Publications & Preprints (see Google Scholar for full list):

Sequence basis of transcription initiation in the human genome, 2023, Kseniia Dudnyk, Donghong Cai*, Chenlai Shi*, Jian Xu, Jian Zhou, Science [Webserver] [Code] [Perspective] (*equal contributions)

An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants, 2023, Bruce Nmezi, Guillermo R. Bey, Talia D. Oranburg, Kseniia Dudnyk, Santana M. Lardo, Nathan Herdman, …, Murad Alturkustani, Robert Hammond, Francois Gros-Louis, Michael Gold, Yungki Park, Geneviève Bernard, Raili Raininko, Jian Zhou, Sarah J. Hainer, Quasar S. Padiath, bioRxiv

TriFold: A New Architecture for Predicting Protein Sequences from Structural Data, 2023, Harish Srinivasan, Jian Zhou, NeurIPS 2023 MLSB Workshop

Dirichlet Diffusion Score Model for biological sequence generation, 2023, Pavel Avdeyev, Chenlai Shi, Yuhao Tan, Kseniia Dudnyk, Jian Zhou, ICML 2023 (International Conference on Machine Learning) [Code]

Accelerating Systematic Prediction of Variant Effects and Sequence Interpretation with Multiplexer Models, 2023, Dennis Tang, Chenlai Shi, Jian Zhou, ICML 2023 Workshop on Computational Biology [Webserver] [Code]

Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription, 2023, Giovanni Botten, Yuannyu Zhang*, Kseniia Dudnyk, Yoon Jung Kim, Xin Liu, Jacob Sanders, Aygun Imanci, Nathalie Droin, Hui Cao, Pranita Kaphle, Kathryn E. Dickerson, Kirthi Kumar, Mingyi Chen, Weina Chen, Eric Solary, Peter Ly, Jian Zhou*, Jian Xu*, Blood (*co-corresponding authors) [Webserver] [Code]

A sequence-based global map of regulatory activity for deciphering human genetics, 2022
Kathleen M. Chen, Aaron K. Wong, Olga G. Troyanskaya*, Jian Zhou*, Nature Genetics (*co-corresponding authors) [Webserver] [Code]

Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale, 2022
​Jian Zhou, Nature Genetics [Webserver] [Code]

Computational approaches for understanding sequence variation effects on the 3D genome architecture, 2022
Pavel Avdeyev, Jian Zhou, Annual Review of Biomedical Data Science

An analytical framework for interpretable and generalizable single-cell data analysis, 2021
​Jian Zhou*, Olga G. Troyanskaya*, Nature Methods (*co-corresponding authors) [Code]

Genome-wide landscape of RNA-binding protein dysregulation reveals a major impact on psychiatric disorder risk, 2020,
Christopher Y. Park, Jian Zhou, Aaron K. Wong, Kathleen M. Chen, Chandra L. Theesfeld,  Robert Darnell, Olga G. Troyanskaya, Nature Genetics

Genomic analyses implicate noncoding de novo variants in congenital heart disease, 2020,
Felix Richter*, Sarah U. Morton*, Seong Won Kim*, Alexander Kitaygorodsky*, Lauren K. Wasson*, Kathleen M Chen*, Jian Zhou, …, Bruce Gelb, Nature Genetics

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development, 2019
​Jian Zhou*, Ignacio E. Schor*, Victoria Yao, Chandra L. Theesfeld, Raquel Marco-Ferreres, Alicja Tadych, Eileen E. M. Furlong, Olga G. Troyanskaya, PLOS Genetics (*co-first authors) [Code]

Whole-genome deep learning analysis identifies contribution of noncoding mutations in autism, 2019
​Jian Zhou*, Christopher Y. Park*, Chandra L. Theesfeld*, Aaron K. Wong, Yuan Yuan, Kirsty Sawicka, Claudia Scheckel, John Fak, Yoko Tajima, Alan Packer, Robert Darnell, Olga Troyanskaya, Nature Genetics (*co-first authors) [Webserver] [Code] [Scientific American] [Sci Show]

Selene: a PyTorch-based deep learning library for sequence-level data, 2019
​Kathleen M. Chen*, Evan Cofer*, Jian Zhou, Olga G. Troyanskaya, Nature Methods [Code]

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk, 2018
​Jian Zhou, Chandra L. Theesfeld, Kevin Yao, Kathleen M. Chen, Aaron K. Wong, Olga G. Troyanskaya, Nature Genetics [Webserver] [Code]

Organoid single-cell profiling identifies a transcriptional signature of glomerular disease, 2018
​Jennifer Harder*, Rajasree Menon*, Edgar A. Otto*, Jian Zhou*, Sean Eddy, Noel Wys, Viji Nair, Cristina Cebrian, Jason R. Spence, Olga Troyanskaya, Jeffrey Hodgin, Roger Wiggins, Benjamin Freedman, Matthias Kretzler, European Renal cDNA Bank, Nephrotic Syndrome Study Network, JCI Insight (*co-first authors)

Predicting effects of noncoding variants with deep learning-based sequence model, 2015
Jian Zhou, Olga G. Troyanskaya, Nature Methods [Webserver] [Code] [News & Views]

Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states, 2015
​Jian Zhou, Olga G. Troyanskaya, Nature Communications

Global Quantitative Modeling of Chromatin Factor Interactions, 2014
Jian Zhou, Olga G. Troyanskaya, PLOS Computational Biology [Code and Dataset]

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney, 2018
​Rajasree Menon, Edgar A. Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu-Chih Chen, Olga Troyanskaya, Jason R. Spence, Matthias Kretzler, Cristina Cebrián, Development

Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction, 2014
Jian Zhou, Olga G. Troyanskaya, ICML 2014 (International Conference on Machine Learning) [Dataset] [Code] [Slides]
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