See also Google Scholar; * for equal contribution, ✝︎ for correspondence, group members highlighted in bold.
Manuscripts & Preprints
- Deep learning modeling of rare noncoding genetic variants in human motor neurons defines CCDC146 as a therapeutic target for ALS
Sai Zhang✝︎, Tobias Moll, Jasper Rubin-Sigler, Sharon Tu, Shuya Li, Enming Yuan, Menghui Liu, Afreen Butt, Calum Harvey, Sarah Gornall, Elham Alhalthli, Allan Shaw, Cleide Dos Santos Souza, Laura Ferraiuolo, Eran Hornstein, Tatyana Shelkovnikova, Charlotte H. van Dijk, Ilia S. Timpanaro, Kevin P. Kenna, Jianyang Zeng, Philip S. Tsao, Pamela J. Shaw, Justin K. Ichida, Johnathan Cooper-Knock✝︎, Michael P. Snyder✝︎
medRxiv, 2024 [Link ]
- A single-cell, isoform-resolved case-control study of frontotemporal dementia reveals cell-type specific and broad splicing dysregulation
Natan Belchikov, Wen Hu, Li Fan, Anoushka Joglekar, Yi He, Careen Foord, Julien Jarroux, Justine Hsu, Shaun Pollard, Shiaoching Gong, Sai Zhang, M. Elizabeth Ross, Alissa Nana Li, Lea T. Grinberg, Salvatore Spina, Bruce L. Miller, Johnathan Cooper-Knock, Michael P. Snyder, William W. Seeley, Priyanka Rao-Ruiz, August B. Smit, Claire D. Clelland, Li Gan, Hagen U. Tilgner
Under submission
- Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity
Sai Zhang, Johnathan Cooper-Knock, Annika K. Weimer, Minyi Shi, Lina Kozhaya, Dera Unutmaz, Calum Harvey, Thomas H. Julian, Cheng Wang, Jingjing Li, Simone Furini, Elisa Frullanti, Francesca Fava, Alessandra Renieri, Cuiping Pan, Jina Song, Paul Billing-Ross, Peng Gao, Xiaotao Shen, Ilia Sarah Timpanaro, Kevin P. Kenna, VA Million Veteran Program, GEN-COVID Network, Mark M. Davis, Philip S. Tsao, Michael P. Snyder
medRxiv, 2021 [ Link ]
- Characterizing information spreading in online social networks
Sai Zhang, Ke Xu, Xi Chen, Xue Liu
arXiv, 2014 [ Link ]
Peer-Reviewed Papers
- Rare and common genetic determinants of mitochondrial function determine severity but not risk of amyotrophic lateral sclerosis
Calum Harvey, Marcel Weinreich, James A.K. Lee, Allan C. Shaw, Laura Ferraiuolo, Heather Mortiboys, Sai Zhang, Paul J. Hop, Ramona A.J. Zwamborn, Kristel van Eijk, Thomas H. Julian, Tobias Moll, Alfredo Iacoangeli, Ahmad Al Khleifat, John P. Quinn, Abigail L. Pfaff, Sulev Kõks, Joanna Poulton, Stephanie L. Battle, Dan E. Arking, Michael P. Snyder, Project MinE ALS Sequencing Consortium, Jan H. Veldink, Kevin P. Kenna, Pamela J. Shaw, Johnathan Cooper-Knock
Heliyon, 10(3):e0000161, e24975, 2024 [ Link ]
- PRS-Net: Interpretable polygenic risk scores via geometric learning
Han Li, Jianyang Zeng✝︎, Michael P. Snyder✝︎, Sai Zhang✝︎
RECOMB 2024 [ Link ]
- Longitudinally tracking personal physiomes for precision management of childhood epilepsy
Peifang Jiang, Feng Gao, Sixing Liu, Sai Zhang, Xicheng Zhang, Zhezhi Xia, Weiqin Zhang, Tiejia Jiang, Jason L. Zhu, Zhaolei Zhang, Qiang Shu, Michael P. Snyder, Jingjing Li
PLOS Digital Health, 1(12):e0000161, 2022 [ Link ]
- Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication
Tobias Moll, Valerie Odon, Calum Harvey, Mark O. Collins, Andrew Peden, John Franklin, Emily Graves, Jack N.G. Marshall, Cleide dos Santos Souza, Sai Zhang, Lydia Castelli, Guillaume Hautbergue, Mimoun Azzouz, David Gordon, Nevan Krogan, Laura Ferraiuolo, Michael P. Snyder, Pamela J. Shaw, Jan Rehwinkel, Johnathan Cooper-Knock
Life Science Alliance, 6(1):e202201449, 2022 [ Link ]
- Systems analysis of de novo mutations in congenital heart diseases identified a protein network in hypoplastic left heart syndrome
Yuejun Wang, Xicheng Zhang, Chi Lam, Hongchao Guo, Cheng Wang, Sai Zhang, Joseph Wu, Michael P. Snyder, Jingjing Li
