Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts

Reed TJ, Tyl MD, Tadych A, Troyanskaya OG, Cristea IM

Nature Methods. 2024 Feb 15. [Website] [Code]


Interpretable neural architecture search and transfer learning for understanding CRISPR/Cas9 off-target enzymatic reactions

Zhang Z, Lamson AR, Shelley M, Troyanskaya O.

Nature Computational Science. 2023 Dec 14.

Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data

Zhang Z, Ruf-Zamojski F, Zamojski M, Bernard DJ, Chen X, Troyanskaya OG, Sealfon SC

Nucleic Acids Res.. 2023 Dec 12.

Automated single-cell omics end-to-end framework with data-driven batch inference

Wang Y, Thistlethwaite W, Tadych A, Ruf-Zamojski F, Bernard DJ, Cappuccio A, Zaslavsky E, Chen X, Sealfon SC, Troyanskaya OG.

bioRxiv. 2023 Nov 14.

Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC.

bioRxiv. 2023 Oct 9.

Atlas of primary cell-type-specific sequence models of gene expression and variant effects

Sokolova K, Theesfeld CL, Wong AK, Zhang Z, Dolinski K, Troyanskaya OG.

Cell Rep Methods. 2023 Sep 13.

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Chen X, Wang Y, Cappuccio A, Cheng WS, Ruf-Zamojski F, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, ... ,Troyanskaya OG, Sealfon SC.

Nature Computational Science. 2023 Jul 25. [Uncovering the genetic circuits that drive diseases]

A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation

Mao W, Miller CM, Nair VD, Ge Y, Amper MAS, Cappuccio A, George MC, Goforth CW, Guevara K, Marjanovic N, ..., Vangeti S, Vasoya M, Weir DL, Zaslavsky E; Biobank Team; Kim-Schulze S, Gnjatic S, Merad M, Letizia AG, Troyanskaya OG, Sealfon SC, Chikina M.

Mol Syst Biol. 2023 Mar 15.

Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease

Zhang Z, Sauerwald N, Cappuccio A, Ramos I, Nair VD, Nudelman G, Zaslavsky E, ... , Letizia AG, Sealfon SC, Troyanskaya OG

Cell Reports Methods. 2023 Feb 27.

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

Brewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, ..., Troyanskaya O, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE.

Sci Transl Med. 2023 Feb 22.

Identifying genes and pathways linking astrocyte regional specificity to Alzheimer’s disease susceptibility

Ran Zhang, Margarete Knudsen, Pedro Del Cioppo Vasques, Alicja Tadych, Patricia Rodriguez-Rodriguez, Paul Greengard, Jean-Pierre Roussarie, Ana Milosevic, Olga Troyanskaya

bioRxiv. 2023 Jan.


Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature

Antonio Cappuccio, Daniel G. Chawla, Xi Chen, Aliza B. Rubenstein, Wan Sze Cheng, Weiguang Mao, Thomas W. Burke, Ephraim L. Tsalik, Elizabeth Petzold, Ricardo Henao, Micah T. McClain, Christopher W. Woods, Maria Chikina, Olga G. Troyanskaya, Stuart C. Sealfon, Steven H. Kleinstein, Elena Zaslavsky

Cell Systems. 2022 Dec 21.

Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection

Sauerwald N, Zhang Z, Ramos I, Nair VD, Soares-Schanoski A, Ge Y, Mao W, Alshammary H, Gonzalez-Reiche AS, van de Guchte A, Goforth CW, Lizewski RA, Lizewski SE, Amper MAS, Vasoya M, Seenarine N, Guevara K, Marjanovic N, Miller CM, Nudelman G, Schilling MA, Sealfon RSG, Termini MS, Vangeti S, Weir DL, Zaslavsky E, Chikina M, Wu YN, Van Bakel H, Letizia AG, Sealfon SC, Troyanskaya OG

Cell Syst. 2022 Nov 1. [Researchers discover behavior of immunity genes leading to worse COVID outcomes for men]

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Roden CA, Dai Y, Giannetti CA, Seim I, Lee M, Sealfon R, McLaughlin GA, Boerneke MA, Iserman C, Wey SA, Ekena JL, Troyanskaya OG, Weeks KM, You L, Chilkoti A, Gladfelter AS.

Nucleic Acids Res. 2022 Aug 15.

