Publications

Shift in MSL1 alternative polyadenylation in response to DNA damage protects cancer cells from chemotherapeutic agent-induced apoptosis.
Alexander K Kunisky, Vivian I Anyaeche, R Samuel Herron, Christopher Y. Park, Hun-Way Hwang.
Cell Reports, 2021.

Tissue-specific enhancer functional networks for associating distal regulatory regions to disease.
Xi Chen, Jian Zhou, Ran Zhang, Aaron K Wong, Christopher Y. Park, Chandra L Theesfeld, Olga G Troyanskaya.
Cell Systems, 2021.

An automated framework for efficiently designing deep convolutional neural networks in genomics G Troyanskaya.
Zijun Zhang, Christopher Y. Park, Chandra L Theesfeld, Olga G Troyanskaya.
Nature Machine Intelligence, 2021.

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk.
Christopher Y. Park^#, Jian Zhou, Aaron K. Wong, Kathleen Chen, Chandra L. Theesfeld, Robert B. Darnell, Olga G. Troyanskaya^#. (# co-corresponding authors)
Nature Genetics, 2021.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate.
Christiane Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis, Christopher Y. Park, Avinash Boppana, Ethan Fritch, Yixuan J Hou, Chandra Theesfeld, Olga G Troyanskaya, Ralph S Baric, Timothy P Sheahan, Kevin Weeks, Amy S Gladfelter.
bioRxiv, 2020.

FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types.
Sarah J Van Driesche, Kirsty Sawicka, Chaolin Zhang, Sharon KY Hung, Christopher Y. Park, John J Fak, Chingwen Yang, Robert B Darnell, Jennifer C Darnell.
bioRxiv, 2019.

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory.
Kirsty Sawicka, Caryn R Hale, Christopher Y. Park, John J Fak, Jodi E Gresack, Sarah J Van Driesche, Jin Joo Kang, Jennifer C Darnell, Robert B Darnell.
eLife, 2019.

Whole-genome deep learning analysis identifies contribution of noncoding mutations to autism risk.
Jian Zhou^*, Christopher Y. Park^★, Chandra L. Theesfeld^*, Yuan Yuan4, Claudia Scheckel, John J Fak, Yoko Tajima, Robert B. Darnell, Olga G. Troyanskaya. (★ co-first authors)
Nature Genetics, 2019.

AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke.
Mariko Kobayashi, Corey Anderson, Corinne Benakis, Michael J Moore, Aldo Mele, John J Fak, Christopher Y. Park, Ping Zhou, Josef Anrather, Costantino Iadecola, Robert B Darnell.
Cell reports, 2019.

Interpretation of an individual functional genomics experiment guided by massive public data.
Young-suk Lee, Aaron K Wong, Alicja Tadych, Boris M Hartmann, Christopher Y. Park, Veronica A DeJesus, Irene Ramos, Elena Zaslavsky, Stuart C Sealfon, Olga G Troyanskaya.
Nature methods, 2018.

ZFP36 RNA-binding proteins restrain T-cell activation and anti-viral immunity.
Michael J Moore, Nathalie E Blachere, John J Fak, Christopher Y. Park, Kirsty Sawicka, Salina Parveen, Ilana Zucker-Scharff, Bruno Moltedo, Alexander Rudensky, Robert Darnell.
eLife, 2018.

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation.
Hun-Way Hwang, Yuhki Saito, Christopher Y. Park, Nathalie E Blachere, Yoko Tajima, John J Fak, Ilana Zucker-Scharff, Robert B Darnell.
Neuron, 2017.

NOVA2-mediated RNA regulatory networks are required for axonal pathfinding during development.
Yuhki Saito, Soledad Miranda-Rottmann, Matteo Ruggiu, Christopher Y. Park, John J. Fak, Jeremy S. Duncan, Brian A Fabella, Roberto Araya, Bernd Fritzsch, A. J. Hudspeth, Robert B. Darnell.
eLife, 2016.

PAPERCLIP identifies novel microRNA targets and a role of CstF64/64tau in promoting non-canonical poly(A) site usage.
Hun-Way Hwang, Christopher Y. Park, Hani Goodarzi, John J. Fak, Aldo Mele, Michael J. Moore, Yuhki Saito, Robert B. Darnell.
Cell Reports, 2016.

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain.
Claudia Scheckel, Elodie Drapeau, Maria A. Frias, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell.
eLife, 2016.

miRNA-target chimeras reveal miRNA 3’-end pairing as a major determinant of Argonaute target specificity.
Michael J Moore, Troels KH Scheel, Joseph M Luna, Christopher Y. Park, John J Fak, Eiko Nishiuchi, Charles M Rice, Robert B Darnell.
Nature Communications, 2015.

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation.
Shengdong Ke, Endalkachew A Alemu, Claudia Mertens, Emily Conn Gantman, John J Fak, Aldo Mele, Bhagwattie Haripal, Ilana Zucker-Scharff, Michael J Moore, Christopher Y. Park, Cathrine Broberg Vågbø, Anna Kusśnierczyk, Arne Klungland, James E Darnell, Robert B Darnell.
Genes & Development, 2015.

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.
Dmitriy Gorenshteyn^*, Elena Zaslavsky^*, Miguel Fribourg^*, Christopher Y. Park^★, Aaron K Wong, Alicja Tadych, Boris M Hartmann, Randy A Albrecht, Adolfo García-Sastre, Steven H Kleinstein, Olga G Troyanskaya, Stuart C Sealfon. (★ co-first authors)
Immunity, 2015.

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.
Christopher Y. Park, Arjun Krishnan, Qian Zhu, Aaron K Wong, Young-Suk Lee, and Olga G Troyanskaya.
Bioinformatics, 2015.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.
Christopher Y. Park^★, Aaron K. Wong^*, Casey S. Greene^*, Jessica Rowland, Yuanfang Guan, Rebecca D. Burdine and Olga G. Troyanskaya. (★ co-first authors)
PLoS Computational Biology, 2013.

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Aaron K. Wong^*, Christopher Y. Park^★, Casey S. Greene^*, Lars A. Bongo, Yuanfang Guan and Olga G. Troyanskaya. (★ co-first authors)
Nucleic Acids Research, 2012.
Selected as NAR Editor’s featured article representing top 5% papers in terms of scientific excellence

Simultaneous genome-wide inference of physical, genetic, regulatory and functional pathway components.
Christopher Y. Park, David C. Hess, Curtis Huttenhower and Olga Troyanskaya.
PLoS Computational Biology, 2010.

Statistical calibration of the SEQUEST XCorr function.
Aaron A. Klammer, Christopher Y. Park and William Stafford Noble.
Journal of Proteome Research, 2009.

Rapid and accurate peptide identification from tandem mass spectra.
Christopher Y. Park^★, Aaron A. Klammer^*, Lukas Käll, Michael J. MacCoss and William Stafford Noble. (★ co-first authors)
Journal of Proteome Research, 2008.