{"id":421359,"date":"2017-08-23T10:40:42","date_gmt":"2017-08-23T17:40:42","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/?post_type=msr-event&#038;p=421359"},"modified":"2025-08-06T11:57:44","modified_gmt":"2025-08-06T18:57:44","slug":"cabi-2017","status":"publish","type":"msr-event","link":"https:\/\/www.microsoft.com\/en-us\/research\/event\/cabi-2017\/","title":{"rendered":"Computational Aspects of Biological Information 2017"},"content":{"rendered":"\n\n<p><strong>Venue:<\/strong> <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/lab\/microsoft-research-new-england\/\" target=\"_blank\" rel=\"noopener noreferrer\">Microsoft Research New England<\/a><br \/>\nHorace Mann Conference Room<br \/>\nFirst Floor Conference Center<br \/>\nOne Memorial Drive, Cambridge, MA<\/p>\n<p><strong>Registration is now closed.<\/strong><\/p>\n<p><strong>Contact:<\/strong> Please email the conference organizers at\u00a0<a href=\"mailto:cabi2017@microsoft.com\">cabi2017@microsoft.com<\/a>.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-768x583.png 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-1024x777.png 1024w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-80x60.png 80w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork.png 2018w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>Computational Aspects of Biological Information (CABI) 2017 is the fifth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2017 will be held at Microsoft Research New England on October 13, 2017 and will\u00a0bring together experts to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.<\/p>\n<h2>Symposium Speakers<\/h2>\n<p>Confirmed speakers include:<\/p>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.med.upenn.edu\/apps\/faculty\/index.php\/g275\/p8507519\">Yoseph Barash<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, University of Pennsylvania<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/statweb.stanford.edu\/~susan\/\">Susan Holmes<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Stanford University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.broadinstitute.org\/bios\/daniel-macarthur-0\">Daniel MacArthur<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Broad Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.broadinstitute.org\/bios\/todd-r-golub\">Todd Golub<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Broad Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/medschool.vanderbilt.edu\/brain-institute\/person\/nancy-j-cox-phd\">Nancy Cox<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Vanderbilt University<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/carlson\/\">Jonathan Carlson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Microsoft<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/bejerano.stanford.edu\/pi.html\">Gill Bejerano<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Stanford University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/www.vedantabio.com\/about\/board-of-directors\">Bernat Olle<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Vedanta Biosciences, Inc.<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/dmse.mit.edu\/faculty\/profile\/anikeeva\">Polina Anikeeva<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/niryosef.wordpress.com\/\">Nir Yoseph<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Berkeley University<\/li>\n<\/ul>\n<h2>Organizing committee<\/h2>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/frcasale\/\" target=\"_blank\" rel=\"noopener noreferrer\">Francesco Casale<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<\/ul>\n<h2>Poster Session<\/h2>\n<p>There will be a poster session in the afternoon. See the Poster Submissions tab for details.<\/p>\n<p><strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution&#8217;s ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution&#8217;s policies.<\/p>\n<p><strong>Arrival Guidance<\/strong><\/p>\n<p>Upon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p>To be considered for the CABI 2017 poster session, please submit the following information to <a href=\"mailto:CABI2017posters@microsoft.com\">CABI2017posters@microsoft.com<\/a> by September 29th. Submissions will be evaluated on a rolling basis. Space is limited, and preference will be given to early submissions.<\/p>\n<p>Posters may be up to 48\u201dW X 36\u201dH.<\/p>\n<ul>\n<li>Presenting author name<\/li>\n<li>Presenting author affiliation\/institution<\/li>\n<li>Presenting author email address<\/li>\n<li>Title<\/li>\n<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\n<li>Abstract (250 words maximum)<\/li>\n<\/ul>\n<p>Please email the conference organizers at <a href=\"mailto:cabi2017@microsoft.com\">cabi2017@microsoft.com<\/a> if you have any questions.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<table class=\"msr-table-schedule\">\n<thead class=\"thead\">\n<tr class=\"tr\">\n<th class=\"th\">Time<\/th>\n<th class=\"th\">Session<\/th>\n<th class=\"th\">Speaker<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"tbody\">\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Opening remarks<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Jennifer Chayes, Microsoft<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Biobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Nancy Cox, Vanderbilt University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Probing Neural Function with Electronic, Optical and Magnetic Materials<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Polina Anikeeva, Massachusetts University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Building a New View of Transcriptome Variations<\/div>\n<\/td>\n<td>Yoseph Barash, University of Pennsylvania<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Rational development of drugs from the human microbiota<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Bernat Olle, Vendata Biosciences, Inc.<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Lunch<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">One genome to rule them all, one genome to find them<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Gill Bejerano, Stanford University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Using Large Scale Genomic Databases to Improve Disease Variant Interpretation<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Daniel MacArthur, Broad Institute<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Single cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Nir Yosef, Berkeley University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break \/ poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Genomic Approaches to Cancer<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Todd Golub, Harvard University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Using the data, all the data; the case of the human microbiome<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Susan Holmes, Stanford University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Project Premonition: Scaling up pathogen surveillance<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Jonathan Carlson, Microsoft<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Closing Remarks<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p>\t<div data-wp-context='{\"items\":[]}' data-wp-interactive=\"msr\/accordion\">\n\t\t\t\t\t<div class=\"clearfix\">\n\t\t\t\t<div\n\t\t\t\t\tclass=\"btn-group align-items-center mb-g float-sm-right\"\n\t\t\t\t\tdata-bi-aN=\"accordion-collapse-controls\"\n\t\t\t\t>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Expand all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onExpandAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tExpand all\t\t\t\t\t<\/button>\n\t\t\t\t\t<span aria-hidden=\"true\"> | <\/span>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Collapse all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onCollapseAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tCollapse all\t\t\t\t\t<\/button>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t<ul class=\"msr-accordion\">\n\t\t\t\t\t\t\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1470\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1470\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1469\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tBiobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1469\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1470\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Nancy Cox<\/p>\n<p>We have applied the PrediXcan method in which we use GTEx as a reference to impute transcript levels for genes and test the association of those imputed transcript levels with ~1800 phenome codes developed for phenome-wide association studies. I will illustrate how we are using the resulting gene x medical phenome catalog to extend discovery research into identification of primary disease mechanism as well as novel approaches to translation of discoveries.