Wong A, Sealfon R, Theesfeld C, Troyanskaya O. Decoding disease: from genomes to networks to phenotypes. Nat Rev Genet. 2021;22(12):774–790. PMCID: 6786975

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

Cofer E, Raimundo J, Tadych A, Yamazaki Y, Wong A, Theesfeld C, Levine M, Troyanskaya O. Modeling transcriptional regulation of model species with deep learning. Genome Res. 2021;31(6):1097–1105. PMCID: PMC8168591

Graim K, Gorenshteyn D, Robinson D, Carriero N, Cahill J, Chakrabarti R, Goldschmidt M, Durham A, Funk J, Storey J, Kristensen V, Theesfeld C, Sorenmo K, Troyanskaya O. Modeling molecular development of breast cancer in canine mammary tumors. Genome Res. 2020;31(2):337–47. PMCID: PMC7849403

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

Iserman C, Roden C, Boerneke M, Sealfon R, McLaughlin G, Jungreis I, Fritch E, Hou Y, Ekena J, Weidmann C, Theesfeld C, Kellis M, Troyanskaya O, Baric R, Sheahan T, Weeks K, Gladfelter A. Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. Mol Cell. 2020;80(6):1078–1091.e6. PMCID: PMC7691212

Menon R, Otto E, Sealfon R, Nair V, Wong A, Theesfeld C, Chen X, Wang Y, Boppana A, Luo J, Yang Y, Kasson P, Schaub J, Berthier C, Eddy S, Lienczewski C, Godfrey B, Dagenais S, Sohaney R, Hartman J, Fermin D, Subramanian L, Looker H, Harder J, Mariani L, Hodgin J, Sexton J, Wobus C, Naik A, Nelson R, Troyanskaya O, Kretzler M. SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease. Kidney Int. 2020;98(6):1502–1518. PMCID: PMC7543950

Menon R, Otto E, Sealfon R, Nair V, Wong A, Theesfeld C, Chen X, Wang Y, Boppanna A, Luo J, Yang Y, Kasson P, Schaub J, Berthier C, Eddy S, Lienczewski C, Godfrey B, Dagenais S, Sohaney R, Hartman J, Fermin D, Subramanian L, Looker H, Harder J, Mariani L, Hodgin J, Sexton J, Wobus C, Naik A, Nelson R, Troyanskaya O, Kretzler M. SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease. medRxiv. 2020;. PMCID: PMC7241118

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

Lee Y-S, Krishnan A, Oughtred R, Rust J, Chang C, Ryu J, Kristensen V, Dolinski K, Theesfeld C, Troyanskaya O. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019;8(2):152–162.e6. PMCID: PMC7374759

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

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

Krishnan A, Zhang R, Yao V, Theesfeld C, Wong A, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya O. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nat Neurosci. 2016;19(11):1454–1462. PMCID: PMC5803797