Yuan-Jyue Chen

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad

ACL 2023 | July 2023

Publication

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Bas W. A. Bögels, Bichlien Nguyen, David Ward, Levena Gascoigne, David P. Schrijver, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Ilja K. Voets, Willem J. M. Mulder, Andrew Phillips, Stephen Mann, Georg Seelig, Karin Strauss, Yuan-Jyue Chen, Tom F. A. de Greef

Nature Nanotechnology | May 2023

Publication Project

A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

Claris Winston, Lee Organick, David Ward, Luis Ceze, Karin Strauss, Yuan-Jyue Chen

ACS Synthetic Biology | February 2022

Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

Robust Digital Molecular Design of Binarized Neural Networks

Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze, Karin Strauss

Leibniz International Proceedings in Informatics (LIPIcs) | September 2021, Vol 205(DNA 27)

Publication DOI Project

Molecular-level similarity search brings computing to DNA data storage

Callista Bee, Yuan-Jyue Chen, Melissa Queen, David Ward, Xiaomeng Liu, Lee Organick, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | August 2021, Vol 12(4764)

DOI Publication Project

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang

Nature Communications | July 2021, Vol 12

Publication Project Project

Quantifying Molecular Bias in DNA Data Storage

Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, Karin Strauss

Nature Communications | June 2020, Vol 11(3264)

Publication DOI PDF Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project

Using Strand Displacing Polymerase To Program Chemical Reaction Networks

Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss, Yuan-Jyue Chen, John Reif

Journal of the American Chemical Society | May 2020, Vol 142(21): pp. 9587-9593

Publication

Probing the Physical Limits of Reliable DNA Data Retrieval

Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze

Nature Communications | January 2020, Vol 11(616)

PDF Publication Project

DNA Assembly for Nanopore Data Storage Readout

Randolph Lopez, Yuan-Jyue Chen, Siena Dumas Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | July 2019, Vol 10:2933

PDF DOI Project

Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells

Gourab Chatterjee, Yuan-Jyue Chen, Georg Seelig

ACS Synthetic Biology | November 2018, Vol 7(12): pp. 2737-2741

Publication

A Content-Addressable DNA Database with Learned Sequence Encodings

Kendall Stewart, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

24th International Conference On DNA Computing and Molecular Programming | October 2018

Video Project

Random Access in Large-Scale DNA Data Storage

Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Doug Carmean, Georg Seelig, Luis Ceze, Karin Strauss

Nature Biotechnology | March 2018, Vol 36(3)

Publication Project

Computing in mammalian cells with nucleic acid strand exchange

Benjamin Groves, Yuan-Jyue Chen, Chiara Zurla, Sergii Pochekailov, Jonathan L. Kirschman, Philip J. Santangelo, Georg Seelig

Nature Nanotechnology | December 2015, Vol 11(3): pp. 287-294

Publication

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Yuan-Jyue Chen, Sundipta D. Rao, Georg Seelig

The Journal of Visualized Experiments | November 2015

Publication

DNA nanotechnology from the test tube to the cell

Yuan-Jyue Chen, Benjamin Groves, Richard A. Muscat, Georg Seelig

Nature Nanotechnology | September 2015, Vol 10: pp. 748-760

Publication

Programmable chemical controllers made from DNA

Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig

Nature Nanotechnology | September 2013, Vol 8: pp. 755-762

Publication Project Project

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad

ACL 2023 | July 2023

Publication

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad

ACL 2023 | July 2023

Publication

A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

Claris Winston, Lee Organick, David Ward, Luis Ceze, Karin Strauss, Yuan-Jyue Chen

ACS Synthetic Biology | February 2022

Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang

Nature Communications | July 2021, Vol 12

Publication Project Project

Quantifying Molecular Bias in DNA Data Storage

Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, Karin Strauss

Nature Communications | June 2020, Vol 11(3264)

Publication DOI PDF Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project

Using Strand Displacing Polymerase To Program Chemical Reaction Networks

Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss, Yuan-Jyue Chen, John Reif

Journal of the American Chemical Society | May 2020, Vol 142(21): pp. 9587-9593

Publication

DNA Assembly for Nanopore Data Storage Readout

Randolph Lopez, Yuan-Jyue Chen, Siena Dumas Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | July 2019, Vol 10:2933