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1472\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1472\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1471\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tProbing Neural Function with Electronic, Optical and Magnetic Materials\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1471\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1472\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Polina Anikeeva<\/p>\n<p>Mammalian nervous system contains billions of neurons that exchange electrical, chemical and mechanical signals. Our ability to study this complexity is limited by the lack of technologies available for interrogating neural circuits across their diverse signaling modalities without inducing a foreign-body reaction. My talk will describe neural interface strategies pursued in my group aimed at mimicking the materials properties and transduction mechanisms of the nervous system. Specifically, I will discuss (1) Fiber-based probes for multifunctional interfaces with the brain and spinal cord circuits; (2) Magnetic nanotransducers for minimally invasive neural stimulation; and (3) Active scaffolds for neural tissue engineering and interrogation.<\/p>\n<p>Fiber-drawing methods can be applied to create multifunctional polymer-based probes capable of simultaneous electrical, optical, and chemical probing of neural tissues in freely moving subjects. Similar engineering principles enable ultra-flexible miniature fiber-probes with geometries inspired by nerves, which permit simultaneous optical excitation and recording of neural activity in the spinal cord allowing for optical control of lower limb movement. Furthermore, fiber-based fabrication can be extended to design of scaffolds that direct neural growth and activity facilitating repair of damaged nerves.<\/p>\n<p>Molecular mechanisms of action potential firing inspire the development of materials-based strategies for direct manipulation of ion transport across neuronal membranes. For example, hysteretic heat dissipation by magnetic nanomaterials can be used to remotely trigger activity of neurons expressing heat-sensitive ion channels. Since the alternating magnetic fields in the low radiofrequency range interact minimally with the biological tissues, the magnetic nanoparticles injected into the brain can act as transducers of wireless magnetothermal deep brain stimulation. Similarly, local hysteretic heating allows magnetic nanoparticles to disrupt protein aggregates associated with neurodegenerative disorders.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1474\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1474\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1473\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tBuilding a New View of Transcriptome Variations\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1473\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1474\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Yoseph Barash<\/p>\n<p>In this talk, I will review some of the challenges and advances we have made in building a new view of transcriptome complexity, along with and the kind of tools that can be used to infer it.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1476\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1476\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1475\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tRational development of drugs from the human microbiota\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1475\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1476\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Bernat Olle<\/p>\n<p>Medicines that modulate the human microbiome hold enormous promise for treatment of immune and infectious diseases, as highlighted by the success of randomized, controlled trials of fecal transplantation for treatment of C. difficile infections and IBD, as well as early pilot data in GvHD. They also pose some unique scientific, translational, manufacturing, and regulatory challenges. Drugs based on defined bacterial consortia (characterized communities of limited numbers of live organisms) could potentially retain some of the beneficial attributes of fecal transplants while being amenable to development as pharmaceutical-grade agents. I will present examples of Vedanta\u2019s efforts to develop first-in-class drugs based on rationally selected bacterial consortia for applications in immune and infectious diseases.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1478\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1478\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1477\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tOne genome to rule them all, one genome to find them\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1477\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1478\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Gill Bejerano<\/p>\n<p>I will highlight some methodologies and examples of finding causal mutations in both medical genomics and comparative genomics contexts.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1480\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1480\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1479\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tUsing Large Scale Genomic Databases to Improve Disease Variant Interpretation\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1479\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1480\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Daniel MacArthur<\/p>\n<p>Rapid advances in sequencing technology have led to the generation of genome-scale DNA sequencing data for more than 2 million individuals worldwide. These data represent incredibly powerful information about the distribution and impact of genetic variation, but major challenges remain to aggregating and harmonizing them. In this presentation I will describe the development of the Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD) databases, which combined represent exome and genome sequencing data for over 135,000 individuals. I will discuss approaches to analyzing genome data at massive scale, and the applications of these data to understanding human variation and gene function.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1482\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1482\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1481\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tSingle cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1481\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1482\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Nir Yoseph<\/p>\n<p>Human immunity relies on coordinated responses of ensembles of cells from various types and functional states. Over the past several decades, substantial work has been done to catalog the cell types, states, and interactions that inform these behaviors. The emerging field of single cell genomics has the potential to make important contributions to this body of work, by providing a way to systematically map previously unknown subsets of cells, predict their functionality, and ultimately modulate their relative abundance so as to favorably tune the emerging immune response. In this talk I will present our recent work, which explored these ideas within the context of HIV-1 infection, using single-cell RNA-Seq of dendritic cells from human donors. Through a combination of computational analysis and experimental validation we were able to identify a highly functional subset of anti-viral dendritic cells that is capable of effectively priming T cell responses in vitro. Furthermore, by integrating knowledge from existing genomics databases we were able to identify and test immunomodulators that increase the relative abundance of this functional subset in-vitro, thus potentially leading to a more potent anti-viral response.