bayesian Networks: Search Methods and Experimental Results
Max Chickering, Dan Geiger, David Heckerman
Proceedings of the Fifth International Workshop on Artificial Intelligence and Statistics | January 1995
-
A Decision-Based View of Causality
David Heckerman, Ross D. Shachter
UAI-P-1994-PG-302-310 | July 1994
Proceedings of the Second Conference on Uncertainty in Artificial Intelligence (UAI1986)
A New Look at Causal Independence
David Heckerman, John S. Breese
UAI-P-1994-PG-286-292 | July 1994
Proceedings of the Ninth Conference on Uncertainty in Artificial Intelligence (UAI1993)
Learning Bayesian Networks: The Combination of Knowledge and Statistical Data
David Heckerman, Dan Geiger, Max Chickering
Machine Learning | March 1994, Vol 20(3): pp. 197-243
Causal Independence for Probability Assessment and Inference Using Bayesian Networks
John S. Breese, David Heckerman
MSR-TR-94-08 | March 1994
Decision-Theoretic Foundations for Causal Reasoning
David Heckerman, Ross Shachter
MSR-TR-94-11 | March 1994
Learning Gaussian Networks
Dan Geiger, David Heckerman
MSR-TR-94-10 | January 1994
Troubleshooting Under Uncertainty
David Heckerman, John S. Breese, Koos Rommelse
MSR-TR-94-07 | January 1994
-
Inference Algorithms for Similarity Networks
Dan Geiger, David Heckerman
MSR-TR-93-09 | July 1993
Proceedings of the IEEE International Conference on Data Mining (ICDM)
Diagnosis of Multiple Faults: A Sensitivity Analysis
David Heckerman, Michael Shwe
MSR-TR-93-11 | June 1993
SPIE Astronomy Telescopes and Instruments
Efficient Approximations for the Marginal Likelihood of Incomplete Data Given a Bayesian Network
Max Chickering, David Heckerman
MSR-TR-96-08 | May 1993
An Approximate Nonmyopic Computation for Value of Information
David Heckerman, Eric Horvitz, Blackford Middleton
January 1993
-
The Certainty-Factor Model
Encyclopedia of Artificial Intelligence, Second Edition | August 1992, pp. 131-138
Toward Normative Expert Systems Part II
David Heckerman, Bharat N. Nathwani
Methods of Information in Medicine | August 1992, Vol 31: pp. 106-116
Toward Normative Expert Systems Part I
David Heckerman, Eric Horvitz, Bharat N. Nathwani
Methods of Information in Medicine | June 1992, Vol 31: pp. 90-105
From Certainty Factors to Belief Networks
David Heckerman, Edward H. Shortliffe
Artificial Intelligence in Medicine | February 1992, pp. 35-52
-
Probabilistic Similarity Networks
Published by MIT Press - Cambridge, MA | August 1991
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part II
Blackford Middleton, Michael Shwe, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | August 1991, Vol 30: pp. 256-267
Advances in Probabilistic Reasoning
Dan Geiger, David Heckerman
Proceedings of the Seventh Conference on Uncertainty in Artificial Intelligence | July 1991
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part I
Michael Shwe, Blackford Middleton, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | May 1991, Vol 30: pp. 241-255
-
Probabilistic Similarity Networks
Networks | August 1990
A Combination of Cutset Conditioning with Clique-tree Propagation in the Pathfinder System
Jaap Suermondt, Gregory F. Cooper, David Heckerman
UAI-P-1990-PG-273-280 | August 1990
SRI International
Integrated Expert Systems and Videodisc in Surgical Pathology: An Overview
B. Nathwani, David Heckerman, Eric Horvitz, T. Lincoln
Human Pathology | August 1990, Vol 21: pp. 11-27
Separable and Transitive Graphoids
Dan Geiger, David Heckerman
UAI-P-1990-PG-538-545 | August 1990
SRC Technical Note 1994-001 (December 1994).
A Tractable Algorithm for Diagnosing Multiple Diseases
UAI-P-1989-PG-174-181 | July 1990
Secure Internet Programming
Similarity Networks for the Construction of Multiple-Fault Belief Networks
UAI-P-1990-PG-32-39 | July 1990
Stanford University Interactive Workspaces Project Technical Note 2001-1
-
Heuristic Abstraction in the Decision-Theoretic Pathfinder System
Eric Horvitz, David Heckerman, Keung-Chi Ng, Bharat Nathwani
Proceedings of the Symposium on Computers in Medical Care, Washington DC, IEEE Press: Silver Springs MD | November 1989
-
An Empirical Comparison of Three Inference Methods
UAI-P-1988-PG-158-169 | August 1988
SIGCOMM 2014
A Method for Temporal Probabilistic Reasoning
Gregory F. Cooper, Eric Horvitz, David Heckerman
KSL-88-30 | July 1988
Knowledge Systems Laboratory
The Myth of Modularity in Rule-Based Systems for Reasoning with Uncertainty
UAI-P-1986-PG-115-122 | January 1988
-
Thinking Backward for Knowledge Acquisition
Ross D. Shachter, David Heckerman
AI Magazine | August 1987, pp. 55-61
A Perspective on Confidence and its use in Focusing Attention During Knowledge Acquisition
David Heckerman, Holly Jimison
UAI-P-1987-PG-123-131 | July 1987
In Proceedings of the Third Workshop on Uncertainty in Artificial Intelligence, Seattle, WA (UAI1987)
On the Expressiveness of Rule-based Systems for Reasoning with Uncertainty
AAAI-87 Proceedings | January 1987
-
An Axiomatic Framework for Belief Updates
UAI-P-1986-PG-123-128 | October 1986
SPIE Astronomy Telescopes and Instruments
Towards a Better Understanding of the INTERNIST-1 Knowledge Base
David Heckerman, Randolph A. Miller
Proceedings of Medinfo, Washington | October 1986
A Framework for Comparing Alternative Formalisms for Plausible Reasoning
Eric Horvitz, David Heckerman, Curtis P. Langlotz
AAAI-86 Proceedings | January 1986
The Use of a Heuristic Problem-Solving Hierarchy to Facilitate the Explanation of Hypothesis-Directed Reasoning
Eric Horvitz, David Heckerman, Bharat Nathwani, Lawrence Fagan
January 1986, pp. 27-31
-
The Inconsistent Use of Measures of Certainty in Artificial Intelligence Research
Uncertainty in Artificial Intelligence Annual Conference on Uncertainty in Artificial Intelligence (UAI-85) | August 1985
-
Diagnostic Strategies in the Hypothesis-Directed PATHFINDER System
Eric Horvitz, David Heckerman, Bharat N. Nathwani, Lawrence M. Fagan
January 1984, pp. 630-636
-
Pressure release superleak sound modes in He II
David Heckerman, Ralph Rosenbaum, Seth Putterman, Gary A. Williams
Journal of Low Temperature Physics | March 1980, Vol 38(5-6): pp. 629-640
-
Surface tension sound in superfluid helium films adsorbed on alumina powder
Ralph Rosenbaum, G. A. Williams, David Heckerman, J. Marcus, D. Scholler, J. Maynard, I. Rudnick
Journal of Low Temperature Physics | December 1979, Vol 37(5): pp. 663-678
Superfluid Two-Phase Sound
Seth Putterman, David Heckerman, Ralph Rosenbaum, Gary Williams
Physical Review Letters | February 1979, Vol 42(9): pp. 580-583
Publications by Research Area
-
Integrated Expert Systems and Videodisc in Surgical Pathology: An Overview
B. Nathwani, David Heckerman, Eric Horvitz, T. Lincoln
Human Pathology | August 1990, Vol 21: pp. 11-27
Pressure release superleak sound modes in He II
David Heckerman, Ralph Rosenbaum, Seth Putterman, Gary A. Williams
Journal of Low Temperature Physics | March 1980, Vol 38(5-6): pp. 629-640
Surface tension sound in superfluid helium films adsorbed on alumina powder
Ralph Rosenbaum, G. A. Williams, David Heckerman, J. Marcus, D. Scholler, J. Maynard, I. Rudnick
Journal of Low Temperature Physics | December 1979, Vol 37(5): pp. 663-678
Superfluid Two-Phase Sound
Seth Putterman, David Heckerman, Ralph Rosenbaum, Gary Williams
Physical Review Letters | February 1979, Vol 42(9): pp. 580-583
Impact of Pre-Adapted HIV Transmission
Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
Nature Medicine | May 2016, Vol 22: pp. 606-613
Bonnie Mathieson Young Investigator Award
Anti-Hepatitis C Virus T-Cell Immunity in the Context of Multiple Exposures to the Virus
Katja Pfafferott, Pooja Deshpande, Elizabeth McKinnon, Shahzma Merani, Andrew Lucas, David Heckerman, Simon Mallal, Mina John, Silvana Gaudieri, Michaela Lucas
June 2015
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
Garbiel R. A. Margarido, David Heckerman
PLoS Comput Biol | April 2015
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of virology | April 2015, Vol 89: pp. 4015-4019
Accurate Liability Estimation Improves Power in Ascertained Case-Control Studies
Omer Weissbrod, Christoph Lippert, Dan Geiger, David Heckerman
Nature Methods | February 2015, Vol 12: pp. 332-334
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of Virology | January 2015
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Bioinformatics | September 2014, pp. btu504
Addendum on the scoring of Gaussian directed acyclic graphical models
Jack Kuipers, Giusi Moffa, David Heckerman
Annal Statistics | August 2014, Vol 42: pp. 1689-1691
HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes
Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker
Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948
Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
Science | July 2014, Vol 345(6193)
Publication Publication Publication Publication Publication Project
Eliciting cytotoxic T-lymphocyte responses from synthetic vectors containing one or two epitopes in a C57BL/6 mouse model using peptide-containing biodegradable microspheres and adjuvants
R. M. Rubsamen, C. V. Herst, P. M. Lloyd, David Heckerman
June 2014
Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
eLife | October 2013
Epigenome-wide association studies without the need for cell-type composition
James Zhou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
Nature Methods | August 2013
Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication
Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm
Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365
The benefits of selecting phenotype-specific variants for applications of mixed models in genomics
Christoph Lippert, Gerald Quon, Eun Yong Kang, Carl Kadie, Jennifer Listgarten, David Heckerman
MSR-TR-2013-138 | May 2013
Influence of HLA-C Expression Level on HIV Control
Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington
Science | April 2013, Vol 340(6128): pp. 87-91
HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes
Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John
AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905
HIV-1 p24gag Derived Conserved Element DNA Vaccine Increases the Breadth of Immune Response in Mice
Viraj Kulkarni, Margherita Rosati, Antonio Valentin, Brunda Ganneru, Ashish K. Singh, Jian Yan, Morgane Rolland, Candido Alicea, Rachel Kelly Beach, Gen-Mu Zhang, Sylvie Le Gall, Kate E. Broderick, Niranjan Y. Sardesai, David Heckerman, Beatriz Mothe, Christian Brander, David B. Weiner, James I. Mullins, George N. Pavlakis, Barbara K. Felber
PLoS ONE | March 2013, pp. e60245
High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control
Zaza M. Ndhlovu, Lori B. Chibnik, Jacqueline Proudfoot, Seanna Vine, Ashley McMullen, Kevin Cesa, Filippos Porichis, R. Brad Jones, Donna Marie Alvino, Meghan G. Hart, Eleni Stampouloglou, Alicja Piechocka-Trocha, Carl Kadie, Florencia Pereyra, David Heckerman, Philip L. De Jager, Bruce D. Walker, Daniel E. Kaufmann
Blood Journal | January 2013, Vol 121(5)
Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins
Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen
January 2013
A powerful and efficient set test for genetic markers that handles confounders
Jennifer Listgarten, Christoph Lippert, Carl Kadie, David Heckerman
Bioinformatics | January 2013
Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme
Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216
Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope
Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder
Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654
Extraneous markers used for genetic similarity leads to loss of power in GWAS and heritability determination
Christoph Lippert, Gerald Quon, Jennifer Listgarten, David Heckerman
MSR-TR-2012-120 | December 2012
Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan
Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura
Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476
Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis
Jessica L. Prince, Daniel T. Claiborne, Jonathan M. Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A. Prentice, Ling Yue, Sundaram A. Vishwanathan, William Kilembe, Paul Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter
PLoS Pathogens | November 2012, pp. e1003041
Co-operative additive effects between HLA alleles in control of HIV-1
Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
PLoS ONE | October 2012, pp. e47799
Patterns of methylation heritability in a genome-wide analysis of four brain regions
Gerald Quon, Christoph Lippert, David Heckerman, Jennifer Listgarten
Nucleic Acids Research | August 2012
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans
Paul J. McLaren, Stephan Ripke, Kimberly Pelak, Amy C. Weintrob, Nikolaos A. Patsopoulos, Xiaoming Jia, Rachel L. Erlich, Niall J. Lennon, Carl Kadie, David Heckerman, Namrata Gupta, David W. Haas, Steven G. Deeks, Florencia Pereyra, Bruce D. Walker, Paul I. W. de Bakker
Human Molecular Genetics | June 2012, Vol 21(19): pp. 4334-4347
Improved linear mixed models for genome-wide association studies
Jennifer Listgarten, Christoph Lippert, Carl Kadie, Robert I. Davidson, Eleazar Eskin, David Heckerman
Nature Methods | May 2012, Vol 9: pp. 3–4
Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243
Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity
Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme
Journal of Virology | April 2012
Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
February 2012
High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection
Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John
Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234
CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Jennifer Zamarreno, Mattia Schiaulini, Cristina Miranda, Marta Ruiz-Riol, Christoph T. Berger, M. Jose Herrero, Eduard Palou, Montse Plana, Morgane Rolland, Ashok Khatri, David Heckerman, Florencia Pereyra, Bruce D. Walker, David Weiner, Roger Paredes, Bonaventura Clotet, Barbara K. Felber, George N. Pavlakis, James I. Mullins, Chirstian Brander
PLoS ONE | January 2012, pp. e29717
HIV-specific CD4 T cell responses to different viral proteins have discordant associations with viral load and clinical outcome
Srinika Ranasinghe, Michael Flanders, Sam Cutler, Damien Z. Soghoian, Musie Ghebremicahel, Isaiah Davis, Madelene Lindqvist, Florencia Pereyra, Bruce D. Walker, David Heckerman, Hendrik Streeck
Journal of Virology | October 2011
A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD
Alan E. Renton, Elisa Majounie, Adrian Waite, Javier Simon-Sanchez, Sara Rollinson, J. Raphael Gibbs, Jennifer C Scymick, Hannu Laaksovirta, John. C. van Swieten, Liisa Myllykangas, Hannu Kalimo, Anders Paetau, Yevgeniya Abramzon, Anne M. Remes, Alice Kaganovich, Sonja W. Scholz, Jamie Duckworth, Jinhui Ding, Daniel W. Harmer, Dena G. Hernandez, Janel O. Johnson, Kin Mok, Mina Ryten, Danyah Trabzuni, Rita J. Guerreiro, Richard W. Orrell, James Neal, Alex Murray, Justin Pearson, Iris E. Jansen, David Sondervan, Harro Seelaar, Derek Blake, Kate Young, Nicola Halliwell, Janis Bennion Callister, Greg Toulson, Anna Richardson, Alex Gerhard, Julie Snowden, David Mann, David Neary, Michael A. Nalls, Terhi Peuralinna, Lilja Jansson, Veli-Matti Isovaiita, Anna-Lotta Kaivorinne, Maarit Holtta-Vuori, Elina Ikonen, Raimo Sulkava, MIchael Benatar, Joanne Wuu, Adriano Chio, Garbiella Restagno, Giuseppe Borghero, Mario Sabatelli, The ITALSGEN Consortium, David Heckerman, Ekaterina ROgaeva, Lorne Zinman, Jeffrey D. Rothstein, MIchael Sendtner, Carsten Drepper, Evan E. Eichler, Can Alkan, Ziedulla Abdullaev, Svetlana D. Pack, Amalia Dutra, Evengenia Pak, John Hardy, Andrew SIngleton, Nigel M. Williams, Peter Heutink, Stuart Pickering-Brown, Huw R. Morris, Pentti J. Tienari, Bryan J. Traynor
Neuron | September 2011, Vol 72(2): pp. 257-268
Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes
Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John
The Journal of Immunology | September 2011
Definition of the viral targets of protective HIV-1-specific T cell responses
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Marcus Daniels, Cristina Miranda, Jennifer Zamarreno, Vanessa Bach, Rosario Zuniga, Susana Perez-Alvarez, Chirstoph T. Berger, Maria C. Puertas, Javier Martinez-Picado, Morgane Rolland, Marilu Farfan, James J. Szinger, William H. Hildebrand, Otto O. Yang, Victor Sanchez-Merino, Chanson J. Brumme, Zabrina L. Brumme, David Heckerman, Todd M. Allen, James I. Mullins, Guadalupe Gomez, Philip J. Goulder, Bruce D. Walker, Jose M. Gatell, Bonaventura Clotet, Better T. Korber, Jorge Sanchez, Chirstian Brander
Journal of Translational Medicine | August 2011, Vol 9(208)
HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100
Conditional Random Fields for Fast, Large-Scale Genome-Wide Association Studies
Jim Huang, Chris Meek, Carl Kadie, David Heckerman
PLoS ONE | July 2011
Variable HIV Peptide Stability in Human Cytosol is Critical to Epitope Presentation and Immune Escape
Estibaliz Lazaro, Carl Kadie, Pamela Stamegna, Shao Chong Zhang, Pauline Gourdain, Nicole Y. Lai, Mei Zhang, Sergio A. Martinez, David Heckerman, Sylvie Le Gall
J Clin Invest | June 2011
Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations
Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M. Carlson, Mark A. Brockman, Swati Mishra, Zabrina L. Brumme, Stephen Hickling, Christopher S.W. Tang, Toshiyuki Miura, Chris Seebregts, David Heckerman, Thumbi Ndung'u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater
April 2011
HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703
Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder
The Journal of Immunology | April 2011
Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences
Morgane Rolland, Nicole Frahm, David C. Nickle, Nebojsa Jojic, Wenjie Deng, Todd M. Allen, Christian Brander, David Heckerman, James I. Mullins
PLoS One | March 2011, Vol 28(6): pp. e17969
Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C
Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u
February 2011
Reduced Replication Capacity of NL4-3 Recombinant Viruses Encoding Reverse Transcriptase Integrase Sequences From HIV-1 Elite Controllers
Zabrina L. Brumme, Chun Li, Toshiyuki Miura, Jennifer Sela, Pamela C. Rosato, Chanson J. Brumme, Tristan J. Markle, Eric Martin, Brian L. Block, Alicja Trocha, Carl Kadie, Todd M. Allen, Florencia Pereyra, David Heckerman, Bruce D. Walker, Mark A. Brockman
J Acquir Immune Defic Syndr. | February 2011
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Science The International HIV Controllers Study | December 2010, Vol 330(6010): pp. 1551-1557
The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms
Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder
Journal of Virology | November 2010
Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection
Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen
Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949
Chromosome 9p21 in Amyotrophic Lateral Sclerosis in Finland: A Genome-Wide Association Study
Hannu Laaksovirta, Terhi Peuralinna, Jennifer C. Schymick, Sonja W. Scholz, Shaoi-Lin Lai, Liisa Myllykangas, Raimo Sulkava, Lilja Jansson, Dena G. Hernandez, J. Raphael Gibbs, Michael A. Nalls, David Heckerman, Pentti J. Tienari, Bryan J. Traynor
The Lancet Neurology | October 2010, pp. 978-985
Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters
Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u
Journal of Virology | October 2010
Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics
Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins
PLoS ONE | September 2010, pp. e12463
Correction for Hidden Confounders in the Genetic Analysis of Gene Expression
Jennifer Listgarten, Carl Kadie, Eric E. Schadt, David Heckerman
September 2010
Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs
Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal
The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377
Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection
Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888
CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription
Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert
The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51
Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences
Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander
JEM | January 2010
Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time
Michiko Koga, Ai Kawana-Tachikawa, David Heckerman, Takashi Odawara, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Toshiyuki Miura, Aikichi Iwamoto
Microbiology and Immunology | January 2010, Vol 54(4): pp. 196-205
PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612
HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins
Zabrina L. Brumme, Mina John, Jonathan M. Carlson, Chanson J. Brumme, Dennison Chan, Mark A. Brockman, Luke C. Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal
August 2009
Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study
Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran
Retrovirology | August 2009
HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
July 2009
Adaptation of HIV-1 to Human Leukocyte Antigen Class I
Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Pendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung'u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder
Nature | April 2009, Vol 458: pp. 641-645
Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles
Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins
AIDS Research and Human Retroviruses | March 2009
HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1
Toshiyuki Miura, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Florencia Pereyra, Alicja Trocha, Brian L. Block, Arne Schneidewind, Todd M. Allen, David Heckerman, Bruce D. Walker
Journal of Virology | January 2009, Vol 83(1): pp. 140-149
HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering
Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder
Journal of Virology | January 2009, pp. JVI.02017-08
Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1
Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen
Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855
Design, Expression, and Processing of Epitomized Hepatitis C Virus-Encoded CTL Epitopes
Daniel Yerly, David Heckerman, Todd Allen, Todd J. Suscovich, Nebojsa Jojic, Carl Kadie, Werner J. Pichler, Andreas Cerny, Christian Brander
The Journal of Immunology | November 2008, Vol 181: pp. 6361-6370
Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman
PLoS Computational Biology | November 2008, Vol 4: pp. e1000225
In Silico Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman
October 2008
Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point
Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder
Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559
Comparison Of Immunogen Designs That Optimize Peptide Coverage: Reply To Fischer et al.
David C Nickle, Nebojsa Jojic, David Heckerman, Darko Kirovski, Vladimir Jojic, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins
PLoS Computational Biology | March 2008, pp. e25
Efficient Control of Population Structure in Model Organism Association Mapping
Hyun Min Kang, Noah A. Zaitlen, Claire M. Wade, Andrew Kirby, David Heckerman, Mark J. Daly, Eleazar Eskin
Genetics | March 2008, Vol 178(3): pp. 1709-1723
Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure
KC Ngumbela, CL Day, Z Mncube, K Nair, D Ramduth, C Thobakgale, E Moodley, S Reddy, C de Pierres, N Mkhwanazi, K Bishop, M van der Stok, N Ismail, I honeyborne, H Crawford, DG Kavanagh, C Rousseau, D Nickle, J Mullins, David Heckerman, B Korber, H Coovadia, P Kiepiela, PJ Goulder, BD Walker
AIDS Res Hum Retroviruses | January 2008, Vol 24(1): pp. 72-82
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads
Morgane Rolland, David Heckerman, Wenjie Deng, Christine M. Rousseau, Hoosen Coovadia, Karen Bishop, Philip J.R. Goulder, Bruce D. Walker, Chirstian Brander, James I. Mullins
PLoS ONE | January 2008, pp. e1424
Statistical Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman
MSR-TR-2008-07 | January 2008
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients
Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter
Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017
HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load
Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins
Journal of Virology | January 2008, Vol 82: pp. 6434-6446
Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection
Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker
Journal of Virology | January 2008, Vol 82: pp. 9216-9227
Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
AIDS | January 2008
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients
Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen
Hepatology | January 2008, Vol 48: pp. 1769-1778
Increased Cytotoxic T-Lymphocyte Epitope Variant Cross-Recognition and Functional Avidity Are Associated with Hepatitis C Virus Clearance
Daniel Yerly, David Heckerman, Todd M. Allen, John V. Chisholm III, Kellie Faircloth, Caitlyn H. Linde, Nicole Frahm, Joerg Timm, Werner J. Pichler, Andreas Cerny, Christian Brander
Journal of Virology | October 2007, Vol 82(6): pp. 3147-3153
A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander, David Heckerman
PLoS Computational Biology | October 2007, Vol 4(10): pp. e188
Extensive HLA class I allele promiscuity among viral CTL epitopes
Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D. Walker, Alessandro Sette, David Heckerman, Bette T. Korber, Christian Brander
European Journal of Immunology | September 2007, Vol 37(9): pp. 2419-2433
Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1
Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan, Jonathan M. Carlson
PLoS Pathogens | July 2007
Leveraging Hierarchical Population Structure in Discrete Association Studies
Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman
PLoS One | July 2007, Vol 2: pp. e591
Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections
Christine M. Rousseau, Gerald H. Learn, Tanmoy Bhattacharya, David C. Nickle, David Heckerman, Senica Chetty, Christian Brander, Philip J. R. Goulder, Bruce D. Walker, Photini Kiepiela, Bette T. Korber, James I. Mullins
Journal of Virology | May 2007
Determining the Number of Non-Spurious Arcs in a Learned DAG Model: Investigation of a Bayesian and a Frequentist Approach
Jennifer Listgarten, David Heckerman
MSR-TR-2007-60 | May 2007
Coping with Viral Diversity in HIV Vaccine Design
David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins
PLoS Computational Biology | April 2007, pp. e75
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations
Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber
Science | January 2007, Vol 315: pp. 1583-1586
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load
Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthia Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Pendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H. Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I. Mullins, David Heckerman, Bruce D. Walker, Philip Goulder
Nature Medicine | December 2006
Identifying the effects of human immune pressure on the evolution of HIV.