PDF DOI Project

Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells

Gourab Chatterjee, Yuan-Jyue Chen, Georg Seelig

ACS Synthetic Biology | November 2018, Vol 7(12): pp. 2737-2741

Publication

Computing in mammalian cells with nucleic acid strand exchange

Benjamin Groves, Yuan-Jyue Chen, Chiara Zurla, Sergii Pochekailov, Jonathan L. Kirschman, Philip J. Santangelo, Georg Seelig

Nature Nanotechnology | December 2015, Vol 11(3): pp. 287-294

Publication

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Yuan-Jyue Chen, Sundipta D. Rao, Georg Seelig

The Journal of Visualized Experiments | November 2015

Publication

DNA nanotechnology from the test tube to the cell

Yuan-Jyue Chen, Benjamin Groves, Richard A. Muscat, Georg Seelig

Nature Nanotechnology | September 2015, Vol 10: pp. 748-760

Publication

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Bas W. A. Bögels, Bichlien Nguyen, David Ward, Levena Gascoigne, David P. Schrijver, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Ilja K. Voets, Willem J. M. Mulder, Andrew Phillips, Stephen Mann, Georg Seelig, Karin Strauss, Yuan-Jyue Chen, Tom F. A. de Greef

Nature Nanotechnology | May 2023

Publication Project

Molecular-level similarity search brings computing to DNA data storage

Callista Bee, Yuan-Jyue Chen, Melissa Queen, David Ward, Xiaomeng Liu, Lee Organick, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | August 2021, Vol 12(4764)

DOI Publication Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project

A Content-Addressable DNA Database with Learned Sequence Encodings

Kendall Stewart, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

24th International Conference On DNA Computing and Molecular Programming | October 2018

Video Project

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Bas W. A. Bögels, Bichlien Nguyen, David Ward, Levena Gascoigne, David P. Schrijver, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Ilja K. Voets, Willem J. M. Mulder, Andrew Phillips, Stephen Mann, Georg Seelig, Karin Strauss, Yuan-Jyue Chen, Tom F. A. de Greef

Nature Nanotechnology | May 2023

Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

Claris Winston, Lee Organick, David Ward, Luis Ceze, Karin Strauss, Yuan-Jyue Chen

ACS Synthetic Biology | February 2022

Publication Project

A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

Claris Winston, Lee Organick, David Ward, Luis Ceze, Karin Strauss, Yuan-Jyue Chen

ACS Synthetic Biology | February 2022

Publication Project

Robust Digital Molecular Design of Binarized Neural Networks

Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze, Karin Strauss

Leibniz International Proceedings in Informatics (LIPIcs) | September 2021, Vol 205(DNA 27)

Publication DOI Project

Molecular-level similarity search brings computing to DNA data storage

Callista Bee, Yuan-Jyue Chen, Melissa Queen, David Ward, Xiaomeng Liu, Lee Organick, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | August 2021, Vol 12(4764)

DOI Publication Project

Quantifying Molecular Bias in DNA Data Storage

Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, Karin Strauss

Nature Communications | June 2020, Vol 11(3264)

Publication DOI PDF Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project

Probing the Physical Limits of Reliable DNA Data Retrieval

Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze

Nature Communications | January 2020, Vol 11(616)

PDF Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

Probing the Physical Limits of Reliable DNA Data Retrieval

Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze

Nature Communications | January 2020, Vol 11(616)

PDF Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

DNA Assembly for Nanopore Data Storage Readout

Randolph Lopez, Yuan-Jyue Chen, Siena Dumas Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | July 2019, Vol 10:2933

PDF DOI Project

Robust Digital Molecular Design of Binarized Neural Networks

Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze, Karin Strauss

Leibniz International Proceedings in Informatics (LIPIcs) | September 2021, Vol 205(DNA 27)

Publication DOI Project

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang

Nature Communications | July 2021, Vol 12

Publication Project Project

Quantifying Molecular Bias in DNA Data Storage

Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, Karin Strauss

Nature Communications | June 2020, Vol 11(3264)

Publication DOI PDF Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project

Probing the Physical Limits of Reliable DNA Data Retrieval

Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze

Nature Communications | January 2020, Vol 11(616)