<\/p>\n<p>While data sets produced by single cell genomics hold unique information, they also pose unique challenges, from idiosyncratic technical limitations to difficulty of interpretability. During this this talk, I will also describe some of the computational tools developed in my group, aiming to address these challenges and realize the potential of single-cell genomics.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1484\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1484\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1483\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tGenomic Approaches to Cancer\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1483\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1484\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Todd Golub<\/p>\n<p>It is now becoming possible to bring powerful genomic methods to bear on the process of cancer drug discovery. This talk will illustrate 1) the use of the Connectivity Map, a large-scale effort to develop a compendium of gene expression signatures of cellular state, 2) the use of PRISM, a new multiplexed, high throughput approach to screening cancer cell lines for anti-cancer activity and resistance, and 3) the use of cancer models (cell lines and patient-derived xenografts) in discovery, with particular focus on clonal drift in these models and the impact of that drift on drug sensitivity.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1486\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1486\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1485\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tUsing the data, all the data; the case of the human microbiome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1485\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1486\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Susan Holmes<\/p>\n<p>Longitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations. Longitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1488\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1488\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1487\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tProject Premonition: Scaling up pathogen surveillance\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1487\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1488\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Jonathan Carlson<\/p>\n<p>Emerging and re-emerging infectious diseases are a central public health concern, with implications for economies and even the stability of nations. The current system for detecting pathogens is entirely reactive, reliant on aggregating local reports by clinicians, and typically takes weeks of symptomatic human infections before detection. Project Premonition aims to detect pathogens before they cause outbreaks, using mosquitoes to sample pathogens in the environment. Turning a mosquito into a device requires new technologies to autonomously locate, robotically collect, and computationally analyze mosquitoes and their genetic payload. \u00a0To this end, we have developed and field tested robotic smart traps that instantaneously classify insects based on wing beat frequencies and other features, allowing real-time monitoring and selective capture of flying insects of interest. The rich data collected from these traps provides unprecedented insight into mosquito foraging behavior, allowing us to predict where and when we\u2019ll find mosquitos, which we expect will allow us to more rapidly locate disease while simultaneously improving the efficacy of mosquito control. Once mosquitos are captured, deep sequencing has the potential to provide insights into the population genetics of the mosquitos, the hosts on which they\u2019ve feed, and pathogens in both mosquitos and hosts. This is essentially a pan metagenomics problem, in which source genetic material may be derived from anywhere on the tree of life, thus motivating very high throughput taxonomic classification methods that leverage all available sequences in public databases. In this talk, I will provide an overview of Project Premonition, results from field trials on the traps, and our algorithmic approach to making a scalable metagenomics pipeline.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Computational Aspects of Biological Information (CABI) 2017 is the fifth one-day symposium on challenges and successes in computational biology. CABI 2017 will be held at Microsoft Research New England on October 13, 2017, and will bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium is open to everyone and registration is free of charge.<\/p>\n","protected":false},"featured_media":421815,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr_startdate":"2017-10-13","msr_enddate":"2017-10-13","msr_location":"Cambridge, MA, USA","msr_expirationdate":"","msr_event_recording_link":"","msr_event_link":"","msr_event_link_redirect":false,"msr_event_time":"9:00 AM \u2013 5:30 PM","msr_hide_region":true,"msr_private_event":false,"msr_hide_image_in_river":0,"footnotes":""},"research-area":[13553],"msr-region":[197900],"msr-event-type":[197944],"msr-video-type":[],"msr-locale":[268875],"msr-program-audience":[],"msr-post-option":[],"msr-impact-theme":[],"class_list":["post-421359","msr-event","type-msr-event","status-publish","has-post-thumbnail","hentry","msr-research-area-medical-health-genomics","msr-region-north-america","msr-event-type-hosted-by-microsoft","msr-locale-en_us"],"msr_about":"<!-- wp:msr\/event-details {\"title\":\"Computational Aspects of Biological Information 2017\",\"backgroundColor\":\"grey\",\"image\":{\"id\":421815,\"url\":\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720.jpg\",\"alt\":\"\"}} \/-->\n\n<!-- wp:msr\/content-tabs --><!-- wp:msr\/content-tab {\"title\":\"About\"} --><!-- wp:freeform --><p><strong>Venue:<\/strong> <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/lab\/microsoft-research-new-england\/\" target=\"_blank\" rel=\"noopener noreferrer\">Microsoft Research New England<\/a><br \/>\nHorace Mann Conference Room<br \/>\nFirst Floor Conference Center<br \/>\nOne Memorial Drive, Cambridge, MA<\/p>\n<p><strong>Registration is now closed.<\/strong><\/p>\n<p><strong>Contact:<\/strong> Please email the conference organizers at\u00a0<a href=\"mailto:cabi2017@microsoft.com\">cabi2017@microsoft.com<\/a>.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-768x583.png 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-1024x777.png 1024w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-80x60.png 80w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork.png 2018w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>Computational Aspects of Biological Information (CABI) 2017 is the fifth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2017 will be held at Microsoft Research New England on October 13, 2017 and will\u00a0bring together experts to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.