Jonathan M. Carlson, Carl Kadie, David Heckerman
December 2006
Learning MHC I – Peptide Binding
Nebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Kadie, Ora Schueler-Furman
June 2006, Vol 22(14): pp. e227-e235
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction
David Heckerman, Carl Kadie, Jennifer Listgarten
MSR-TR-2005-127 | September 2005
Joint Discovery Of Haplotype Blocks And Complex Trait Associations From SNP Sequences
Nebojsa Jojic, Vladimir Jojic, David Heckerman
UAI-P-2004-PG-286-292 | July 2004
Symposium on Networked Systems Design and Implemenentation (NSDI)
Efficient Approximations for Learning Phylogenetic HMM Models from Data
Vladimir Jojic, Nebojsa Jojic, Chris Meek, Daniel Geiger, Adam Siepel, David Haussler, David Heckerman
MSR-TR-2003-62 | October 2003
-
Learning Mixtures Of Smooth, Nonuniform Deformation Models For Probabilistic Image Matching
Nebojsa Jojic, Brendan J. Frey, Patrice Simard, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, Key West, FL | May 2001
The Learning-Curve Sampling Method Applied to Model-Based Clustering
Chris Meek, Bo Thiesson, David Heckerman
Journal of Machine Learning Research | February 2001, Vol 2: pp. 397-418
Also appears as Technical Report MSR-TR-01-34, Microsoft Research, February, 2001.
Fast Learning from Sparse Data
Max Chickering, David Heckerman
MSR-TR-2000-15 | August 1999
Proceedings of the Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON
The Compilation of Decision Models
David Heckerman, John Breese, Eric Horvitz
March 1999
Stratified Exponential Families: Graphical Models and Model Selection
Dan Geiger, David Heckerman, Henry King, Chris Meek
MSR-TR-98-31 | July 1998
The Lumiere Project: Bayesian User Modeling for Inferring the Goals and Needs of Software Users
Eric Horvitz, Jack Breese, David Heckerman, David Hovel, Koos Rommelse
Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence, Madison, WI, July 1998, Morgan Kaufmann: San Francisco. | July 1998
Inferring Informational Goals from Free-Text Queries: A Bayesian Approach
MSR-TR-1998-5 | July 1998
Proceedings of the Fourth Conference on Uncertainty in Artificial Intelligence (UAI1988)
A Bayesian Approach to Filtering Junk E-Mail
David Heckerman, Eric Horvitz, Mehran Sahami, Susan Dumais
AAAI Workshop on Learning for Text Categorization | July 1998
Learning Mixtures of DAG Models
Bo Thiesson, Chris Meek, Max Chickering, David Heckerman
MSR-TR-97-30 | December 1997
Revised May 1998
Models and Selection Criteria for Regression and Classification
David Heckerman, Chris Meek
MSR-TR-97-08 | August 1997
Symposium on Discrete Algorithms
A Bayesian Approach To Learning Bayesian Networks With Local Structure
Max Chickering, David Heckerman, Chris Meek
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, ® Providence, RI | August 1997
Structure and Parameter Learning for Causal Independence and Causal Interaction Models
Chris Meek, David Heckerman
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, Providence, RI | August 1997
Embedded Bayesian Network Classifiers
David Heckerman, Chris Meek
MSR-TR-97-06 | March 1997
Decision-Theoretic Case-Based Reasoning
John S. Breese, David Heckerman
MSR-TR-95-03 | May 1996
IEEE Transactions on Systems, Man, and Cybernetics
Decision-Theoretic Troubleshooting: A Framework for Repair and Experiment
John S. Breese, David Heckerman
MSR-TR-96-06 | March 1996
Probabilistic Independence Networks for Hidden Markov Probability Models
Padhraic Smyth, David Heckerman, Michael I. Jordan
MSR-TR-96-03 | January 1996
Learning Bayesian Networks: A Unification for Discrete and Gaussian Domains
David Heckerman, Dan Geiger
UAI-P-1995-PG-274-284 | August 1995
Robotics Science and System Workshop on Task and Motion Planning
A Characterization of the Dirichlet Distribution with Application to Learning Bayesian Networks
Dan Geiger, David Heckerman
UAI-P-1995-PG-196-207 | August 1995
Real-Time Graphics Architectures, Algorithms, and Programming Systems: Project Technical Report
A Bayesian Approach to Learning Causal Networks
MSR-TR-95-04 | August 1995
Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence (UAI1995)
A Definition and Graphical Representation for Causality
Proceedings of Eleventh Conference on Uncertainty in Artificial Intelligence, Montreal, Quebec | May 1995
Decision-Theoretic Troubleshooting
David Heckerman, John S. Breese, Koos Rommelse
CACM | May 1995
Real-World Applications of Bayesian Networks
David Heckerman, Abe Mamdani, Michael P. Wellman
Communications of the ACM | March 1995, Vol 38(3): pp. 24-26
Learning Bayesian Networks: Search Methods and Experimental Results
Max Chickering, Dan Geiger, David Heckerman
Proceedings of the Fifth International Workshop on Artificial Intelligence and Statistics | January 1995
A New Look at Causal Independence
David Heckerman, John S. Breese
UAI-P-1994-PG-286-292 | July 1994
Proceedings of the Ninth Conference on Uncertainty in Artificial Intelligence (UAI1993)
A Decision-Based View of Causality
David Heckerman, Ross D. Shachter
UAI-P-1994-PG-302-310 | July 1994
Proceedings of the Second Conference on Uncertainty in Artificial Intelligence (UAI1986)
Learning Bayesian Networks: The Combination of Knowledge and Statistical Data
David Heckerman, Dan Geiger, Max Chickering
Machine Learning | March 1994, Vol 20(3): pp. 197-243
Learning Gaussian Networks
Dan Geiger, David Heckerman
MSR-TR-94-10 | January 1994
Troubleshooting Under Uncertainty
David Heckerman, John S. Breese, Koos Rommelse
MSR-TR-94-07 | January 1994
Diagnosis of Multiple Faults: A Sensitivity Analysis
David Heckerman, Michael Shwe
MSR-TR-93-11 | June 1993
SPIE Astronomy Telescopes and Instruments
Efficient Approximations for the Marginal Likelihood of Incomplete Data Given a Bayesian Network
Max Chickering, David Heckerman
MSR-TR-96-08 | May 1993
An Approximate Nonmyopic Computation for Value of Information
David Heckerman, Eric Horvitz, Blackford Middleton
January 1993
Toward Normative Expert Systems Part II
David Heckerman, Bharat N. Nathwani
Methods of Information in Medicine | August 1992, Vol 31: pp. 106-116
The Certainty-Factor Model
Encyclopedia of Artificial Intelligence, Second Edition | August 1992, pp. 131-138
Toward Normative Expert Systems Part I
David Heckerman, Eric Horvitz, Bharat N. Nathwani
Methods of Information in Medicine | June 1992, Vol 31: pp. 90-105
From Certainty Factors to Belief Networks
David Heckerman, Edward H. Shortliffe
Artificial Intelligence in Medicine | February 1992, pp. 35-52
Probabilistic Similarity Networks
Published by MIT Press - Cambridge, MA | August 1991
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part II
Blackford Middleton, Michael Shwe, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | August 1991, Vol 30: pp. 256-267
Advances in Probabilistic Reasoning
Dan Geiger, David Heckerman
Proceedings of the Seventh Conference on Uncertainty in Artificial Intelligence | July 1991
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part I
Michael Shwe, Blackford Middleton, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | May 1991, Vol 30: pp. 241-255
Probabilistic Similarity Networks
Networks | August 1990
Separable and Transitive Graphoids
Dan Geiger, David Heckerman
UAI-P-1990-PG-538-545 | August 1990
SRC Technical Note 1994-001 (December 1994).
A Combination of Cutset Conditioning with Clique-tree Propagation in the Pathfinder System
Jaap Suermondt, Gregory F. Cooper, David Heckerman
UAI-P-1990-PG-273-280 | August 1990
SRI International
Similarity Networks for the Construction of Multiple-Fault Belief Networks
UAI-P-1990-PG-32-39 | July 1990
Stanford University Interactive Workspaces Project Technical Note 2001-1
A Tractable Algorithm for Diagnosing Multiple Diseases
UAI-P-1989-PG-174-181 | July 1990
Secure Internet Programming
Heuristic Abstraction in the Decision-Theoretic Pathfinder System
Eric Horvitz, David Heckerman, Keung-Chi Ng, Bharat Nathwani
Proceedings of the Symposium on Computers in Medical Care, Washington DC, IEEE Press: Silver Springs MD | November 1989
An Empirical Comparison of Three Inference Methods
UAI-P-1988-PG-158-169 | August 1988
SIGCOMM 2014
A Method for Temporal Probabilistic Reasoning
Gregory F. Cooper, Eric Horvitz, David Heckerman
KSL-88-30 | July 1988
Knowledge Systems Laboratory
The Myth of Modularity in Rule-Based Systems for Reasoning with Uncertainty
UAI-P-1986-PG-115-122 | January 1988
Thinking Backward for Knowledge Acquisition
Ross D. Shachter, David Heckerman
AI Magazine | August 1987, pp. 55-61
A Perspective on Confidence and its use in Focusing Attention During Knowledge Acquisition
David Heckerman, Holly Jimison
UAI-P-1987-PG-123-131 | July 1987
In Proceedings of the Third Workshop on Uncertainty in Artificial Intelligence, Seattle, WA (UAI1987)
On the Expressiveness of Rule-based Systems for Reasoning with Uncertainty
AAAI-87 Proceedings | January 1987
An Axiomatic Framework for Belief Updates
UAI-P-1986-PG-123-128 | October 1986
SPIE Astronomy Telescopes and Instruments
Towards a Better Understanding of the INTERNIST-1 Knowledge Base
David Heckerman, Randolph A. Miller
Proceedings of Medinfo, Washington | October 1986
The Use of a Heuristic Problem-Solving Hierarchy to Facilitate the Explanation of Hypothesis-Directed Reasoning
Eric Horvitz, David Heckerman, Bharat Nathwani, Lawrence Fagan
January 1986, pp. 27-31
A Framework for Comparing Alternative Formalisms for Plausible Reasoning
Eric Horvitz, David Heckerman, Curtis P. Langlotz
AAAI-86 Proceedings | January 1986
The Inconsistent Use of Measures of Certainty in Artificial Intelligence Research
Uncertainty in Artificial Intelligence Annual Conference on Uncertainty in Artificial Intelligence (UAI-85) | August 1985
Diagnostic Strategies in the Hypothesis-Directed PATHFINDER System
Eric Horvitz, David Heckerman, Bharat N. Nathwani, Lawrence M. Fagan
January 1984, pp. 630-636
Probabilistic Interpretations for MYCIN’s Certainty Factors
UAI-P-1985-PG-9-20 | November 2016
In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA
Computational and Statistical Issues in Personalized Medicine
Christoph Lippert, David Heckerman
XRDS: Crossroads, The ACM Magazine for Students - Computational Biology | July 2015, Vol 24(4): pp. 24-27
Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
October 2014
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas S. Richardson
Kybernetika | July 2014
Epigenome-wide association studies without the need for cell-type composition
James Zhou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
Nature Methods | August 2013
FaST-LMM-Select for addressing confounding from spatial structure and rare variants
Jennifer Listgarten, Christoph Lippert, David Heckerman
MSR-TR-2013-137 | April 2013
Second International Enterprise Distributed Object Computing Workshop (EDOC )
Causal Independence for Knowledge Acquisition and Inference
MSR-TR-93-10 | March 2013
Asymptotic Model Selection for Directed Networks with Hidden Variables
Dan Geiger, David Heckerman, Chris Meek
MSR-TR-96-07 | February 2013
An Experimental Comparison of Several Clustering and Initialization Methods
Marina Meila, David Heckerman
MSR-TR-98-06 | January 2013
Improved Learning in U.S. History and Decision Competence with Decision-Focused Curriculum
David Jacobson, Andrew Parker, Chris Spetzler, Wandi Bruine de Bruin, Keith Hollenbeck, David Heckerman, Baruch Fischhoff
PLoS ONE | September 2012
Conditional Random Fields for Fast, Large-Scale Genome-Wide Association Studies
Jim Huang, Chris Meek, Carl Kadie, David Heckerman
PLoS ONE | July 2011
Pearl Causality and the Value of Control
Ross Shachter, David Heckerman
Heuristics, Probability and Causality: A Tribute to Judea Pearl | May 2010
Beyond Atopy: Multiple Patterns of Sensitization in Relation to Asthma in a Birth Cohort Study
Angela Simpson, Vincent Y. Tan, John Winn, Markus Svensén, Christopher Bishop, David Heckerman, Iain Buchan, Adnan Custovic
American Journal of Respiratory and Critical Care Medicine | February 2010, Vol 181: pp. 1200-1206
Update on the Pathfinder Project
David Heckerman, Eric Horvitz, Bharat Nathwani
Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care | May 2009
Problem Formulation as the Reduction of a Decision Model
UAI-P-1990-PG-82-89 | May 2009
SRC Technical Note 1998-004 (March 1998). Rejected by Information Processing Letters.