Cell Systems, 13:1-16, 2022 [ Link ]
- Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine
Xiaotao Shen, Wei Shao, Chuchu Wang, Liang Liang, Songjie Chen, Sai Zhang, Mirabela Rusu, Michael P. Snyder
Briefings In Bioinformatics, bbac331, 2022 [ Link ]
- Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity
Sai Zhang, Johnathan Cooper-Knock, Annika K. Weimer, Minyi Shi, Lina Kozhaya, Dera Unutmaz, Calum Harvey, Thomas H. Julian, Simone Furini, Elisa Frullanti, Francesca Fava, Alessandra Renieri, Peng Gao, Xiaotao Shen, Illia Sarah Timpanaro, Kevin P. Kenna, J. Kenneth Baillie, Mark M. Davis, Philip S. Tsao, Michael P. Snyder
Cell Systems, 13(8):598-614, 2022 [ Link, Cover Article ]
[ Stanford Medicine News, GenomeWeb, EurekAlert!, New Scientist, Science Daily, Medical Xpress, GEN ]
- Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
Peng Gao, Xiaotao Shen, Xinyue Zhang, Chao Jiang, Sai Zhang, Xin Zhou, Sophia Miryam Schüssler-Fiorenza Rose, Michael P. Snyder
Genome Research, 32:1-16, 2022 [ Link ]
- Unbiased metabolome screen leads to personalised medicine strategy for amyotrophic lateral sclerosis
Sarah Boddy, Mahjabin Islam, Tobias Moll, Julian Kurz, David Burrows, Alexander McGown, Anushka Bhargava, Thomas H. Julian, Calum Harvey, Jack N.G. Marshall, Benjamin P.C. Hall, Scott P. Allen, Kevin P. Kenna, Eleanor Sanderson, Sai Zhang, Tennore Ramesh, Michael P. Snyder, Pamela J. Shaw, Christopher McDermott, Johnathan Cooper-Knock
Brain Communications, fcac069, 2022 [ Link ]
- Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis
Sai Zhang, Johnathan Cooper-Knock, Annika K. Weimer, Minyi Shi, Tobias Moll, Jack N.G. Marshall, Calum Harvey, Helia Ghahremani Nezhad, John Franklin, Cleide dos Santos Souza, Ke Ning, Cheng Wang, Jingjing Li, Allison A. Dilliott, Sali Farhan, Eran Elhaik, Iris Pasniceanu, Matthew R. Livesey, Chen Eitan, Eran Hornstein, Kevin P. Kenna, Project MinE ALS Sequencing Consortium, Jan H. Veldink, Laura Ferraiuolo, Pamela J. Shaw, Michael P. Snyder
Neuron, 110(6):992-1008, 2022 [ Link, Cover Article, Preview ]
[ Nature Reviews Neurology Research Highlight, Stanford Medicine News, Sheffield News, EurekAlert!, The Register, Science Daily, GEN, Tech Explorist, Medical Xpress, BioArt ]
- A review of Mendelian randomization in amyotrophic lateral sclerosis
Thomas H. Julian, Sarah Boddy, Mahjabin Islam, Julian Kurz, Katherine J. Whittaker, Tobias Moll, Calum Harvey, Sai Zhang, Michael P. Snyder, Christopher McDermott, Johnathan Cooper-Knock, Pamela J. Shaw
Brain, 2021 [ Link ]
- Membrane lipid raft homeostasis is directly linked to neurodegeneration
Tobias Moll, Jack N.G. Marshall, Nikita Soni, Sai Zhang, Johnathan Cooper-Knock, Pamela J. Shaw
Essays in Biochemistry, EBC20210026, 2021 [ Link ]
- Advances in the genetic classification of amyotrophic lateral sclerosis
Johnathan Cooper-Knock, Calum Harvey, Sai Zhang, Tobias Moll, Ilia Sarah Timpanaro, Kevin P. Kenna, Alfredo Iacoangeli, Jan H. Veldink
Current Opinion in Neurology, 33:000–000, 2021 [ Link ]
- Physical exercise is a risk factor for amyotrophic lateral sclerosis: Convergent evidence from Mendelian randomisation, transcriptomics and risk genotypes
Thomas H. Julian, Nicholas Glascow, A. Dylan Fisher Barry, Tobias Moll, Calum Harvey, Yann C. Klimentidis, Michelle Newell, Sai Zhang, Michael P. Snyder, Johnathan Cooper-Knock, Pamela J. Shaw
EBioMedicine, 68:103397, 2021 [ Link ]
- Precision medicine in women with epilepsy: The challenge, systematic review and future direction
Yi Li, Sai Zhang, Michael P. Snyder, Kimford J. Meador
Epilepsy & Behavior, 118:107928, 2021 [ Link ]
- Characterizing RNA pseudouridylation by convolutional neural networks
Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng
Genomics, Proteomics & Bioinformatics, 2021 [ Link ]
- DeepRibSt: A multi-feature convolutional neural network for predicting ribosome stalling
Yuan Zhang, Sai Zhang, Xizhi He, Jing Lu, Xieping Gao
Multimedia Tools and Applications, 80:17239–17255, 2021 [ Link ]
- Rare variant burden analysis within enhancers identifies CAV1 as a new ALS risk gene
Johnathan Cooper-Knock, Sai Zhang, Kevin P. Kenna, Tobias Moll, John P. Franklin, Samantha Allen, Helia Ghahremani Nezhad, Alfredo Iacoangeli, Nancy Y. Yacovzada, Chen Eitan, Eran Hornstein, Eran Elhaik, Petra Celadova, Daniel Bose, Sali Farhan, Simon Fishilevich, Doron Lancet, Karen E. Morrison, Christopher E. Shaw, Ammar Al-Chalabi, Project MinE ALS Sequencing Consortium, Jan H. Veldink, Janine Kirby, Michael P. Snyder, Pamela J. Shaw
Cell Reports, 33(9):108456, 2020 [ Link ]
- Gene-environment interaction in the era of precision medicine
Jingjing Li, Xiao Li, Sai Zhang, Michael P. Snyder
Cell, 177(1):38-44, 2019 [ Link ]
- DeepHINT: Understanding HIV-1 integration via deep learning with attention
Hailin Hu, An Xiao, Sai Zhang, Yangyang Li, Xuanling Shi, Tao Jiang, Linqi Zhang, Lei Zhang, Jianyang Zeng
Bioinformatics, 35(10):1660-1667, 2019 [ Link ]
- Decoding the genomics of abdominal aortic aneurysm
Jingjing Li*, Cuiping Pan*, Sai Zhang*, Joshua M. Spin, Alicia Deng, Lawrence L.K. Leung, Ronald L. Dalman, Philip S. Tsao, Michael P. Snyder
Cell, 174(6):1361-1372, 2018 [ Link, Video Abstract ]
[ Francis Collins' Twitter, Nature Research Highlight, Stanford Medicine News, Stanford Scope, NIH Research Matters, EurekAlert!, GenomeWeb, Science Daily, Medical Xpress ]
- Reconstructing spatial organizations of chromosomes through manifold learning
Guangxiang Zhu, Wenxuan Deng, Hailin Hu, Rui Ma, Sai Zhang, Jinglin Yang, Jian Peng, Tommy Kaplan, Jianyang Zeng
Nucleic Acids Research, 46(8):e50, 2018 [ Link ]
- Analysis of ribosome stalling and translation elongation dynamics by deep learning
Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng
Cell Systems, 5(3):212-220, 2017 [ Link ]; RECOMB 2017
- TITER: Predicting translation initiation sites by deep learning
Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng
Bioinformatics, 33(14):i234-i242, 2017 [ Link ]; ISMB/ECCB 2017
- Elastic restricted Boltzmann machines for cancer data analysis
Sai Zhang, Muxuan Liang, Zhongjun Zhou, Chen Zhang, Ning Chen, Ting Chen, Jianyang Zeng
Quantitative Biology, 5(2):159-172, 2017 [ Link, Cover Article ]
- A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data
Shuya Li, Fanghong Dong, Yuexin Wu, Sai Zhang, Chen Zhang, Xiao Liu, Tao Jiang, Jianyang Zeng
Nucleic Acids Research, 45(14):e129, 2017 [ Link ]
- A deep learning framework for modeling structural features of RNA-binding protein targets
Sai Zhang, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng, Jianyang Zeng
Nucleic Acids Research, 44(4):e32, 2016 [ Link ]
- Constructing structure ensembles of intrinsically disordered proteins from chemical shift data
Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng
Journal of Computational Biology, 23(5):300-310, 2016 [ Link ]; RECOMB 2015
- Measurement and analysis of online social networks
Ke Xu, Sai Zhang, Hao Chen, Haitao Li
Chinese Journal of Computers, 37(1):165-188, 2014 [ Link ]
Patents
- Processes for genetic and clinical data evaluation and classification of complex human traits
Jingjing Li, Sai Zhang, Michael P. Snyder, Cuiping Pan, Philip S. Tsao
US16/961,120, 2021 [ Link ]
- Systems and methods for predicting genetic diseases
Sai Zhang, Jingjing Li, Michael P. Snyder
US16/248,314, 2019 [ Link ]