<\/p>\n<h2>Symposium Speakers<\/h2>\n<p>Confirmed speakers include:<\/p>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.med.upenn.edu\/apps\/faculty\/index.php\/g275\/p8507519\">Yoseph Barash<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, University of Pennsylvania<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/statweb.stanford.edu\/~susan\/\">Susan Holmes<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Stanford University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.broadinstitute.org\/bios\/daniel-macarthur-0\">Daniel MacArthur<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Broad Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/www.broadinstitute.org\/bios\/todd-r-golub\">Todd Golub<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Broad Institute<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/medschool.vanderbilt.edu\/brain-institute\/person\/nancy-j-cox-phd\">Nancy Cox<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Vanderbilt University<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/carlson\/\">Jonathan Carlson<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Microsoft<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/bejerano.stanford.edu\/pi.html\">Gill Bejerano<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Stanford University<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/www.vedantabio.com\/about\/board-of-directors\">Bernat Olle<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Vedanta Biosciences, Inc.<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"http:\/\/dmse.mit.edu\/faculty\/profile\/anikeeva\">Polina Anikeeva<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Massachusetts Institute of Technology<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" target=\"_blank\" href=\"https:\/\/niryosef.wordpress.com\/\">Nir Yoseph<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>, Berkeley University<\/li>\n<\/ul>\n<h2>Organizing committee<\/h2>\n<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/frcasale\/\" target=\"_blank\" rel=\"noopener noreferrer\">Francesco Casale<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>,\u00a0Microsoft Research<\/li>\n<\/ul>\n<h2>Poster Session<\/h2>\n<p>There will be a poster session in the afternoon. See the Poster Submissions tab for details.<\/p>\n<p><strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution&#8217;s ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution&#8217;s policies.<\/p>\n<p><strong>Arrival Guidance<\/strong><\/p>\n<p>Upon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Poster Submissions\"} --><!-- wp:freeform --><p>To be considered for the CABI 2017 poster session, please submit the following information to <a href=\"mailto:CABI2017posters@microsoft.com\">CABI2017posters@microsoft.com<\/a> by September 29th. Submissions will be evaluated on a rolling basis. Space is limited, and preference will be given to early submissions.<\/p>\n<p>Posters may be up to 48\u201dW X 36\u201dH.<\/p>\n<ul>\n<li>Presenting author name<\/li>\n<li>Presenting author affiliation\/institution<\/li>\n<li>Presenting author email address<\/li>\n<li>Title<\/li>\n<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\n<li>Abstract (250 words maximum)<\/li>\n<\/ul>\n<p>Please email the conference organizers at <a href=\"mailto:cabi2017@microsoft.com\">cabi2017@microsoft.com<\/a> if you have any questions.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Agenda\"} --><!-- wp:freeform --><table class=\"msr-table-schedule\">\n<thead class=\"thead\">\n<tr class=\"tr\">\n<th class=\"th\">Time<\/th>\n<th class=\"th\">Session<\/th>\n<th class=\"th\">Speaker<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"tbody\">\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Opening remarks<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Jennifer Chayes, Microsoft<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Biobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Nancy Cox, Vanderbilt University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Probing Neural Function with Electronic, Optical and Magnetic Materials<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Polina Anikeeva, Massachusetts University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Building a New View of Transcriptome Variations<\/div>\n<\/td>\n<td>Yoseph Barash, University of Pennsylvania<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Rational development of drugs from the human microbiota<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Bernat Olle, Vendata Biosciences, Inc.<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Lunch<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">One genome to rule them all, one genome to find them<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Gill Bejerano, Stanford University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Using Large Scale Genomic Databases to Improve Disease Variant Interpretation<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Daniel MacArthur, Broad Institute<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Single cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Nir Yosef, Berkeley University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Coffee break \/ poster session<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Genomic Approaches to Cancer<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Todd Golub, Harvard University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Using the data, all the data; the case of the human microbiome<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Susan Holmes, Stanford University<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Project Premonition: Scaling up pathogen surveillance<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Jonathan Carlson, Microsoft<\/div>\n<\/td>\n<\/tr>\n<tr class=\"tr\">\n<td class=\"td-1-4\">\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div>\n<\/td>\n<td>\n<div class=\"msr-table-schedule-cell\">Closing Remarks<\/div>\n<\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- wp:msr\/content-tab {\"title\":\"Abstracts\"} --><!-- wp:freeform --><p>\t<div data-wp-context='{\"items\":[]}' data-wp-interactive=\"msr\/accordion\">\n\t\t\t\t\t<div class=\"clearfix\">\n\t\t\t\t<div\n\t\t\t\t\tclass=\"btn-group align-items-center mb-g float-sm-right\"\n\t\t\t\t\tdata-bi-aN=\"accordion-collapse-controls\"\n\t\t\t\t>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Expand all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllExpanded\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onExpandAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tExpand all\t\t\t\t\t<\/button>\n\t\t\t\t\t<span aria-hidden=\"true\"> | <\/span>\n\t\t\t\t\t<button\n\t\t\t\t\t\tclass=\"btn btn-link m-0\"\n\t\t\t\t\t\tdata-bi-cN=\"Collapse all\"\n\t\t\t\t\t\tdata-wp-bind--aria-controls=\"state.ariaControls\"\n\t\t\t\t\t\tdata-wp-bind--aria-expanded=\"state.ariaExpanded\"\n\t\t\t\t\t\tdata-wp-bind--disabled=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-class--inactive=\"state.isAllCollapsed\"\n\t\t\t\t\t\tdata-wp-on--click=\"actions.onCollapseAll\"\n\t\t\t\t\t\ttype=\"button\"\n\t\t\t\t\t>\n\t\t\t\t\t\tCollapse all\t\t\t\t\t<\/button>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t<ul class=\"msr-accordion\">\n\t\t\t\t\t\t\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1470\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1470\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1469\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tBiobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1469\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1470\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Nancy Cox<\/p>\n<p>We have applied the PrediXcan method in which we use GTEx as a reference to impute transcript levels for genes and test the association of those imputed transcript levels with ~1800 phenome codes developed for phenome-wide association studies. I will illustrate how we are using the resulting gene x medical phenome catalog to extend discovery research into identification of primary disease mechanism as well as novel approaches to translation of discoveries.