Continuous Time Dynamic Topic Models
Chong Wang, David Blei, David Heckerman
UAI-P-2008-PG-579-586 | July 2008
Tech Report 2003 61
Reflection and Action Under Scarce Resources: Theoretical Principles and Empirical Study
Eric Horvitz, Gregory Cooper, David Heckerman
November 2007
Considering Cost Asymmetry in Learning Classifiers
Francis Bach, David Heckerman, Eric Horvitz
Machine Learning Research | October 2005, Vol 7: pp. 1713-1741
Using Epitomes To Model Genetic Diversity: Rational Design Of HIV Vaccines
Nebojsa Jojic, Vladimir Jojic, Brendan J. Frey, Chris Meek, David Heckerman
NIPS | May 2005
Large-Sample Learning of Bayesian Networks is NP-Hard
Max Chickering, David Heckerman, Chris Meek
Journal of Machine Learning Research | December 2004, Vol 5: pp. 1287-1330
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas Richardson
MSR-TR-2004-94 | September 2004
A Characterization of the Dirichlet Distribution Through Global and Local Independence
Dan Geiger, David Heckerman
MSR-TR-94-16 | November 2003
Annal Statistics
An MDP-Based Recommender System
Guy Shani, Ronen I. Brafman, David Heckerman
UAI-P-2002-PG-453-460 | August 2002
Proceedings of Twentieth Conference on Uncertainty in Artificial Intelligence, Banff, Canada, UAI Press
CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence
Carl Kadie, Chris Meek, David Heckerman
MSR-TR-2002-46 | August 2002
Proceedings of Twenty Fourth Conference on Uncertainty in Artificial Intelligence, Helsinki, Finland, UAI Press
An Evaluation of the Diagnostic Accuracy of Pathfinder
David Heckerman, Bharat N. Nathwani
Comput Biomed Res | November 2001, Vol 25(1): pp. 56-74
-
Improved Learning in U.S. History and Decision Competence with Decision-Focused Curriculum
David Jacobson, Andrew Parker, Chris Spetzler, Wandi Bruine de Bruin, Keith Hollenbeck, David Heckerman, Baruch Fischhoff
PLoS ONE | September 2012
-
Stopping Spam
Joshua Goodman, David Heckerman, Robert Rounthwaite
Scientific American | April 2005, Vol 292: pp. 42-49
-
Dependency Networks for Inference, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
MSR-TR-2000-16 | October 2000
Proceedings of the International Conference on Dependable Systems and Networks
Targeted Advertising with Inventory Management
Max Chickering, David Heckerman
MSR-TR-2000-49 | October 2000
ACM Special Interest Group on E-Commerce (EC00), ® Minneapolis, MN
Visualization of Navigation Patterns on a Web Site Using Model Based Clustering
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
MSR-TR-2000-18 | March 2000
Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
Proceedings of Sixteenth Conference on Uncertainty in Artificial Intelligence, ® Stanford, CA | January 2000
Towards a Better Understanding of the INTERNIST-1 Knowledge Base
David Heckerman, Randolph A. Miller
Proceedings of Medinfo, Washington | October 1986
Model-Based Clustering and Visualization of Navigation Patterns on a Web Site
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
Data Mining and Knowledge Discovery | October 2003, Vol 7(4): pp. 399-424
Also in KDD 2000
Autoregressive Tree Models For Time-Series Analysis
Chris Meek, Max Chickering, David Heckerman
Proceedings of the Second International SIAM Conference on Data Mining | August 2002
-
Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point
Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder
Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559
Combinatorics of The Vaccine Design Problem: Definition and An Algorithm
Darko Kirovski, David Heckerman, Nebojsa Jojic
MSR-TR-2007-148 | November 2007
Efficient Approximations for Learning Phylogenetic HMM Models from Data
Vladimir Jojic, Nebojsa Jojic, Chris Meek, Daniel Geiger, Adam Siepel, David Haussler, David Heckerman
MSR-TR-2003-62 | October 2003
-
Computationally Efficient Methods for Selecting Among Mixtures of Graphical Models
Max Chickering, David Heckerman, Chris Meek
Bayesian Statistics 6 | Published by Oxford University Press | 1999 | Bayesian Statistics 6 edition
A Characterization of the Bivariate Normal-Wishart Distribution
Dan Geiger, David Heckerman
MSR-TR-95-53 | November 1995
Decision-Theoretic Foundations for Causal Reasoning
David Heckerman, Ross Shachter
MSR-TR-94-11 | March 1994
Causal Independence for Probability Assessment and Inference Using Bayesian Networks
John S. Breese, David Heckerman
MSR-TR-94-08 | March 1994
Linear mixed model for heritability estimation that explicitly addresses environmental variation
David Heckerman, Deepti Gurdasani, Carl Kadie, Cristina Pomilla, Tommy Carstensen, Hilary Martin, Kenneth Ekoru, Rebecca N. Nsubuga, Gerald Ssenyomo, Anatoli Kamali, Pontiano Kaleebu, Christian Widmer, Manjinder S. Sandhu
Proceedings of the National Academy of Sciences | April 2016
An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data
Christoph Lippert, Jennifer Listgarten, Bob Davidson, Jeff Baxter, Hoifung Poon, Carl Kadie, David Heckerman
Scientific Reports | January 2013, Vol 3
FaST linear mixed models for genome-wide association studies
Christoph Lippert, Jennifer Listgarten, Ying Liu, Carl Kadie, Bob Davidson, David Heckerman
Nature Methods | October 2011, Vol 8: pp. 833-835
-
The Learning-Curve Sampling Method Applied to Model-Based Clustering
Chris Meek, Bo Thiesson, David Heckerman
Journal of Machine Learning Research | February 2001, Vol 2: pp. 397-418
Also appears as Technical Report MSR-TR-01-34, Microsoft Research, February, 2001.
Accelerating EM For Large Databases
Bo Thiesson, Chris Meek, David Heckerman
Machine Learning | January 2001, Vol 45: pp. 279-299
Also appears as Technical Report MSR-TR-99-31, Microsoft Research, May, 1999 (Revised February, 2001).
Learning Bayesian Networks From Dependency Networks: A Preliminary Study
Geoff Hulten, Max Chickering, David Heckerman
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, ® Key West, FL | January 2001
The Learning-Curve Method Applied To Clustering
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, ® Key West, Florida | January 2001
Goal-Oriented Clustering
Max Chickering, David Heckerman, Chris Meek, John Platt, Bo Thiesson
MSR-TR-2000-82 | May 2000
A Decision-Theoretic Approach to Targeted Advertising
Max Chickering, David Heckerman
MSR-TR-2000-17 | February 2000
Proceedings of the International Conference on Functional Programming
Fast Learning from Sparse Data
Max Chickering, David Heckerman
MSR-TR-2000-15 | August 1999
Proceedings of the Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON
Empirical Analysis of Predictive Algorithms for Collaborative Filtering
John S. Breese, David Heckerman, Carl Kadie
MSR-TR-98-12 | May 1998
Inductive Learning Algorithms and Representations for Text Categorization
Susan Dumais, John Platt, David Heckerman, Mehran Sahami
7th International Conference on Information and Knowledge Management | January 1998
Learning Mixtures of DAG Models
Bo Thiesson, Chris Meek, Max Chickering, David Heckerman
MSR-TR-97-30 | December 1997
Revised May 1998
A Comparison of Scientific and Engineering Criteria for Bayesian Model Selection
David Heckerman, Max Chickering
MSR-TR-96-12 | June 1996
Tools and Algorithms for the Construction and Analysis of Systems (TACAS '07)
Decision-Theoretic Case-Based Reasoning
John S. Breese, David Heckerman
MSR-TR-95-03 | May 1996
IEEE Transactions on Systems, Man, and Cybernetics
On Finding A Cycle Basis With A Shortest Maximal Cycle
Max Chickering, Dan Geiger, David Heckerman
Information Processing Letters | August 1995, Vol 54: pp. 55-58
A Bayesian Approach to Learning Causal Networks
MSR-TR-95-04 | August 1995
Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence (UAI1995)
Decision-Theoretic Troubleshooting
David Heckerman, John S. Breese, Koos Rommelse
CACM | May 1995
Learning Bayesian Networks: The Combination of Knowledge and Statistical Data
David Heckerman, Dan Geiger, Max Chickering
Machine Learning | March 1994, Vol 20(3): pp. 197-243
Learning Gaussian Networks
Dan Geiger, David Heckerman
MSR-TR-94-10 | January 1994
Inference Algorithms for Similarity Networks
Dan Geiger, David Heckerman
MSR-TR-93-09 | July 1993
Proceedings of the IEEE International Conference on Data Mining (ICDM)
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Bioinformatics | September 2014, pp. btu504
Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
MSR-TR-2008-97 | July 2008
Large-Sample Learning of Bayesian Networks is NP-Hard
Max Chickering, David Heckerman, Chris Meek
Journal of Machine Learning Research | December 2004, Vol 5: pp. 1287-1330
Probabilistic Models for Relational Data
David Heckerman, Chris Meek, Daphne Koller
MSR-TR-2004-30 | March 2004
Probabilistic Entity-Relationship Models, PRMs and Plate Models
David Heckerman, Chris Meek, Daphne Koller
Introduction to Statistical Relational Learning | Published by MIT Press | 2004
Model-Based Clustering and Visualization of Navigation Patterns on a Web Site
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
Data Mining and Knowledge Discovery | October 2003, Vol 7(4): pp. 399-424
Also in KDD 2000
Staged Mixture Modeling and Boosting
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence | August 2002
CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence
Carl Kadie, Chris Meek, David Heckerman
MSR-TR-2002-46 | August 2002
Proceedings of Twenty Fourth Conference on Uncertainty in Artificial Intelligence, Helsinki, Finland, UAI Press
-
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Bioinformatics | September 2014, pp. btu504
Estimating false discovery rates for contingency tables
Jonathan M. Carlson, David Heckerman, Guy Shani
MSR-TR-2009-53 | May 2009
-
Quantifying the Uncertainty in Heritability
Nicholas Furlotte, David Heckerman, Christoph Lippert
MSR-TR-2014-161 | March 2014
-
Learning Bayesian Networks From Dependency Networks: A Preliminary Study
Geoff Hulten, Max Chickering, David Heckerman
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, ® Key West, FL | January 2001
Parameter Priors for Directed Acyclic Graphical Models and the Characterization of Several Probability Distributions
Dan Geiger, David Heckerman
MSR-TR-98-67 | January 2001
Computationally Efficient Methods For Selecting Among Mixtures Of Graphical Models, With Discussion
Bo Thiesson, Chris Meek, David Maxwell Chickering, David Heckerman
Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting | Published by Oxford University Press | 1999 | Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting edition
Editors: Bernardo, J., Berger, J., Dawid, A., and Smith, A.
