Cappuccio A, Chawla D, Chen X, Rubenstein A, Cheng W, Mao W, Burke T, Tsalik E, Petzold E, Henao R, McClain M, Woods C, Chikina M, Troyanskaya O, Sealfon S, Kleinstein S, Zaslavsky E. Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature. Cell Syst. 2022;13(12):989–1001.e8. PMID: 36549275

Sauerwald N, Zhang Z, Ramos I, Nair V, Soares-Schanoski A, Ge Y, Mao W, Alshammary H, Gonzalez-Reiche A, van de Guchte A, Goforth C, Lizewski R, Lizewski S, Amper M, Vasoya M, Seenarine N, Guevara K, Marjanovic N, Miller C, Nudelman G, Schilling M, Sealfon R, Termini M, Vangeti S, Weir D, Zaslavsky E, Chikina M, Wu Y, van Bakel H, Letizia A, Sealfon S, Troyanskaya O. Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Syst. 2022;13(11):924–931.e4. PMCID: PMC9623453

Lizewski R, Sealfon R, Park S, Smith G, Porter C, Gonzalez-Reiche A, Ge Y, Miller C, Goforth C, Pincas H, Termini M, Ramos I, Nair V, Lizewski S, Alshammary H, Cer R, Chen H, George M-C, Arnold C, Glang L, Long K, Malagon F, Marayag J, Nunez E, Rice G, Ana E, Schilling M, Smith D, Sugiharto V, Sun P, van de Guchte A, Khan Z, Dutta J, Vangeti S, Voegtly L, Weir D, Metcalf J, Troyanskaya O, Bishop-Lilly K, Grenfell B, van Bakel H, Letizia A, Sealfon S. SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology. 2022;33(6):797–807. PMCID: PMC9531985

Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res. 2022;50(14):8168–8192. PMCID: PMC9371935

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

Hansen J, Sealfon R, Menon R, Eadon M, Lake B, Steck B, Anjani K, Parikh S, Sigdel T, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto E, Rivera M, Rose M, Anderton C, Shapiro J, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer I, Hodgin J, Barisoni L, Naik A, Sharma K, Sarwal M, Zhang K, Himmelfarb J, Rovin B, El-Achkar T, Laszik Z, He J, Dagher P, Valerius T, Jain S, Satlin L, Troyanskaya O, Kretzler M, Iyengar R, Azeloglu E, Kidney Precision Medicine Project. A reference tissue atlas for the human kidney. Sci Adv. 2022;8(23):eabn4965. PMCID: PMC9176741

Soares-Schanoski A, Sauerwald N, Goforth C, Periasamy S, Weir D, Lizewski S, Lizewski R, Ge Y, Kuzmina N, Nair V, Vangeti S, Marjanovic N, Cappuccio A, Cheng W, Mofsowitz S, Miller C, Yu X, George M-C, Zaslavsky E, Bukreyev A, Troyanskaya O, Sealfon S, Letizia A, Ramos I. Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19. Front Immunol. 2022;13:821730. PMCID: PMC9037090

Zhang Z, Zamojski M, Smith G, Willis T, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper M, Vasoya M, Cheng W, Zaslavsky E, Nair V, Turgeon J, Bernard D, Troyanskaya O, Andoniadou C, Sealfon S, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell Rep. 2022;38(10):110467. PMCID: PMC8957708

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

Meyer M, Wang Y, Edwards D, Smith G, Rubenstein A, Ramanathan P, Mire C, Pietzsch C, Chen X, Ge Y, Cheng W, Henry C, Woods A, Ma L, Stewart-Jones G, Bock K, Minai M, Nagata B, Periasamy S, Shi P-Y, Graham B, Moore I, Ramos I, Troyanskaya O, Zaslavsky E, Carfi A, Sealfon S, Bukreyev A. Attenuated activation of pulmonary immune cells in mRNA-1273-vaccinated hamsters after SARS-CoV-2 infection. J Clin Invest. 2021;131(20). PMCID: PMC8516449

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

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

Li V, Zhang Z, Troyanskaya O. CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinformatics. 2021;37(Suppl_1):i342-i348. PMCID: PMC8275342

Ruf-Zamojski F, Zhang Z, Zamojski M, Smith G, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon R, Nair V, Seenarine N, Amper M, Zhou X, Ongaro L, Toufaily C, Schang G, Nery J, Bartlett A, Aldridge A, Jain N, Childs G, Troyanskaya O, Ecker J, Turgeon J, Welt C, Bernard D, Sealfon S. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021;12(1):2677. PMCID: PMC8113460