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1472\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1472\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1471\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tProbing Neural Function with Electronic, Optical and Magnetic Materials\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1471\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1472\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Polina Anikeeva<\/p>\n<p>Mammalian nervous system contains billions of neurons that exchange electrical, chemical and mechanical signals. Our ability to study this complexity is limited by the lack of technologies available for interrogating neural circuits across their diverse signaling modalities without inducing a foreign-body reaction. My talk will describe neural interface strategies pursued in my group aimed at mimicking the materials properties and transduction mechanisms of the nervous system. Specifically, I will discuss (1) Fiber-based probes for multifunctional interfaces with the brain and spinal cord circuits; (2) Magnetic nanotransducers for minimally invasive neural stimulation; and (3) Active scaffolds for neural tissue engineering and interrogation.<\/p>\n<p>Fiber-drawing methods can be applied to create multifunctional polymer-based probes capable of simultaneous electrical, optical, and chemical probing of neural tissues in freely moving subjects. Similar engineering principles enable ultra-flexible miniature fiber-probes with geometries inspired by nerves, which permit simultaneous optical excitation and recording of neural activity in the spinal cord allowing for optical control of lower limb movement. Furthermore, fiber-based fabrication can be extended to design of scaffolds that direct neural growth and activity facilitating repair of damaged nerves.<\/p>\n<p>Molecular mechanisms of action potential firing inspire the development of materials-based strategies for direct manipulation of ion transport across neuronal membranes. For example, hysteretic heat dissipation by magnetic nanomaterials can be used to remotely trigger activity of neurons expressing heat-sensitive ion channels. Since the alternating magnetic fields in the low radiofrequency range interact minimally with the biological tissues, the magnetic nanoparticles injected into the brain can act as transducers of wireless magnetothermal deep brain stimulation. Similarly, local hysteretic heating allows magnetic nanoparticles to disrupt protein aggregates associated with neurodegenerative disorders.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1474\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1474\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1473\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tBuilding a New View of Transcriptome Variations\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1473\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1474\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Yoseph Barash<\/p>\n<p>In this talk, I will review some of the challenges and advances we have made in building a new view of transcriptome complexity, along with and the kind of tools that can be used to infer it.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1476\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1476\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1475\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tRational development of drugs from the human microbiota\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1475\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1476\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Bernat Olle<\/p>\n<p>Medicines that modulate the human microbiome hold enormous promise for treatment of immune and infectious diseases, as highlighted by the success of randomized, controlled trials of fecal transplantation for treatment of C. difficile infections and IBD, as well as early pilot data in GvHD. They also pose some unique scientific, translational, manufacturing, and regulatory challenges. Drugs based on defined bacterial consortia (characterized communities of limited numbers of live organisms) could potentially retain some of the beneficial attributes of fecal transplants while being amenable to development as pharmaceutical-grade agents. I will present examples of Vedanta\u2019s efforts to develop first-in-class drugs based on rationally selected bacterial consortia for applications in immune and infectious diseases.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1478\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1478\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1477\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tOne genome to rule them all, one genome to find them\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1477\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1478\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Gill Bejerano<\/p>\n<p>I will highlight some methodologies and examples of finding causal mutations in both medical genomics and comparative genomics contexts.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1480\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1480\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1479\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tUsing Large Scale Genomic Databases to Improve Disease Variant Interpretation\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1479\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1480\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Daniel MacArthur<\/p>\n<p>Rapid advances in sequencing technology have led to the generation of genome-scale DNA sequencing data for more than 2 million individuals worldwide. These data represent incredibly powerful information about the distribution and impact of genetic variation, but major challenges remain to aggregating and harmonizing them. In this presentation I will describe the development of the Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD) databases, which combined represent exome and genome sequencing data for over 135,000 individuals. I will discuss approaches to analyzing genome data at massive scale, and the applications of these data to understanding human variation and gene function.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1482\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1482\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1481\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tSingle cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1481\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1482\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Nir Yoseph<\/p>\n<p>Human immunity relies on coordinated responses of ensembles of cells from various types and functional states. Over the past several decades, substantial work has been done to catalog the cell types, states, and interactions that inform these behaviors. The emerging field of single cell genomics has the potential to make important contributions to this body of work, by providing a way to systematically map previously unknown subsets of cells, predict their functionality, and ultimately modulate their relative abundance so as to favorably tune the emerging immune response. In this talk I will present our recent work, which explored these ideas within the context of HIV-1 infection, using single-cell RNA-Seq of dendritic cells from human donors. Through a combination of computational analysis and experimental validation we were able to identify a highly functional subset of anti-viral dendritic cells that is capable of effectively priming T cell responses in vitro. Furthermore, by integrating knowledge from existing genomics databases we were able to identify and test immunomodulators that increase the relative abundance of this functional subset in-vitro, thus potentially leading to a more potent anti-viral response.<\/p>\n<p>While data sets produced by single cell genomics hold unique information, they also pose unique challenges, from idiosyncratic technical limitations to difficulty of interpretability. During this this talk, I will also describe some of the computational tools developed in my group, aiming to address these challenges and realize the potential of single-cell genomics.