A Tutorial on Learning With Bayesian Networks
MSR-TR-95-06 | March 1995
Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes
Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker
Journal of Virology | January 2008, pp. JVI.00535-8
-
ARMA Time-Series Modeling with Graphical Models
Bo Thiesson, Max Chickering, David Heckerman, Chris Meek
Proceedings of the Twentieth Conference on Uncertainty in Artificial Intelligence | July 2004
-
A Bayesian Approach to Causal Discovery
David Heckerman, Chris Meek, Gregory Cooper
Computation, Causation, and Discovery | Published by AAAI Press | 2006 | Computation, Causation, and Discovery edition
ISBN: 978-3-540-30609-2
Publications by Type
-
The Learning-Curve Sampling Method Applied to Model-Based Clustering
Chris Meek, Bo Thiesson, David Heckerman
Journal of Machine Learning Research | February 2001, Vol 2: pp. 397-418
Also appears as Technical Report MSR-TR-01-34, Microsoft Research, February, 2001.
Accelerating EM For Large Databases
Bo Thiesson, Chris Meek, David Heckerman
Machine Learning | January 2001, Vol 45: pp. 279-299
Also appears as Technical Report MSR-TR-99-31, Microsoft Research, May, 1999 (Revised February, 2001).
On Finding A Cycle Basis With A Shortest Maximal Cycle
Max Chickering, Dan Geiger, David Heckerman
Information Processing Letters | August 1995, Vol 54: pp. 55-58
Real-World Applications of Bayesian Networks
David Heckerman, Abe Mamdani, Michael P. Wellman
Communications of the ACM | March 1995, Vol 38(3): pp. 24-26
Learning Bayesian Networks: The Combination of Knowledge and Statistical Data
David Heckerman, Dan Geiger, Max Chickering
Machine Learning | March 1994, Vol 20(3): pp. 197-243
Toward Normative Expert Systems Part II
David Heckerman, Bharat N. Nathwani
Methods of Information in Medicine | August 1992, Vol 31: pp. 106-116
The Certainty-Factor Model
Encyclopedia of Artificial Intelligence, Second Edition | August 1992, pp. 131-138
Toward Normative Expert Systems Part I
David Heckerman, Eric Horvitz, Bharat N. Nathwani
Methods of Information in Medicine | June 1992, Vol 31: pp. 90-105
From Certainty Factors to Belief Networks
David Heckerman, Edward H. Shortliffe
Artificial Intelligence in Medicine | February 1992, pp. 35-52
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part II
Blackford Middleton, Michael Shwe, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | August 1991, Vol 30: pp. 256-267
Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base Part I
Michael Shwe, Blackford Middleton, David Heckerman, Max Henrion, Eric Horvitz, Harold Lehmann, Gregory Cooper
Methods of Information in Medicine | May 1991, Vol 30: pp. 241-255
Probabilistic Similarity Networks
Networks | August 1990
Integrated Expert Systems and Videodisc in Surgical Pathology: An Overview
B. Nathwani, David Heckerman, Eric Horvitz, T. Lincoln
Human Pathology | August 1990, Vol 21: pp. 11-27
Thinking Backward for Knowledge Acquisition
Ross D. Shachter, David Heckerman
AI Magazine | August 1987, pp. 55-61
Diagnostic Strategies in the Hypothesis-Directed PATHFINDER System
Eric Horvitz, David Heckerman, Bharat N. Nathwani, Lawrence M. Fagan
January 1984, pp. 630-636
Pressure release superleak sound modes in He II
David Heckerman, Ralph Rosenbaum, Seth Putterman, Gary A. Williams
Journal of Low Temperature Physics | March 1980, Vol 38(5-6): pp. 629-640
Surface tension sound in superfluid helium films adsorbed on alumina powder
Ralph Rosenbaum, G. A. Williams, David Heckerman, J. Marcus, D. Scholler, J. Maynard, I. Rudnick
Journal of Low Temperature Physics | December 1979, Vol 37(5): pp. 663-678
Superfluid Two-Phase Sound
Seth Putterman, David Heckerman, Ralph Rosenbaum, Gary Williams
Physical Review Letters | February 1979, Vol 42(9): pp. 580-583
Impact of Pre-Adapted HIV Transmission
Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert
Nature Medicine | May 2016, Vol 22: pp. 606-613
Bonnie Mathieson Young Investigator Award
Computational and Statistical Issues in Personalized Medicine
Christoph Lippert, David Heckerman
XRDS: Crossroads, The ACM Magazine for Students - Computational Biology | July 2015, Vol 24(4): pp. 24-27
Anti-Hepatitis C Virus T-Cell Immunity in the Context of Multiple Exposures to the Virus
Katja Pfafferott, Pooja Deshpande, Elizabeth McKinnon, Shahzma Merani, Andrew Lucas, David Heckerman, Simon Mallal, Mina John, Silvana Gaudieri, Michaela Lucas
June 2015
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
Garbiel R. A. Margarido, David Heckerman
PLoS Comput Biol | April 2015
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of virology | April 2015, Vol 89: pp. 4015-4019
Accurate Liability Estimation Improves Power in Ascertained Case-Control Studies
Omer Weissbrod, Christoph Lippert, Dan Geiger, David Heckerman
Nature Methods | February 2015, Vol 12: pp. 332-334
Immune screening identifies novel T cell targets encoded by anti-sense reading frames of HIV-1
Christopher T. Berger, Anuska Llano, Jonathan M. Carlson, Zabrina L. Brumme, Mark A. Brockman, Samandhy Cedeno, P. Richard Harrigan, Daniel E. Kaufmann, David Heckerman, Andreas Meyerhans, Christian Brander
Journal of Virology | January 2015
Further Improvements to Linear Mixed Models for Genome-Wide Association Studies
Christian Widmer, Christoph Lippert, Omer Weissbrod, Nicolo Fusi, Carl Kadie, Robert Davidson, Jennifer Listgarten, David Heckerman
October 2014
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Bioinformatics | September 2014, pp. btu504
Addendum on the scoring of Gaussian directed acyclic graphical models
Jack Kuipers, Giusi Moffa, David Heckerman
Annal Statistics | August 2014, Vol 42: pp. 1689-1691
HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes
Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B Davis, Charles E DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, Bruce D Walker
Journal of Virology | August 2014, Vol 88(22): pp. 12937-12948
Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
Science | July 2014, Vol 345(6193)
Publication Publication Publication Publication Publication Project
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas S. Richardson
Kybernetika | July 2014
Eliciting cytotoxic T-lymphocyte responses from synthetic vectors containing one or two epitopes in a C57BL/6 mouse model using peptide-containing biodegradable microspheres and adjuvants
R. M. Rubsamen, C. V. Herst, P. M. Lloyd, David Heckerman
June 2014
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Jennifer Listgarten, Christoph Lippert, Nicolo Fusi, David Heckerman, Jonathan M. Carlson
eLife | October 2013
Epigenome-wide association studies without the need for cell-type composition
James Zhou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
Nature Methods | August 2013
Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication
Justine Sunshine, Moon Kim, Jonathan M. Carlson, David Heckerman, Julie Czartoski, Stephen A. Migueles, Janine Maenza, M. Juliana McElrath, James I. Mullins, Nicole Frahm
Journal of Virology | August 2013, Vol 88(2): pp. 1354-1365
Influence of HLA-C Expression Level on HIV Control
Richard Apps, Ying Qi, Jonathan M. Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington
Science | April 2013, Vol 340(6128): pp. 87-91
HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes
Corine Bronke, Coral-Ann M. Almeida, Elizabeth McKinnon, Steven G. Roberts, Niamh M. Keane, Abha Chopra, Jonathan M. Carlson, David Heckerman, Simon Mallal, Mina John
AIDS, Basic Science | March 2013, Vol 27(6): pp. 899-905
HIV-1 p24gag Derived Conserved Element DNA Vaccine Increases the Breadth of Immune Response in Mice
Viraj Kulkarni, Margherita Rosati, Antonio Valentin, Brunda Ganneru, Ashish K. Singh, Jian Yan, Morgane Rolland, Candido Alicea, Rachel Kelly Beach, Gen-Mu Zhang, Sylvie Le Gall, Kate E. Broderick, Niranjan Y. Sardesai, David Heckerman, Beatriz Mothe, Christian Brander, David B. Weiner, James I. Mullins, George N. Pavlakis, Barbara K. Felber
PLoS ONE | March 2013, pp. e60245
High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control
Zaza M. Ndhlovu, Lori B. Chibnik, Jacqueline Proudfoot, Seanna Vine, Ashley McMullen, Kevin Cesa, Filippos Porichis, R. Brad Jones, Donna Marie Alvino, Meghan G. Hart, Eleni Stampouloglou, Alicja Piechocka-Trocha, Carl Kadie, Florencia Pereyra, David Heckerman, Philip L. De Jager, Bruce D. Walker, Daniel E. Kaufmann
Blood Journal | January 2013, Vol 121(5)
An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data
Christoph Lippert, Jennifer Listgarten, Bob Davidson, Jeff Baxter, Hoifung Poon, Carl Kadie, David Heckerman
Scientific Reports | January 2013, Vol 3
Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins
Christian L Boutwell, Jonathan M. Carlson, Tien-Ho Lin, Aaron Seese, Karen A Power, Jian Peng, Yanhua Tang, Zabrina L Brumme, David Heckerman, Arne Schneidewind, Todd M Allen
January 2013
A powerful and efficient set test for genetic markers that handles confounders
Jennifer Listgarten, Christoph Lippert, Carl Kadie, David Heckerman
Bioinformatics | January 2013
Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme
Journal of Virololgy | December 2012, Vol 86(24): pp. 13202-13216
Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope
Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan M. Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder
Journal of Virololgy | December 2012, Vol 86(23): pp. 12643-12654
Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan
Shigeru Nomura, Noriaki Hosoya, Zabrina L. Brumme, Mark A. Brockman, Tadashi Kikuchi, Michiko Koga, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Jonathan M. Carlson, David Heckerman, Ai Kawana-Tachikawa, Aikichi Iwamoto, Toshiyuki Miura
Journal of Virology | November 2012, Vol 87(3): pp. 1465-1476
Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis
Jessica L. Prince, Daniel T. Claiborne, Jonathan M. Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A. Prentice, Ling Yue, Sundaram A. Vishwanathan, William Kilembe, Paul Geopfert, Matthew A. Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A. Derdeyn, Jiaming Tang, David Heckerman, Richard A. Kaslow, Susan A. Allen, Eric Hunter
PLoS Pathogens | November 2012, pp. e1003041
Co-operative additive effects between HLA alleles in control of HIV-1
Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
PLoS ONE | October 2012, pp. e47799
Improved Learning in U.S. History and Decision Competence with Decision-Focused Curriculum
David Jacobson, Andrew Parker, Chris Spetzler, Wandi Bruine de Bruin, Keith Hollenbeck, David Heckerman, Baruch Fischhoff
PLoS ONE | September 2012
Patterns of methylation heritability in a genome-wide analysis of four brain regions
Gerald Quon, Christoph Lippert, David Heckerman, Jennifer Listgarten
Nucleic Acids Research | August 2012
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans
Paul J. McLaren, Stephan Ripke, Kimberly Pelak, Amy C. Weintrob, Nikolaos A. Patsopoulos, Xiaoming Jia, Rachel L. Erlich, Niall J. Lennon, Carl Kadie, David Heckerman, Namrata Gupta, David W. Haas, Steven G. Deeks, Florencia Pereyra, Bruce D. Walker, Paul I. W. de Bakker
Human Molecular Genetics | June 2012, Vol 21(19): pp. 4334-4347
Improved linear mixed models for genome-wide association studies
Jennifer Listgarten, Christoph Lippert, Carl Kadie, Robert I. Davidson, Eleazar Eskin, David Heckerman
Nature Methods | May 2012, Vol 9: pp. 3–4
Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
Journal of Virology | May 2012, Vol 86(9): pp. 5230-5243
Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity
Mark A. Brockman, Denis R. Chopera, Alex Olvera, Chanson J. Brumme, Jennifer Sela, Tristan J. Markle, Eric Martin, Jonathan M. Carlson, Anh Q. Le, Rachel McGovern, Peter K. Cheung, Anthony D. Kelleher, Heiko Jessen, Martin Markowitz, Eric Rosenberg, Nicole Frahm, Jorge Sanchez, Simon Mallal, Mina John, P. Richard Harrigan, David Heckerman, Christian Brander, Bruce D. Walker, Zabrina L. Brumme
Journal of Virology | April 2012
Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models
Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
February 2012
