Chen K, Wong A, Troyanskaya O, Zhou J. A sequence-based global map of regulatory activity for deciphering human genetics. Nat Genet. 2022;54(7):940–949. PMCID: PMC9279145

Zhou J, Troyanskaya O. Author Correction: An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2022;19(3):370. PMID: 35165450

Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021;18(11):1317–1321. PMCID: PMC8959118

Lindström N, Sealfon R, Chen X, Parvez R, Ransick A, Brandine G, Guo J, Hill B, Tran T, Kim A, Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs B, Thornton M, McMahon J, Smith A, Ruffins S, Armit C, Troyanskaya O, McMahon A. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell. 2021;56(16):2381–2398.e6. PMCID: PMC8396064

Chen X, Zhou J, Zhang R, Wong A, Park C, Theesfeld C, Troyanskaya O. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease. Cell Syst. 2021;12(4):353–362.e6. PMID: 33689683

Park C, Zhou J, Wong A, Chen K, Theesfeld C, Darnell R, Troyanskaya O. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet. 2021;53(2):166–173. PMCID: PMC7886016

El-Achkar T, Eadon M, Menon R, Lake B, Sigdel T, Alexandrov T, Parikh S, Zhang G, Dobi D, Dunn K, Otto E, Anderton C, Carson J, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu E, Sealfon R, Winfree S, Steck B, He Y, D’Agati V, Iyengar R, Troyanskaya O, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin B, Dagher P, Sharma K, Sarwal M, Hodgin J, Alpers C, Kretzler M, Jain S. A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. Physiol Genomics. 2021;53(1):1–11. PMCID: PMC7847045

Richter F, Morton S, Kim S, Kitaygorodsky A, Wasson L, Chen K, Zhou J, Qi H, Patel N, DePalma S, Parfenov M, Homsy J, Gorham J, Manheimer K, Velinder M, Farrell A, Marth G, Schadt E, Kaltman J, Newburger J, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter G, Bernstein D, Chung W, Srivastava D, Tristani-Firouzi M, Troyanskaya O, Dickel D, Shen Y, Seidman J, Seidman C, Gelb B. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet. 2020;52(8):769–777. PMCID: PMC7415662

Zhou J, Schor I, Yao V, Theesfeld C, Marco-Ferreres R, Tadych A, Furlong E, Troyanskaya O. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412

Shrine N, Guyatt A, Erzurumluoglu M, Jackson V, Hobbs B, Melbourne C, Batini C, Fawcett K, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve N, Obeidat M, Zhao J, Wielscher M, Understanding Society Scientific Group, Weiss S, Kentistou K, Cook J, Sun B, Zhou J, Hui J, Karrasch S, Imboden M, Harris S, Marten J, Enroth S, Kerr S, Surakka I, Vitart V, Lehtimäki T, Allen R, Bakke P, Beaty T, Bleecker E, Bossé Y, Brandsma C-A, Chen Z, Crapo J, Danesh J, DeMeo D, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell A, Hao K, Hoffman J, Hokanson J, Homuth G, Joshi P, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville J, Murray A, Nickle D, Packer R, Parker M, Paynton M, Porteous D, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin D, Smith B, Artigas M, Sparrow D, Tal-Singer R, Timmers P, Van den Berge M, Whittaker J, Woodruff P, Yerges-Armstrong L, Troyanskaya O, Raitakari O, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary I, Probst-Hensch N, Schulz H, James A, Wilson J, Stubbe B, Zeggini E, Jarvelin M-R, Wareham N, Silverman E, Hayward C, Morris A, Butterworth A, Scott R, Walters R, Meyers D, Cho M, Strachan D, Hall I, Tobin M, Wain L. Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet. 2019;51(6):1067. PMID: 31110354

Zhou J, Park C, Theesfeld C, Wong A, Yuan Y, Scheckel C, Fak J, Funk J, Yao K, Tajima Y, Packer A, Darnell R, Troyanskaya O. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019;51(6):973–980. PMCID: PMC6758908

Harder J, Menon R, Otto E, Zhou J, Eddy S, Wys N, O’Connor C, Luo J, Nair V, Cebrian C, Spence J, Bitzer M, Troyanskaya O, Hodgin J, Wiggins R, Freedman B, Kretzler M, European Renal cDNA Bank (ERCB), Nephrotic Syndrome Study Network (NEPTUNE). Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019;4(1). PMCID: PMC6485369

Shrine N, Guyatt A, Erzurumluoglu M, Jackson V, Hobbs B, Melbourne C, Batini C, Fawcett K, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve N, Obeidat M, Zhao J, Wielscher M, Weiss S, Kentistou K, Cook J, Sun B, Zhou J, Hui J, Karrasch S, Imboden M, Harris S, Marten J, Enroth S, Kerr S, Surakka I, Vitart V, Lehtimäki T, Allen R, Bakke P, Beaty T, Bleecker E, Bossé Y, Brandsma C-A, Chen Z, Crapo J, Danesh J, DeMeo D, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell A, Hao K, Hoffman J, Hokanson J, Homuth G, Joshi P, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville J, Murray A, Nickle D, Packer R, Parker M, Paynton M, Porteous D, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin D, Smith B, Artigas M, Sparrow D, Tal-Singer R, Timmers P, Van den Berge M, Whittaker J, Woodruff P, Yerges-Armstrong L, Troyanskaya O, Raitakari O, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary I, Probst-Hensch N, Schulz H, James A, Wilson J, Stubbe B, Zeggini E, Jarvelin M-R, Wareham N, Silverman E, Hayward C, Morris A, Butterworth A, Scott R, Walters R, Meyers D, Cho M, Strachan D, Hall I, Tobin M, Wain L, Understanding Society Scientific Group. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet. 2019;51(3):481–493. PMCID: PMC6397078

Chen K, Cofer E, Zhou J, Troyanskaya O. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMCID: PMC7148117

Zhou J, Theesfeld C, Yao K, Chen K, Wong A, Troyanskaya O. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018;50(8):1171–1179. PMCID: PMC6094955

Zhou J, Troyanskaya O. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015;12(10):931–4. PMCID: PMC4768299

Zhou J, Troyanskaya O. Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. Nat Commun. 2016;7:10528. PMCID: PMC4742914