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1484\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1484\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1483\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tGenomic Approaches to Cancer\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1483\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1484\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Todd Golub<\/p>\n<p>It is now becoming possible to bring powerful genomic methods to bear on the process of cancer drug discovery. This talk will illustrate 1) the use of the Connectivity Map, a large-scale effort to develop a compendium of gene expression signatures of cellular state, 2) the use of PRISM, a new multiplexed, high throughput approach to screening cancer cell lines for anti-cancer activity and resistance, and 3) the use of cancer models (cell lines and patient-derived xenografts) in discovery, with particular focus on clonal drift in these models and the impact of that drift on drug sensitivity.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1486\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1486\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1485\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tUsing the data, all the data; the case of the human microbiome\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1485\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1486\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Susan Holmes<\/p>\n<p>Longitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations. Longitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t<li class=\"m-0\" data-wp-context='{\"id\":\"accordion-content-1488\"}' data-wp-init=\"callbacks.init\">\n\t\t<div class=\"accordion-header\">\n\t\t\t<button\n\t\t\t\taria-controls=\"accordion-content-1488\"\n\t\t\t\tclass=\"btn btn-collapse\"\n\t\t\t\tdata-wp-bind--aria-expanded=\"state.isExpanded\"\n\t\t\t\tdata-wp-on--click=\"actions.onClick\"\n\t\t\t\tid=\"accordion-button-1487\"\n\t\t\t\ttype=\"button\"\n\t\t\t>\n\t\t\t\tProject Premonition: Scaling up pathogen surveillance\t\t\t<\/button>\n\t\t<\/div>\n\t\t<div\n\t\t\taria-labelledby=\"accordion-button-1487\"\n\t\t\tclass=\"msr-accordion__content\"\n\t\t\tdata-wp-bind--inert=\"!state.isExpanded\"\n\t\t\tdata-wp-run=\"callbacks.run\"\n\t\t\tid=\"accordion-content-1488\"\n\t\t>\n\t\t\t<div class=\"msr-accordion__body\">\n\t\t\t\t<p><strong>Speaker:<\/strong> Jonathan Carlson<\/p>\n<p>Emerging and re-emerging infectious diseases are a central public health concern, with implications for economies and even the stability of nations. The current system for detecting pathogens is entirely reactive, reliant on aggregating local reports by clinicians, and typically takes weeks of symptomatic human infections before detection. Project Premonition aims to detect pathogens before they cause outbreaks, using mosquitoes to sample pathogens in the environment. Turning a mosquito into a device requires new technologies to autonomously locate, robotically collect, and computationally analyze mosquitoes and their genetic payload. \u00a0To this end, we have developed and field tested robotic smart traps that instantaneously classify insects based on wing beat frequencies and other features, allowing real-time monitoring and selective capture of flying insects of interest. The rich data collected from these traps provides unprecedented insight into mosquito foraging behavior, allowing us to predict where and when we\u2019ll find mosquitos, which we expect will allow us to more rapidly locate disease while simultaneously improving the efficacy of mosquito control. Once mosquitos are captured, deep sequencing has the potential to provide insights into the population genetics of the mosquitos, the hosts on which they\u2019ve feed, and pathogens in both mosquitos and hosts. This is essentially a pan metagenomics problem, in which source genetic material may be derived from anywhere on the tree of life, thus motivating very high throughput taxonomic classification methods that leverage all available sequences in public databases. In this talk, I will provide an overview of Project Premonition, results from field trials on the traps, and our algorithmic approach to making a scalable metagenomics pipeline.<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<span id=\"label-external-link\" class=\"sr-only\" aria-hidden=\"true\">Opens in a new tab<\/span><\/p>\n<!-- \/wp:freeform --><!-- \/wp:msr\/content-tab --><!-- \/wp:msr\/content-tabs -->","tab-content":[{"id":0,"name":"About","content":"<img class=\"size-medium wp-image-293573 alignright\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cabi2016_top_badge-artwork-300x228.png\" alt=\"Computational Aspects of Biological Information 2016\" width=\"300\" height=\"228\" \/>Computational Aspects of Biological Information (CABI) 2017 is the fifth one-day symposium\u00a0on challenges and successes in computational biology. CABI 2017 will be held at Microsoft Research New England on October 13, 2017 and will\u00a0bring together experts to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. The symposium\u00a0is open to everyone and registration is free of charge. Lunch will be served.\r\n<h2>Symposium Speakers<\/h2>\r\nConfirmed speakers include:\r\n<ul>\r\n \t<li><a href=\"https:\/\/www.med.upenn.edu\/apps\/faculty\/index.php\/g275\/p8507519\">Yoseph Barash<\/a>, University of Pennsylvania<\/li>\r\n \t<li><a href=\"http:\/\/statweb.stanford.edu\/~susan\/\">Susan Holmes<\/a>, Stanford University<\/li>\r\n \t<li><a href=\"https:\/\/www.broadinstitute.org\/bios\/daniel-macarthur-0\">Daniel MacArthur<\/a>, Broad Institute<\/li>\r\n \t<li><a href=\"https:\/\/www.broadinstitute.org\/bios\/todd-r-golub\">Todd Golub<\/a>, Broad Institute<\/li>\r\n \t<li><a href=\"https:\/\/medschool.vanderbilt.edu\/brain-institute\/person\/nancy-j-cox-phd\">Nancy Cox<\/a>, Vanderbilt University<\/li>\r\n \t<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/carlson\/\">Jonathan Carlson<\/a>, Microsoft<\/li>\r\n \t<li><a href=\"http:\/\/bejerano.stanford.edu\/pi.html\">Gill Bejerano<\/a>, Stanford University<\/li>\r\n \t<li><a href=\"http:\/\/www.vedantabio.com\/about\/board-of-directors\">Bernat Olle<\/a>, Vedanta Biosciences, Inc.<\/li>\r\n \t<li><a href=\"http:\/\/dmse.mit.edu\/faculty\/profile\/anikeeva\">Polina Anikeeva<\/a>, Massachusetts Institute of Technology<\/li>\r\n \t<li><a href=\"https:\/\/niryosef.wordpress.com\/\">Nir Yoseph<\/a>, Berkeley University<\/li>\r\n<\/ul>\r\n<h2>Organizing committee<\/h2>\r\n<ul>\r\n \t<li><a href=\"http:\/\/nicolofusi.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Nicolo Fusi<\/a>,\u00a0Microsoft Research<\/li>\r\n \t<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/people\/frcasale\/\" target=\"_blank\" rel=\"noopener noreferrer\">Francesco Casale<\/a>,\u00a0Microsoft Research<\/li>\r\n \t<li><a href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/jennl\/\" target=\"_blank\" rel=\"noopener noreferrer\">Jennifer Listgarten<\/a>,\u00a0Microsoft Research<\/li>\r\n<\/ul>\r\n<h2>Poster Session<\/h2>\r\nThere will be a poster session in the afternoon. See the Poster Submissions tab for details.\r\n\r\n<strong>Hospitality Notice for University and Government Employees: <\/strong>Microsoft Research is providing hospitality at this event. Please consult with your institution to determine whether you can accept meals and other hospitality under your institution's ethics rules and any other laws that might apply. By accepting our invitation, you confirm that this invitation is compliant with your institution's policies.\r\n\r\n<strong>Arrival Guidance<\/strong>\r\n\r\nUpon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room."},{"id":1,"name":"Poster Submissions","content":"To be considered for the CABI 2017 poster session, please submit the following information to <a href=\"mailto:CABI2017posters@microsoft.com\">CABI2017posters@microsoft.com<\/a> by September 29th. Submissions will be evaluated on a rolling basis. Space is limited, and preference will be given to early submissions.\r\n\r\nPosters may be up to 48\u201dW X 36\u201dH.