High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection
Niamh M. Keane, Stevens G. Roberts, Coral-Ann M. Almedia, Tanya Krishnan, Abha Chopra, Emma Demaine, Rebecca Laird, Monika Tschochner, Jonathan M. Carlson, Simon Mallal, David Heckerman, Ian James, Mina John
Immunology and Cell Biology | February 2012, Vol 90(2): pp. 224-234
CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Jennifer Zamarreno, Mattia Schiaulini, Cristina Miranda, Marta Ruiz-Riol, Christoph T. Berger, M. Jose Herrero, Eduard Palou, Montse Plana, Morgane Rolland, Ashok Khatri, David Heckerman, Florencia Pereyra, Bruce D. Walker, David Weiner, Roger Paredes, Bonaventura Clotet, Barbara K. Felber, George N. Pavlakis, James I. Mullins, Chirstian Brander
PLoS ONE | January 2012, pp. e29717
HIV-specific CD4 T cell responses to different viral proteins have discordant associations with viral load and clinical outcome
Srinika Ranasinghe, Michael Flanders, Sam Cutler, Damien Z. Soghoian, Musie Ghebremicahel, Isaiah Davis, Madelene Lindqvist, Florencia Pereyra, Bruce D. Walker, David Heckerman, Hendrik Streeck
Journal of Virology | October 2011
FaST linear mixed models for genome-wide association studies
Christoph Lippert, Jennifer Listgarten, Ying Liu, Carl Kadie, Bob Davidson, David Heckerman
Nature Methods | October 2011, Vol 8: pp. 833-835
A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD
Alan E. Renton, Elisa Majounie, Adrian Waite, Javier Simon-Sanchez, Sara Rollinson, J. Raphael Gibbs, Jennifer C Scymick, Hannu Laaksovirta, John. C. van Swieten, Liisa Myllykangas, Hannu Kalimo, Anders Paetau, Yevgeniya Abramzon, Anne M. Remes, Alice Kaganovich, Sonja W. Scholz, Jamie Duckworth, Jinhui Ding, Daniel W. Harmer, Dena G. Hernandez, Janel O. Johnson, Kin Mok, Mina Ryten, Danyah Trabzuni, Rita J. Guerreiro, Richard W. Orrell, James Neal, Alex Murray, Justin Pearson, Iris E. Jansen, David Sondervan, Harro Seelaar, Derek Blake, Kate Young, Nicola Halliwell, Janis Bennion Callister, Greg Toulson, Anna Richardson, Alex Gerhard, Julie Snowden, David Mann, David Neary, Michael A. Nalls, Terhi Peuralinna, Lilja Jansson, Veli-Matti Isovaiita, Anna-Lotta Kaivorinne, Maarit Holtta-Vuori, Elina Ikonen, Raimo Sulkava, MIchael Benatar, Joanne Wuu, Adriano Chio, Garbiella Restagno, Giuseppe Borghero, Mario Sabatelli, The ITALSGEN Consortium, David Heckerman, Ekaterina ROgaeva, Lorne Zinman, Jeffrey D. Rothstein, MIchael Sendtner, Carsten Drepper, Evan E. Eichler, Can Alkan, Ziedulla Abdullaev, Svetlana D. Pack, Amalia Dutra, Evengenia Pak, John Hardy, Andrew SIngleton, Nigel M. Williams, Peter Heutink, Stuart Pickering-Brown, Huw R. Morris, Pentti J. Tienari, Bryan J. Traynor
Neuron | September 2011, Vol 72(2): pp. 257-268
Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant Epitopes
Coral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan M. Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John
The Journal of Immunology | September 2011
Definition of the viral targets of protective HIV-1-specific T cell responses
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Marcus Daniels, Cristina Miranda, Jennifer Zamarreno, Vanessa Bach, Rosario Zuniga, Susana Perez-Alvarez, Chirstoph T. Berger, Maria C. Puertas, Javier Martinez-Picado, Morgane Rolland, Marilu Farfan, James J. Szinger, William H. Hildebrand, Otto O. Yang, Victor Sanchez-Merino, Chanson J. Brumme, Zabrina L. Brumme, David Heckerman, Todd M. Allen, James I. Mullins, Guadalupe Gomez, Philip J. Goulder, Bruce D. Walker, Jose M. Gatell, Bonaventura Clotet, Better T. Korber, Jorge Sanchez, Chirstian Brander
Journal of Translational Medicine | August 2011, Vol 9(208)
HIV-1 Adaptation to NK-Cell-Mediated Immune Pressure
Galit Alter, David Heckerman, Arne Schneidewind, Lena Fadda, Carl Kadie, Jonathan M. Carlson, Cesar Oniangue-Ndza, Maureen Martin, Bin Li, Salim I. Khakoo, Mary Carrington, Todd M. Allen, Marcus Altfeld
Nature International weekly journal of science | August 2011, Vol 476: pp. 96-100
Conditional Random Fields for Fast, Large-Scale Genome-Wide Association Studies
Jim Huang, Chris Meek, Carl Kadie, David Heckerman
PLoS ONE | July 2011
Variable HIV Peptide Stability in Human Cytosol is Critical to Epitope Presentation and Immune Escape
Estibaliz Lazaro, Carl Kadie, Pamela Stamegna, Shao Chong Zhang, Pauline Gourdain, Nicole Y. Lai, Mei Zhang, Sergio A. Martinez, David Heckerman, Sylvie Le Gall
J Clin Invest | June 2011
Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations
Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M. Carlson, Mark A. Brockman, Swati Mishra, Zabrina L. Brumme, Stephen Hickling, Christopher S.W. Tang, Toshiyuki Miura, Chris Seebregts, David Heckerman, Thumbi Ndung'u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Bloemfotnein-Oxford Collaborative Group, Cloete van Vuuren, John Frater
April 2011
HLA-A*7401-Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703
Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan M. Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder
The Journal of Immunology | April 2011
Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences
Morgane Rolland, Nicole Frahm, David C. Nickle, Nebojsa Jojic, Wenjie Deng, Todd M. Allen, Christian Brander, David Heckerman, James I. Mullins
PLoS One | March 2011, Vol 28(6): pp. e17969
Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C
Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u
February 2011
Reduced Replication Capacity of NL4-3 Recombinant Viruses Encoding Reverse Transcriptase Integrase Sequences From HIV-1 Elite Controllers
Zabrina L. Brumme, Chun Li, Toshiyuki Miura, Jennifer Sela, Pamela C. Rosato, Chanson J. Brumme, Tristan J. Markle, Eric Martin, Brian L. Block, Alicja Trocha, Carl Kadie, Todd M. Allen, Florencia Pereyra, David Heckerman, Bruce D. Walker, Mark A. Brockman
J Acquir Immune Defic Syndr. | February 2011
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Science The International HIV Controllers Study | December 2010, Vol 330(6010): pp. 1551-1557
The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms
Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung'u, David Heckerman, Eric Hunter, Philip J. R. Goulder
Journal of Virology | November 2010
Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection
Mark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan M. Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen
Journal of Virology | November 2010, Vol 84(22): pp. 11937-11949
Chromosome 9p21 in Amyotrophic Lateral Sclerosis in Finland: A Genome-Wide Association Study
Hannu Laaksovirta, Terhi Peuralinna, Jennifer C. Schymick, Sonja W. Scholz, Shaoi-Lin Lai, Liisa Myllykangas, Raimo Sulkava, Lilja Jansson, Dena G. Hernandez, J. Raphael Gibbs, Michael A. Nalls, David Heckerman, Pentti J. Tienari, Bryan J. Traynor
The Lancet Neurology | October 2010, pp. 978-985
Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters
Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u
Journal of Virology | October 2010
Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics
Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J. R. Goulder, Bruce D. Walker, Christian Brander, David Heckerman, James I. Mullins
PLoS ONE | September 2010, pp. e12463
Correction for Hidden Confounders in the Genetic Analysis of Gene Expression
Jennifer Listgarten, Carl Kadie, Eric E. Schadt, David Heckerman
September 2010
Adaptive Interactions between HLA and HIV-1: Highly Divergent Selection Imposed by HLA Class I Molecules with Common Supertype Motifs
Mina John, David Heckerman, Ian James, Lawrence P. Park, Jonathan M. Carlson, Abha Chopra, Silvana Gaudieri, David Nolan, David W. Haas, Sharon A. Riddler, Richard Haubrich, Simon Mallal
The Journal of Immunology | March 2010, Vol 184(8): pp. 4368-4377
Beyond Atopy: Multiple Patterns of Sensitization in Relation to Asthma in a Birth Cohort Study
Angela Simpson, Vincent Y. Tan, John Winn, Markus Svensén, Christopher Bishop, David Heckerman, Iain Buchan, Adnan Custovic
American Journal of Respiratory and Critical Care Medicine | February 2010, Vol 181: pp. 1200-1206
Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection
Alasdair Leslie, Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Carl Kadie, Thumbi Ndung'u, Christian Brander, Hoosen Coovadia, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
Journal of Virology | February 2010, Vol 84(19): pp. 9879-9888
CD8 T Cell Response and Evolutionary Pressure to HIV-1 Cryptic Epitopes Derived from Antisense Transcription
Anju Bansal, Jonathan M. Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David N. Levy, Sonya Heath, Jianming Tang, Richard A Kaslow, Bruce D. Walker, Thumbi Ndung'u, Philip J. Goulder, David Heckerman, Eric Hunter, Paul A. Goepfert
The Journal of Experimental Medicine | January 2010, Vol 207(1): pp. 51
Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences
Christopher T. Berger, Jonathan M. Carlson, Chanson J. Brumme, Kari L. Hartman, Zabrina L. Brumme, Leah M. Henry, Pamela C. Rosato, Alicja Piechocka-Trocha, Mark A. Brockman, P. Richard Harrigan, David Heckerman, Daniel E. Kaufmann, Christian Brander
JEM | January 2010
Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time
Michiko Koga, Ai Kawana-Tachikawa, David Heckerman, Takashi Odawara, Hitomi Nakamura, Tomohiko Koibuchi, Takeshi Fujii, Toshiyuki Miura, Aikichi Iwamoto
Microbiology and Immunology | January 2010, Vol 54(4): pp. 196-205
PhyloDet: A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
Bioinformatics | October 2009, Vol 25(19): pp. 2611-2612
HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins
Zabrina L. Brumme, Mina John, Jonathan M. Carlson, Chanson J. Brumme, Dennison Chan, Mark A. Brockman, Luke C. Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal
August 2009
Unique Features of HLA-mediated HIV Evolution in a Mexican Cohort: A Comparative Study
Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran
Retrovirology | August 2009
HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
July 2009
Adaptation of HIV-1 to Human Leukocyte Antigen Class I
Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Pendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung'u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder
Nature | April 2009, Vol 458: pp. 641-645
Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles
Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins
AIDS Research and Human Retroviruses | March 2009
HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1
Toshiyuki Miura, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Florencia Pereyra, Alicja Trocha, Brian L. Block, Arne Schneidewind, Todd M. Allen, David Heckerman, Bruce D. Walker
Journal of Virology | January 2009, Vol 83(1): pp. 140-149
HLA footprints on HIV-1 are associated with inter-clade polymorphisms and intra-clade phylogenetic clustering
Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan M. Carlson, David Heckerman, Thumbi Ndung'u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder
Journal of Virology | January 2009, pp. JVI.02017-08
Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1
Yaoyu E. Wang, Bin Li, Jonathan M. Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen
Journal of Virology | January 2009, Vol 83(4): pp. 1845-1855
Design, Expression, and Processing of Epitomized Hepatitis C Virus-Encoded CTL Epitopes
Daniel Yerly, David Heckerman, Todd Allen, Todd J. Suscovich, Nebojsa Jojic, Carl Kadie, Werner J. Pichler, Andreas Cerny, Christian Brander
The Journal of Immunology | November 2008, Vol 181: pp. 6361-6370
Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman
PLoS Computational Biology | November 2008, Vol 4: pp. e1000225
In Silico Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman
October 2008
Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point
Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Isobella Honeyborne, Jonathan M. Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. Goulder
Journal of Virology | September 2008, Vol 82(17): pp. 8548-8559
Comparison Of Immunogen Designs That Optimize Peptide Coverage: Reply To Fischer et al.