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

de Boer I, Alpers C, Azeloglu E, Balis U, Barasch J, Barisoni L, Blank K, Bomback A, Brown K, Dagher P, Dighe A, Eadon M, El-Achkar T, Gaut J, Hacohen N, He Y, Hodgin J, Jain S, Kellum J, Kiryluk K, Knight R, Laszik Z, Lienczewski C, Mariani L, McClelland R, Menez S, Moledina D, Mooney S, O’Toole J, Palevsky P, Parikh C, Poggio E, Rosas S, Rosengart M, Sarwal M, Schaub J, Sedor J, Sharma K, Steck B, Toto R, Troyanskaya O, Tuttle K, Vazquez M, Waikar S, Williams K, Wilson F, Zhang K, Iyengar R, Kretzler M, Himmelfarb J, Kidney Precision Medicine Project. Rationale and design of the Kidney Precision Medicine Project. Kidney Int. 2021;99(3):498–510. PMCID: PMC8330551

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

Letizia A, Ramos I, Obla A, Goforth C, Weir D, Ge Y, Bamman M, Dutta J, Ellis E, Estrella L, George M-C, Gonzalez-Reiche A, Graham W, van de Guchte A, Gutierrez R, Jones F, Kalomoiri A, Lizewski R, Lizewski S, Marayag J, Marjanovic N, Millar E, Nair V, Nudelman G, Nunez E, Pike B, Porter C, Regeimbal J, Rirak S, Ana E, Sealfon R, Sebra R, Simons M, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya O, van Bakel H, Sealfon S. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. N Engl J Med. 2020;383(25):2407–2416. PMCID: PMC7675690

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

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

Dannenfelser R, Allen G, VanderSluis B, Koegel A, Levinson S, Stark S, Yao V, Tadych A, Troyanskaya O, Lim W. Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies. Cell Syst. 2020;11(3):215–228.e5. PMCID: PMC7814417

Ledo J, Zhang R, Mesin L, Mourão-Sá D, Azevedo E, Troyanskaya O, Bustos V, Greengard P. Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development. PLoS One. 2020;15(8):e0237773. PMCID: PMC7444478

Ledo J, Liebmann T, Zhang R, Chang J, Azevedo E, Wong E, Silva H, Troyanskaya O, Bustos V, Greengard P. Presenilin 1 phosphorylation regulates amyloid-β degradation by microglia. Mol Psychiatry. 2021;26(10):5620–5635. PMCID: PMC7881060

Orange D, Yao V, Sawicka K, Fak J, Frank M, Parveen S, Blachere N, Hale C, Zhang F, Raychaudhuri S, Troyanskaya O, Darnell R. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. N Engl J Med. 2020;383(3):218–228. PMCID: PMC7546156

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

Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt E, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof P, Heiman M, Dolinski K, Flajolet M, Troyanskaya O, Greengard P. Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis. Neuron. 2020;107(5):821–835.e12. PMCID: PMC7580783

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

Sealfon R, Mariani L, Kretzler M, Troyanskaya O. Machine learning, the kidney, and genotype-phenotype analysis. Kidney Int. 2020;97(6):1141–1149. PMCID: PMC8048707

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

Zhu Q, Tekpli X, Troyanskaya O, Kristensen V. Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. Bioinformatics. 2020;36(4):994–999. PMCID: PMC7031777

Sargin D, Chottekalapanda R, Perit K, Yao V, Chu D, Sparks D, Kalik S, Power S, Troyanskaya O, Schmidt E, Greengard P, Lambe E. Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons. Mol Psychiatry. 2020;25(5):1112–1129. PMCID: PMC7031043

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

Lee Y-S, Wong A, Tadych A, Hartmann B, Park C, DeJesus V, Ramos I, Zaslavsky E, Sealfon S, Troyanskaya O. Interpretation of an individual functional genomics experiment guided by massive public data. Nat Methods. 2018;15(12):1049–1052. PMCID: PMC6941785

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

Bradley P, Gibney P, Botstein D, Troyanskaya O, Rabinowitz J. Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems. 2019;4(1). PMCID: PMC6392091

Yao V, Kaletsky R, Keyes W, Mor D, Wong A, Sohrabi S, Murphy C, Troyanskaya O. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol. 2018;. PMCID: PMC7021177

Yao V, Wong A, Troyanskaya O. Enabling Precision Medicine through Integrative Network Models. J Mol Biol. 2018;430(18 Pt A):2913–2923. PMID: 30003887

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

Kaletsky R, Yao V, Williams A, Runnels A, Tadych A, Zhou S, Troyanskaya O, Murphy C. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet. 2018;14(8):e1007559. PMCID: PMC6105014

Wong A, Krishnan A, Troyanskaya O. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 2018;46(W1):W65-W70. PMCID: PMC6030827

Watson E, Olin-Sandoval V, Hoy M, Li C-H, Louisse T, Yao V, Mori A, Holdorf A, Troyanskaya O, Ralser M, Walhout A. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. Elife. 2016;5. PMCID: PMC4951191

Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Vollan H, Haakensen V, Helland Åslaug, Naume B, Caldas C, Børresen-Dale A-L, Kristensen V, Troyanskaya O. Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity. Oncotarget. 2017;8(34):57121–57133. PMCID: PMC5593630