\r\n<ul>\r\n \t<li>Presenting author name<\/li>\r\n \t<li>Presenting author affiliation\/institution<\/li>\r\n \t<li>Presenting author email address<\/li>\r\n \t<li>Title<\/li>\r\n \t<li>Complete list of authors (first name last name).\u00a0 Please do not list author affiliations.<\/li>\r\n \t<li>Abstract (250 words maximum)<\/li>\r\n<\/ul>\r\nPlease email the conference organizers at <a href=\"mailto:cabi2017@microsoft.com\">cabi2017@microsoft.com<\/a> if you have any questions."},{"id":2,"name":"Agenda","content":"<table class=\"msr-table-schedule\">\r\n<thead class=\"thead\">\r\n<tr class=\"tr\">\r\n<th class=\"th\">Time<\/th>\r\n<th class=\"th\">Session<\/th>\r\n<th class=\"th\">Speaker<\/th>\r\n<\/tr>\r\n<\/thead>\r\n<tbody class=\"tbody\">\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">9:00 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Registration and coffee service<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">9:50 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Opening remarks<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Jennifer Chayes, Microsoft<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">10:00 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Biobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Nancy Cox, Vanderbilt University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">10:30 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Probing Neural Function with Electronic, Optical and Magnetic Materials<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Polina Anikeeva, Massachusetts University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">11:00 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Coffee break<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">11:15 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Building a New View of Transcriptome Variations<\/div><\/td>\r\n<td>Yoseph Barash, University of Pennsylvania<\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">11:45 AM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Rational development of drugs from the human microbiota<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Bernat Olle, Vendata Biosciences, Inc.<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">12:15 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Lunch<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">1:00 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Poster session<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">1:30 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">One genome to rule them all, one genome to find them<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Gill Bejerano, Stanford University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">2:00 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Using Large Scale Genomic Databases to Improve Disease Variant Interpretation<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Daniel MacArthur, Broad Institute<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">2:30 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Single cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Nir Yosef, Berkeley University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">3:00 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Coffee break \/ poster session<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">3:45 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Genomic Approaches to Cancer<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Todd Golub, Harvard University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">4:15 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Using the data, all the data; the case of the human microbiome<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Susan Holmes, Stanford University<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">4:45 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Project Premonition: Scaling up pathogen surveillance<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Jonathan Carlson, Microsoft<\/div><\/td>\r\n<\/tr>\r\n<tr class=\"tr\">\r\n<td class=\"td-1-4\">\r\n<div class=\"msr-table-schedule-cell\">5:15 PM<\/div><\/td>\r\n<td>\r\n<div class=\"msr-table-schedule-cell\">Closing Remarks<\/div><\/td>\r\n<td><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>"},{"id":3,"name":"Abstracts","content":"[accordion]\r\n[panel header=\"Biobanks Provide Unique Opportunities for Discovery and Translation: Data Integration across Phenome, Genome, and Transcriptome\"]\r\n<strong>Speaker:<\/strong> Nancy Cox\r\n\r\nWe have applied the PrediXcan method in which we use GTEx as a reference to impute transcript levels for genes and test the association of those imputed transcript levels with ~1800 phenome codes developed for phenome-wide association studies. I will illustrate how we are using the resulting gene x medical phenome catalog to extend discovery research into identification of primary disease mechanism as well as novel approaches to translation of discoveries.\r\n[\/panel]\r\n[panel header=\"Probing Neural Function with Electronic, Optical and Magnetic Materials\"]\r\n<strong>Speaker:<\/strong> Polina Anikeeva\r\n\r\nMammalian nervous system contains billions of neurons that exchange electrical, chemical and mechanical signals. Our ability to study this complexity is limited by the lack of technologies available for interrogating neural circuits across their diverse signaling modalities without inducing a foreign-body reaction. My talk will describe neural interface strategies pursued in my group aimed at mimicking the materials properties and transduction mechanisms of the nervous system. Specifically, I will discuss (1) Fiber-based probes for multifunctional interfaces with the brain and spinal cord circuits; (2) Magnetic nanotransducers for minimally invasive neural stimulation; and (3) Active scaffolds for neural tissue engineering and interrogation.\r\n\r\nFiber-drawing methods can be applied to create multifunctional polymer-based probes capable of simultaneous electrical, optical, and chemical probing of neural tissues in freely moving subjects. Similar engineering principles enable ultra-flexible miniature fiber-probes with geometries inspired by nerves, which permit simultaneous optical excitation and recording of neural activity in the spinal cord allowing for optical control of lower limb movement. Furthermore, fiber-based fabrication can be extended to design of scaffolds that direct neural growth and activity facilitating repair of damaged nerves.\r\n\r\nMolecular mechanisms of action potential firing inspire the development of materials-based strategies for direct manipulation of ion transport across neuronal membranes. For example, hysteretic heat dissipation by magnetic nanomaterials can be used to remotely trigger activity of neurons expressing heat-sensitive ion channels. Since the alternating magnetic fields in the low radiofrequency range interact minimally with the biological tissues, the magnetic nanoparticles injected into the brain can act as transducers of wireless magnetothermal deep brain stimulation. Similarly, local hysteretic heating allows magnetic nanoparticles to disrupt protein aggregates associated with neurodegenerative disorders.\r\n[\/panel]\r\n[panel header=\"Building a New View of Transcriptome Variations\"]\r\n<strong>Speaker:<\/strong> Yoseph Barash\r\n\r\nIn this talk, I will review some of the challenges and advances we have made in building a new view of transcriptome complexity, along with and the kind of tools that can be used to infer it.\r\n[\/panel]\r\n[panel header=\"Rational development of drugs from the human microbiota\"]\r\n<strong>Speaker:<\/strong> Bernat Olle\r\n\r\nMedicines that modulate the human microbiome hold enormous promise for treatment of immune and infectious diseases, as highlighted by the success of randomized, controlled trials of fecal transplantation for treatment of C. difficile infections and IBD, as well as early pilot data in GvHD. They also pose some unique scientific, translational, manufacturing, and regulatory challenges. Drugs based on defined bacterial consortia (characterized communities of limited numbers of live organisms) could potentially retain some of the beneficial attributes of fecal transplants while being amenable to development as pharmaceutical-grade agents. I will present examples of Vedanta\u2019s efforts to develop first-in-class drugs based on rationally selected bacterial consortia for applications in immune and infectious diseases.