David C Nickle, Nebojsa Jojic, David Heckerman, Darko Kirovski, Vladimir Jojic, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins
PLoS Computational Biology | March 2008, pp. e25
Efficient Control of Population Structure in Model Organism Association Mapping
Hyun Min Kang, Noah A. Zaitlen, Claire M. Wade, Andrew Kirby, David Heckerman, Mark J. Daly, Eleazar Eskin
Genetics | March 2008, Vol 178(3): pp. 1709-1723
Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure
KC Ngumbela, CL Day, Z Mncube, K Nair, D Ramduth, C Thobakgale, E Moodley, S Reddy, C de Pierres, N Mkhwanazi, K Bishop, M van der Stok, N Ismail, I honeyborne, H Crawford, DG Kavanagh, C Rousseau, D Nickle, J Mullins, David Heckerman, B Korber, H Coovadia, P Kiepiela, PJ Goulder, BD Walker
AIDS Res Hum Retroviruses | January 2008, Vol 24(1): pp. 72-82
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads
Morgane Rolland, David Heckerman, Wenjie Deng, Christine M. Rousseau, Hoosen Coovadia, Karen Bishop, Philip J.R. Goulder, Bruce D. Walker, Chirstian Brander, James I. Mullins
PLoS ONE | January 2008, pp. e1424
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients
Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, Eric Hunter
Journal of Experimental Medicine | January 2008, Vol 205: pp. 1009-1017
HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load
Christine M. Rousseau, Marcus G. Daniels, Jonathan M. Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins
Journal of Virology | January 2008, Vol 82: pp. 6434-6446
Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection
Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker
Journal of Virology | January 2008, Vol 82: pp. 9216-9227
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients
Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan M. Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen
Hepatology | January 2008, Vol 48: pp. 1769-1778
Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes
Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan M. Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker
Journal of Virology | January 2008, pp. JVI.00535-8
Increased Cytotoxic T-Lymphocyte Epitope Variant Cross-Recognition and Functional Avidity Are Associated with Hepatitis C Virus Clearance
Daniel Yerly, David Heckerman, Todd M. Allen, John V. Chisholm III, Kellie Faircloth, Caitlyn H. Linde, Nicole Frahm, Joerg Timm, Werner J. Pichler, Andreas Cerny, Christian Brander
Journal of Virology | October 2007, Vol 82(6): pp. 3147-3153
A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander, David Heckerman
PLoS Computational Biology | October 2007, Vol 4(10): pp. e188
Extensive HLA class I allele promiscuity among viral CTL epitopes
Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D. Walker, Alessandro Sette, David Heckerman, Bette T. Korber, Christian Brander
European Journal of Immunology | September 2007, Vol 37(9): pp. 2419-2433
Leveraging Hierarchical Population Structure in Discrete Association Studies
Jonathan M. Carlson, Carl Kadie, Simon Mallal, David Heckerman
PLoS One | July 2007, Vol 2: pp. e591
Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections
Christine M. Rousseau, Gerald H. Learn, Tanmoy Bhattacharya, David C. Nickle, David Heckerman, Senica Chetty, Christian Brander, Philip J. R. Goulder, Bruce D. Walker, Photini Kiepiela, Bette T. Korber, James I. Mullins
Journal of Virology | May 2007
Coping with Viral Diversity in HIV Vaccine Design
David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins
PLoS Computational Biology | April 2007, pp. e75
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations
Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan M. Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber
Science | January 2007, Vol 315: pp. 1583-1586
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load
Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthia Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Pendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H. Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I. Mullins, David Heckerman, Bruce D. Walker, Philip Goulder
Nature Medicine | December 2006
Learning MHC I – Peptide Binding
Nebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Kadie, Ora Schueler-Furman
June 2006, Vol 22(14): pp. e227-e235
Considering Cost Asymmetry in Learning Classifiers
Francis Bach, David Heckerman, Eric Horvitz
Machine Learning Research | October 2005, Vol 7: pp. 1713-1741
Stopping Spam
Joshua Goodman, David Heckerman, Robert Rounthwaite
Scientific American | April 2005, Vol 292: pp. 42-49
Large-Sample Learning of Bayesian Networks is NP-Hard
Max Chickering, David Heckerman, Chris Meek
Journal of Machine Learning Research | December 2004, Vol 5: pp. 1287-1330
Model-Based Clustering and Visualization of Navigation Patterns on a Web Site
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
Data Mining and Knowledge Discovery | October 2003, Vol 7(4): pp. 399-424
Also in KDD 2000
An Evaluation of the Diagnostic Accuracy of Pathfinder
David Heckerman, Bharat N. Nathwani
Comput Biomed Res | November 2001, Vol 25(1): pp. 56-74
-
Learning Mixtures Of Smooth, Nonuniform Deformation Models For Probabilistic Image Matching
Nebojsa Jojic, Brendan J. Frey, Patrice Simard, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, Key West, FL | May 2001
Learning Bayesian Networks From Dependency Networks: A Preliminary Study
Geoff Hulten, Max Chickering, David Heckerman
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, ® Key West, FL | January 2001
The Learning-Curve Method Applied To Clustering
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of Eighth International Workshop on Artificial Intelligence and Statistics, ® Key West, Florida | January 2001
Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
Proceedings of Sixteenth Conference on Uncertainty in Artificial Intelligence, ® Stanford, CA | January 2000
The Compilation of Decision Models
David Heckerman, John Breese, Eric Horvitz
March 1999
The Lumiere Project: Bayesian User Modeling for Inferring the Goals and Needs of Software Users
Eric Horvitz, Jack Breese, David Heckerman, David Hovel, Koos Rommelse
Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence, Madison, WI, July 1998, Morgan Kaufmann: San Francisco. | July 1998
A Bayesian Approach to Filtering Junk E-Mail
David Heckerman, Eric Horvitz, Mehran Sahami, Susan Dumais
AAAI Workshop on Learning for Text Categorization | July 1998
Inductive Learning Algorithms and Representations for Text Categorization
Susan Dumais, John Platt, David Heckerman, Mehran Sahami
7th International Conference on Information and Knowledge Management | January 1998
A Bayesian Approach To Learning Bayesian Networks With Local Structure
Max Chickering, David Heckerman, Chris Meek
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, ® Providence, RI | August 1997
Structure and Parameter Learning for Causal Independence and Causal Interaction Models
Chris Meek, David Heckerman
Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence, Providence, RI | August 1997
A Definition and Graphical Representation for Causality
Proceedings of Eleventh Conference on Uncertainty in Artificial Intelligence, Montreal, Quebec | May 1995
Decision-Theoretic Troubleshooting
David Heckerman, John S. Breese, Koos Rommelse
CACM | May 1995
Learning Bayesian Networks: Search Methods and Experimental Results
Max Chickering, Dan Geiger, David Heckerman
Proceedings of the Fifth International Workshop on Artificial Intelligence and Statistics | January 1995
An Approximate Nonmyopic Computation for Value of Information
David Heckerman, Eric Horvitz, Blackford Middleton
January 1993
Advances in Probabilistic Reasoning
Dan Geiger, David Heckerman
Proceedings of the Seventh Conference on Uncertainty in Artificial Intelligence | July 1991
Heuristic Abstraction in the Decision-Theoretic Pathfinder System
Eric Horvitz, David Heckerman, Keung-Chi Ng, Bharat Nathwani
Proceedings of the Symposium on Computers in Medical Care, Washington DC, IEEE Press: Silver Springs MD | November 1989
On the Expressiveness of Rule-based Systems for Reasoning with Uncertainty
AAAI-87 Proceedings | January 1987
Towards a Better Understanding of the INTERNIST-1 Knowledge Base
David Heckerman, Randolph A. Miller
Proceedings of Medinfo, Washington | October 1986
A Framework for Comparing Alternative Formalisms for Plausible Reasoning
Eric Horvitz, David Heckerman, Curtis P. Langlotz
AAAI-86 Proceedings | January 1986
The Inconsistent Use of Measures of Certainty in Artificial Intelligence Research
Uncertainty in Artificial Intelligence Annual Conference on Uncertainty in Artificial Intelligence (UAI-85) | August 1985
Linear mixed model for heritability estimation that explicitly addresses environmental variation
David Heckerman, Deepti Gurdasani, Carl Kadie, Cristina Pomilla, Tommy Carstensen, Hilary Martin, Kenneth Ekoru, Rebecca N. Nsubuga, Gerald Ssenyomo, Anatoli Kamali, Pontiano Kaleebu, Christian Widmer, Manjinder S. Sandhu
Proceedings of the National Academy of Sciences | April 2016
Literome: PubMed-scale Genomic Knowledge Base in the Cloud
Hoifung Poon, Chris Quirk, Charlie DeZiel, David Heckerman
Bioinformatics 2014 | May 2014
Pearl Causality and the Value of Control
Ross Shachter, David Heckerman
Heuristics, Probability and Causality: A Tribute to Judea Pearl | May 2010
Update on the Pathfinder Project
David Heckerman, Eric Horvitz, Bharat Nathwani
Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care | May 2009
Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan M. Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan
AIDS | January 2008
Reflection and Action Under Scarce Resources: Theoretical Principles and Empirical Study
Eric Horvitz, Gregory Cooper, David Heckerman
November 2007
Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1
Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan, Jonathan M. Carlson
PLoS Pathogens | July 2007
Identifying the effects of human immune pressure on the evolution of HIV.