PDF Publication Project

A Content-Addressable DNA Database with Learned Sequence Encodings

Kendall Stewart, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

24th International Conference On DNA Computing and Molecular Programming | October 2018

Video Project

Random Access in Large-Scale DNA Data Storage

Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Doug Carmean, Georg Seelig, Luis Ceze, Karin Strauss

Nature Biotechnology | March 2018, Vol 36(3)

Publication Project

Programmable chemical controllers made from DNA

Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig

Nature Nanotechnology | September 2013, Vol 8: pp. 755-762

Publication Project Project

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad

ACL 2023 | July 2023

Publication

A Content-Addressable DNA Database with Learned Sequence Encodings

Kendall Stewart, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

24th International Conference On DNA Computing and Molecular Programming | October 2018

Video Project

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Bas W. A. Bögels, Bichlien Nguyen, David Ward, Levena Gascoigne, David P. Schrijver, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Ilja K. Voets, Willem J. M. Mulder, Andrew Phillips, Stephen Mann, Georg Seelig, Karin Strauss, Yuan-Jyue Chen, Tom F. A. de Greef

Nature Nanotechnology | May 2023

Publication Project

A Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools

Claris Winston, Lee Organick, David Ward, Luis Ceze, Karin Strauss, Yuan-Jyue Chen

ACS Synthetic Biology | February 2022

Publication Project

Synthetic DNA applications in information technology

Linda C. Meiser, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss, Luis Ceze, Robert N. Grass

Nature Communications | January 2022

Publication

Robust Digital Molecular Design of Binarized Neural Networks

Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze, Karin Strauss

Leibniz International Proceedings in Informatics (LIPIcs) | September 2021, Vol 205(DNA 27)

Publication DOI Project

Molecular-level similarity search brings computing to DNA data storage

Callista Bee, Yuan-Jyue Chen, Melissa Queen, David Ward, Xiaomeng Liu, Lee Organick, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | August 2021, Vol 12(4764)

DOI Publication Project

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang

Nature Communications | July 2021, Vol 12

Publication Project Project

Quantifying Molecular Bias in DNA Data Storage

Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, Karin Strauss

Nature Communications | June 2020, Vol 11(3264)

Publication DOI PDF Project

Using Strand Displacing Polymerase To Program Chemical Reaction Networks

Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss, Yuan-Jyue Chen, John Reif

Journal of the American Chemical Society | May 2020, Vol 142(21): pp. 9587-9593

Publication

Probing the Physical Limits of Reliable DNA Data Retrieval

Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze

Nature Communications | January 2020, Vol 11(616)

PDF Publication Project

DNA Assembly for Nanopore Data Storage Readout

Randolph Lopez, Yuan-Jyue Chen, Siena Dumas Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Georg Seelig, Karin Strauss, Luis Ceze

Nature Communications | July 2019, Vol 10:2933

PDF DOI Project

Nucleic Acid Strand Displacement with Synthetic mRNA Inputs in Living Mammalian Cells

Gourab Chatterjee, Yuan-Jyue Chen, Georg Seelig

ACS Synthetic Biology | November 2018, Vol 7(12): pp. 2737-2741

Publication

Random Access in Large-Scale DNA Data Storage

Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Doug Carmean, Georg Seelig, Luis Ceze, Karin Strauss

Nature Biotechnology | March 2018, Vol 36(3)

Publication Project

Computing in mammalian cells with nucleic acid strand exchange

Benjamin Groves, Yuan-Jyue Chen, Chiara Zurla, Sergii Pochekailov, Jonathan L. Kirschman, Philip J. Santangelo, Georg Seelig

Nature Nanotechnology | December 2015, Vol 11(3): pp. 287-294

Publication

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Yuan-Jyue Chen, Sundipta D. Rao, Georg Seelig

The Journal of Visualized Experiments | November 2015

Publication

DNA nanotechnology from the test tube to the cell

Yuan-Jyue Chen, Benjamin Groves, Richard A. Muscat, Georg Seelig

Nature Nanotechnology | September 2015, Vol 10: pp. 748-760

Publication

Programmable chemical controllers made from DNA

Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig

Nature Nanotechnology | September 2013, Vol 8: pp. 755-762

Publication Project Project

Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis Ceze

May 2020

Author's Version DOI PDF Project