\r\n[\/panel]\r\n[panel header=\"One genome to rule them all, one genome to find them\"]\r\n<strong>Speaker:<\/strong> Gill Bejerano\r\n\r\nI will highlight some methodologies and examples of finding causal mutations in both medical genomics and comparative genomics contexts.\r\n[\/panel]\r\n[panel header=\"Using Large Scale Genomic Databases to Improve Disease Variant Interpretation\"]\r\n<strong>Speaker:<\/strong> Daniel MacArthur\r\n\r\nRapid advances in sequencing technology have led to the generation of genome-scale DNA sequencing data for more than 2 million individuals worldwide. These data represent incredibly powerful information about the distribution and impact of genetic variation, but major challenges remain to aggregating and harmonizing them. In this presentation I will describe the development of the Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD) databases, which combined represent exome and genome sequencing data for over 135,000 individuals. I will discuss approaches to analyzing genome data at massive scale, and the applications of these data to understanding human variation and gene function.\r\n[\/panel]\r\n[panel header=\"Single cell genomics: tools for computational analysis with application to innate immune response to HIV-1 infection\"]\r\n<strong>Speaker:<\/strong> Nir Yoseph\r\n\r\nHuman immunity relies on coordinated responses of ensembles of cells from various types and functional states. Over the past several decades, substantial work has been done to catalog the cell types, states, and interactions that inform these behaviors. The emerging field of single cell genomics has the potential to make important contributions to this body of work, by providing a way to systematically map previously unknown subsets of cells, predict their functionality, and ultimately modulate their relative abundance so as to favorably tune the emerging immune response. In this talk I will present our recent work, which explored these ideas within the context of HIV-1 infection, using single-cell RNA-Seq of dendritic cells from human donors. Through a combination of computational analysis and experimental validation we were able to identify a highly functional subset of anti-viral dendritic cells that is capable of effectively priming T cell responses in vitro. Furthermore, by integrating knowledge from existing genomics databases we were able to identify and test immunomodulators that increase the relative abundance of this functional subset in-vitro, thus potentially leading to a more potent anti-viral response.\r\n\r\nWhile data sets produced by single cell genomics hold unique information, they also pose unique challenges, from idiosyncratic technical limitations to difficulty of interpretability. During this this talk, I will also describe some of the computational tools developed in my group, aiming to address these challenges and realize the potential of single-cell genomics.\r\n[\/panel]\r\n[panel header=\"Genomic Approaches to Cancer\"]\r\n<strong>Speaker:<\/strong> Todd Golub\r\n\r\nIt is now becoming possible to bring powerful genomic methods to bear on the process of cancer drug discovery. This talk will illustrate 1) the use of the Connectivity Map, a large-scale effort to develop a compendium of gene expression signatures of cellular state, 2) the use of PRISM, a new multiplexed, high throughput approach to screening cancer cell lines for anti-cancer activity and resistance, and 3) the use of cancer models (cell lines and patient-derived xenografts) in discovery, with particular focus on clonal drift in these models and the impact of that drift on drug sensitivity.\r\n[\/panel]\r\n[panel header=\"Using the data, all the data; the case of the human microbiome\"]\r\n<strong>Speaker:<\/strong> Susan Holmes\r\n\r\nLongitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations. Longitudinal studies using perturbations enable us to study the resilience of the human microbiome. These are particularly informative in the case of antibiotic courses and colonic clean-out. The heterogeneity of the sources of information (time, phylogenetic trees, community networks, samples, batches, noise levels, sequences) pose real visualization and analytic challenges that we have overcome using interactive multivariate mappings. These enable simple tree-aware projections and account for uncertainties using Bayesian MCMC implementations.\r\n[\/panel]\r\n[panel header=\"Project Premonition: Scaling up pathogen surveillance\"]\r\n<strong>Speaker:<\/strong> Jonathan Carlson\r\n\r\nEmerging and re-emerging infectious diseases are a central public health concern, with implications for economies and even the stability of nations. The current system for detecting pathogens is entirely reactive, reliant on aggregating local reports by clinicians, and typically takes weeks of symptomatic human infections before detection. Project Premonition aims to detect pathogens before they cause outbreaks, using mosquitoes to sample pathogens in the environment. Turning a mosquito into a device requires new technologies to autonomously locate, robotically collect, and computationally analyze mosquitoes and their genetic payload. \u00a0To this end, we have developed and field tested robotic smart traps that instantaneously classify insects based on wing beat frequencies and other features, allowing real-time monitoring and selective capture of flying insects of interest. The rich data collected from these traps provides unprecedented insight into mosquito foraging behavior, allowing us to predict where and when we\u2019ll find mosquitos, which we expect will allow us to more rapidly locate disease while simultaneously improving the efficacy of mosquito control. Once mosquitos are captured, deep sequencing has the potential to provide insights into the population genetics of the mosquitos, the hosts on which they\u2019ve feed, and pathogens in both mosquitos and hosts. This is essentially a pan metagenomics problem, in which source genetic material may be derived from anywhere on the tree of life, thus motivating very high throughput taxonomic classification methods that leverage all available sequences in public databases. In this talk, I will provide an overview of Project Premonition, results from field trials on the traps, and our algorithmic approach to making a scalable metagenomics pipeline.\r\n[\/panel]\r\n[\/accordion]"}],"msr_startdate":"2017-10-13","msr_enddate":"2017-10-13","msr_event_time":"9:00 AM \u2013 5:30 PM","msr_location":"Cambridge, MA, USA","msr_event_link":"","msr_event_recording_link":"","msr_startdate_formatted":"October 13, 2017","msr_register_text":"Watch now","msr_cta_link":"","msr_cta_text":"","msr_cta_bi_name":"","featured_image_thumbnail":"<img width=\"960\" height=\"360\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720.jpg\" class=\"img-object-cover\" alt=\"\" decoding=\"async\" loading=\"lazy\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720.jpg 1920w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720-300x113.jpg 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720-768x288.jpg 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2017\/08\/CABI2017_Header_1920X720-1024x384.jpg 1024w\" sizes=\"auto, (max-width: 960px) 100vw, 960px\" \/>","event_excerpt":"Computational Aspects of Biological Information (CABI) 2017 is the fifth one-day symposium on challenges and successes in computational biology. CABI 2017 will be held at Microsoft Research New England on October 13, 2017, and will bring together experts in the Boston\/Cambridge area to discuss computational solutions to problems in biology, including systems biology, genomics, and related areas. 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