Jonathan M. Carlson, Carl Kadie, David Heckerman
December 2006
Using Epitomes To Model Genetic Diversity: Rational Design Of HIV Vaccines
Nebojsa Jojic, Vladimir Jojic, Brendan J. Frey, Chris Meek, David Heckerman
NIPS | May 2005
ARMA Time-Series Modeling with Graphical Models
Bo Thiesson, Max Chickering, David Heckerman, Chris Meek
Proceedings of the Twentieth Conference on Uncertainty in Artificial Intelligence | July 2004
Autoregressive Tree Models For Time-Series Analysis
Chris Meek, Max Chickering, David Heckerman
Proceedings of the Second International SIAM Conference on Data Mining | August 2002
Staged Mixture Modeling and Boosting
Chris Meek, Bo Thiesson, David Heckerman
Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence | August 2002
-
Parameter Priors for Directed Acyclic Graphical Models and the Characterization of Several Probability Distributions
Dan Geiger, David Heckerman
MSR-TR-98-67 | January 2001
Dependency Networks for Inference, Collaborative Filtering, and Data Visualization
David Heckerman, Max Chickering, Chris Meek, Robert Rounthwaite, Carl Kadie
MSR-TR-2000-16 | October 2000
Proceedings of the International Conference on Dependable Systems and Networks
Targeted Advertising with Inventory Management
Max Chickering, David Heckerman
MSR-TR-2000-49 | October 2000
ACM Special Interest Group on E-Commerce (EC00), ® Minneapolis, MN
Goal-Oriented Clustering
Max Chickering, David Heckerman, Chris Meek, John Platt, Bo Thiesson
MSR-TR-2000-82 | May 2000
Visualization of Navigation Patterns on a Web Site Using Model Based Clustering
Igor Cadez, David Heckerman, Chris Meek, Padhraic Smyth, Steven White
MSR-TR-2000-18 | March 2000
A Decision-Theoretic Approach to Targeted Advertising
Max Chickering, David Heckerman
MSR-TR-2000-17 | February 2000
Proceedings of the International Conference on Functional Programming
Fast Learning from Sparse Data
Max Chickering, David Heckerman
MSR-TR-2000-15 | August 1999
Proceedings of the Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON
Stratified Exponential Families: Graphical Models and Model Selection
Dan Geiger, David Heckerman, Henry King, Chris Meek
MSR-TR-98-31 | July 1998
Inferring Informational Goals from Free-Text Queries: A Bayesian Approach
MSR-TR-1998-5 | July 1998
Proceedings of the Fourth Conference on Uncertainty in Artificial Intelligence (UAI1988)
Empirical Analysis of Predictive Algorithms for Collaborative Filtering
John S. Breese, David Heckerman, Carl Kadie
MSR-TR-98-12 | May 1998
Learning Mixtures of DAG Models
Bo Thiesson, Chris Meek, Max Chickering, David Heckerman
MSR-TR-97-30 | December 1997
Revised May 1998
Models and Selection Criteria for Regression and Classification
David Heckerman, Chris Meek
MSR-TR-97-08 | August 1997
Symposium on Discrete Algorithms
Embedded Bayesian Network Classifiers
David Heckerman, Chris Meek
MSR-TR-97-06 | March 1997
A Comparison of Scientific and Engineering Criteria for Bayesian Model Selection
David Heckerman, Max Chickering
MSR-TR-96-12 | June 1996
Tools and Algorithms for the Construction and Analysis of Systems (TACAS '07)
Decision-Theoretic Case-Based Reasoning
John S. Breese, David Heckerman
MSR-TR-95-03 | May 1996
IEEE Transactions on Systems, Man, and Cybernetics
Decision-Theoretic Troubleshooting: A Framework for Repair and Experiment
John S. Breese, David Heckerman
MSR-TR-96-06 | March 1996
Probabilistic Independence Networks for Hidden Markov Probability Models
Padhraic Smyth, David Heckerman, Michael I. Jordan
MSR-TR-96-03 | January 1996
A Characterization of the Bivariate Normal-Wishart Distribution
Dan Geiger, David Heckerman
MSR-TR-95-53 | November 1995
Learning Bayesian Networks: A Unification for Discrete and Gaussian Domains
David Heckerman, Dan Geiger
UAI-P-1995-PG-274-284 | August 1995
Robotics Science and System Workshop on Task and Motion Planning
A Characterization of the Dirichlet Distribution with Application to Learning Bayesian Networks
Dan Geiger, David Heckerman
UAI-P-1995-PG-196-207 | August 1995
Real-Time Graphics Architectures, Algorithms, and Programming Systems: Project Technical Report
A Bayesian Approach to Learning Causal Networks
MSR-TR-95-04 | August 1995
Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence (UAI1995)
A Tutorial on Learning With Bayesian Networks
MSR-TR-95-06 | March 1995
A New Look at Causal Independence
David Heckerman, John S. Breese
UAI-P-1994-PG-286-292 | July 1994
Proceedings of the Ninth Conference on Uncertainty in Artificial Intelligence (UAI1993)
A Decision-Based View of Causality
David Heckerman, Ross D. Shachter
UAI-P-1994-PG-302-310 | July 1994
Proceedings of the Second Conference on Uncertainty in Artificial Intelligence (UAI1986)
Decision-Theoretic Foundations for Causal Reasoning
David Heckerman, Ross Shachter
MSR-TR-94-11 | March 1994
Causal Independence for Probability Assessment and Inference Using Bayesian Networks
John S. Breese, David Heckerman
MSR-TR-94-08 | March 1994
Learning Gaussian Networks
Dan Geiger, David Heckerman
MSR-TR-94-10 | January 1994
Troubleshooting Under Uncertainty
David Heckerman, John S. Breese, Koos Rommelse
MSR-TR-94-07 | January 1994
Inference Algorithms for Similarity Networks
Dan Geiger, David Heckerman
MSR-TR-93-09 | July 1993
Proceedings of the IEEE International Conference on Data Mining (ICDM)
Diagnosis of Multiple Faults: A Sensitivity Analysis
David Heckerman, Michael Shwe
MSR-TR-93-11 | June 1993
SPIE Astronomy Telescopes and Instruments
Efficient Approximations for the Marginal Likelihood of Incomplete Data Given a Bayesian Network
Max Chickering, David Heckerman
MSR-TR-96-08 | May 1993
Separable and Transitive Graphoids
Dan Geiger, David Heckerman
UAI-P-1990-PG-538-545 | August 1990
SRC Technical Note 1994-001 (December 1994).
A Combination of Cutset Conditioning with Clique-tree Propagation in the Pathfinder System
Jaap Suermondt, Gregory F. Cooper, David Heckerman
UAI-P-1990-PG-273-280 | August 1990
SRI International
Similarity Networks for the Construction of Multiple-Fault Belief Networks
UAI-P-1990-PG-32-39 | July 1990
Stanford University Interactive Workspaces Project Technical Note 2001-1
A Tractable Algorithm for Diagnosing Multiple Diseases
UAI-P-1989-PG-174-181 | July 1990
Secure Internet Programming
An Empirical Comparison of Three Inference Methods
UAI-P-1988-PG-158-169 | August 1988
SIGCOMM 2014
A Method for Temporal Probabilistic Reasoning
Gregory F. Cooper, Eric Horvitz, David Heckerman
KSL-88-30 | July 1988
Knowledge Systems Laboratory
The Myth of Modularity in Rule-Based Systems for Reasoning with Uncertainty
UAI-P-1986-PG-115-122 | January 1988
A Perspective on Confidence and its use in Focusing Attention During Knowledge Acquisition
David Heckerman, Holly Jimison
UAI-P-1987-PG-123-131 | July 1987
In Proceedings of the Third Workshop on Uncertainty in Artificial Intelligence, Seattle, WA (UAI1987)
An Axiomatic Framework for Belief Updates
UAI-P-1986-PG-123-128 | October 1986
SPIE Astronomy Telescopes and Instruments
Probabilistic Interpretations for MYCIN’s Certainty Factors
UAI-P-1985-PG-9-20 | November 2016
In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA
Quantifying the Uncertainty in Heritability
Nicholas Furlotte, David Heckerman, Christoph Lippert
MSR-TR-2014-161 | March 2014
The benefits of selecting phenotype-specific variants for applications of mixed models in genomics
Christoph Lippert, Gerald Quon, Eun Yong Kang, Carl Kadie, Jennifer Listgarten, David Heckerman
MSR-TR-2013-138 | May 2013
FaST-LMM-Select for addressing confounding from spatial structure and rare variants
Jennifer Listgarten, Christoph Lippert, David Heckerman
MSR-TR-2013-137 | April 2013
Second International Enterprise Distributed Object Computing Workshop (EDOC )
Causal Independence for Knowledge Acquisition and Inference
MSR-TR-93-10 | March 2013
Asymptotic Model Selection for Directed Networks with Hidden Variables
Dan Geiger, David Heckerman, Chris Meek
MSR-TR-96-07 | February 2013
An Experimental Comparison of Several Clustering and Initialization Methods
Marina Meila, David Heckerman
MSR-TR-98-06 | January 2013
Extraneous markers used for genetic similarity leads to loss of power in GWAS and heritability determination
Christoph Lippert, Gerald Quon, Jennifer Listgarten, David Heckerman
MSR-TR-2012-120 | December 2012
Problem Formulation as the Reduction of a Decision Model
UAI-P-1990-PG-82-89 | May 2009
SRC Technical Note 1998-004 (March 1998). Rejected by Information Processing Letters.
Estimating false discovery rates for contingency tables
Jonathan M. Carlson, David Heckerman, Guy Shani
MSR-TR-2009-53 | May 2009
Continuous Time Dynamic Topic Models
Chong Wang, David Blei, David Heckerman
UAI-P-2008-PG-579-586 | July 2008
Tech Report 2003 61
Det. (Distance Encoded Tree): A Scalable Visualization Tool for Mapping Multiple Traits to Large Evolutionary Trees
Bongshin Lee, Lev Nachmanson, George Robertson, Jonathan M. Carlson, David Heckerman
MSR-TR-2008-97 | July 2008
Statistical Resolution of Ambiguous HLA Typing Data
Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman
MSR-TR-2008-07 | January 2008
Combinatorics of The Vaccine Design Problem: Definition and An Algorithm
Darko Kirovski, David Heckerman, Nebojsa Jojic
MSR-TR-2007-148 | November 2007
Determining the Number of Non-Spurious Arcs in a Learned DAG Model: Investigation of a Bayesian and a Frequentist Approach
Jennifer Listgarten, David Heckerman
MSR-TR-2007-60 | May 2007
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction
David Heckerman, Carl Kadie, Jennifer Listgarten
MSR-TR-2005-127 | September 2005
Variations on Undirected Graphical Models and their Relationships
David Heckerman, Chris Meek, Thomas Richardson
MSR-TR-2004-94 | September 2004
Joint Discovery Of Haplotype Blocks And Complex Trait Associations From SNP Sequences
Nebojsa Jojic, Vladimir Jojic, David Heckerman
UAI-P-2004-PG-286-292 | July 2004
Symposium on Networked Systems Design and Implemenentation (NSDI)
Probabilistic Models for Relational Data
David Heckerman, Chris Meek, Daphne Koller
MSR-TR-2004-30 | March 2004
A Characterization of the Dirichlet Distribution Through Global and Local Independence
Dan Geiger, David Heckerman
MSR-TR-94-16 | November 2003
Annal Statistics
Efficient Approximations for Learning Phylogenetic HMM Models from Data
Vladimir Jojic, Nebojsa Jojic, Chris Meek, Daniel Geiger, Adam Siepel, David Haussler, David Heckerman
MSR-TR-2003-62 | October 2003
An MDP-Based Recommender System
Guy Shani, Ronen I. Brafman, David Heckerman
UAI-P-2002-PG-453-460 | August 2002
Proceedings of Twentieth Conference on Uncertainty in Artificial Intelligence, Banff, Canada, UAI Press
CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence
Carl Kadie, Chris Meek, David Heckerman
MSR-TR-2002-46 | August 2002
Proceedings of Twenty Fourth Conference on Uncertainty in Artificial Intelligence, Helsinki, Finland, UAI Press
-
Probabilistic Similarity Networks
Published by MIT Press - Cambridge, MA | August 1991
-
The Use of a Heuristic Problem-Solving Hierarchy to Facilitate the Explanation of Hypothesis-Directed Reasoning
Eric Horvitz, David Heckerman, Bharat Nathwani, Lawrence Fagan
January 1986, pp. 27-31
-
Computationally Efficient Methods for Selecting Among Mixtures of Graphical Models
Max Chickering, David Heckerman, Chris Meek
Bayesian Statistics 6 | Published by Oxford University Press | 1999 | Bayesian Statistics 6 edition
Computationally Efficient Methods For Selecting Among Mixtures Of Graphical Models, With Discussion
Bo Thiesson, Chris Meek, David Maxwell Chickering, David Heckerman
Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting | Published by Oxford University Press | 1999 | Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting edition
Editors: Bernardo, J., Berger, J., Dawid, A., and Smith, A.
A Bayesian Approach to Causal Discovery
David Heckerman, Chris Meek, Gregory Cooper
Computation, Causation, and Discovery | Published by AAAI Press | 2006 | Computation, Causation, and Discovery edition
ISBN: 978-3-540-30609-2
Probabilistic Entity-Relationship Models, PRMs and Plate Models
David Heckerman, Chris Meek, Daphne Koller
Introduction to Statistical Relational Learning | Published by MIT Press | 2004