SARS-CoV-2 outbreak dynamics in an isolated US military recruit training center with rigorous prevention measures

Lizewski RA, Sealfon RSG, Park SW, Smith GR, Porter CK, Gonzalez-Reiche AS, Ge Y, Miller CM, Goforth CW, Pincas H, ..., Vangeti S, Voegtly LJ, Weir DL, Metcalf CJE, Troyanskaya OG, Bishop-Lilly KA, Grenfell BT, van Bakel H, Letizia AG, Sealfon SC.

Epidemiology. 2022 Aug 9.

A sequence-based global map of regulatory activity for deciphering human genetics

Chen KM, Wong AK, Troyanskaya OG, Zhou J.

Nature Genetics. 2022 Jul 11. [Website] [Code]

A reference tissue atlas for the human kidney

Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, ..., Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU; Kidney Precision Medicine Project.

Sci Adv. 2022 Jun 8.

An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes

Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim TG, Nirschl CJ, Devi KSP, Olson WC Jr, Slingluff CL Jr, Engelhard VH, Garraway L, Regev A, Minkis K, Yoon CH, Troyanskaya O, Elemento O, Suárez-Fariñas M, Anandasabapathy N.

Cancer Cell. 2022 May 10.

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

Soares-Schanoski A, Sauerwald N, Goforth CW, Periasamy S, Weir DL, Lizewski S, Lizewski R, Ge Y, Kuzmina NA, Nair VD, ..., Mofsowitz S, Miller CM, Yu XB, George MC, Zaslavsky E, Bukreyev A, Troyanskaya OG, Sealfon SC, Letizia AG, Ramos I.

Front Immunol. 2022 Apr 28.

Molecular Characterization of Membranous Nephropathy

Sealfon R, Mariani L, Avila-Casado C, Nair V, Menon R, Funk J, Wong A, Lerner G, Hayashi N, Troyanskaya O, Kretzler M, Beck LH Jr.

J Am Soc Nephrol. 2022 Apr 28.

Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms

Zhang Z, Zamojski M, Smith GR, Willis TL, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper MAS, Vasoya M, Cheng WS, Zaslavsky E, Nair VD, Turgeon JL, Bernard DJ, Troyanskaya OG, Andoniadou CL, Sealfon SC, Ruf-Zamojski F.

Cell Rep. 2022 Mar 9.


Attenuated activation of pulmonary immune cells in mRNA-1273 vaccinated hamsters after SARS-CoV-2 infection

Meyer M, Wang Y, Edwards D, Smith GR, Rubenstein AB, Ramanathan P, Mire CE, Pietzsch C, Chen X, Ge Y, ..., Periasamy S, Shi PY, Graham BS, Moore IN, Ramos I, Troyanskaya OG, Zaslavsky E, Carfi A, Sealfon SC, Bukreyev A.

J Clin Invest. 2021 Aug 27.

Spatial transcriptional mapping of the human nephrogenic program

Lindström NO, Sealfon R, Chen X, Parvez RK, Ransick A, De Sena Brandine G, Guo J, Hill B, ..., Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs BH, Thornton ME, McMahon JA, Smith AD, Ruffins SW, Armit C, Troyanskaya OG, McMahon AP.

Dev Cell. 2021 Aug 24. [Website]

Decoding disease: from genomes to networks to phenotypes

Wong AK, Sealfon RS, Theesfeld CL, Troyanskaya OG

Nature Reviews Genetics. 2021 Aug 2.

Machine learning methods to model multicellular complexity and tissue specificity

Sealfon RS, Wong AK, Troyanskaya OG

Nature Reviews. 2021 Jul 15.

Single nucleus multi-omics regulatory landscape of the murine pituitary

Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon RG, ..., Bartlett A, Aldridge A, Jain N, Childs GV, Troyanskaya OG, Ecker JR, Turgeon JL, Welt CK, Bernard DJ, Sealfon SC.

Nat Commun. 2021 May 12.

Viable virus shedding during SARS-CoV-2 reinfection

Letizia AG, Smith DR, Ge Y, Ramos I, Sealfon R, Goforth C, Gonzalez-Reiche AS,... Troyanskaya OG, van Bakel H, Sealfon SC

Lancet Respir Med. 2021 May.

Modeling transcriptional regulation of model species with deep learning

Cofer EM, Raimundo J, Tadych A, Yamazaki Y, Wong AK, Theesfeld CL, Levine MS, Troyanskaya OG.

Genome Res. 2021 Apr 23. [Website]

An automated framework for efficiently designing deep convolutional neural networks in genomics

Zhang Z*, Park CY, Theesfeld CL, Troyanskaya OG.

Nature Machine Intelligence. 2021 Mar 15. [Website] [Code]

Tissue-specific enhancer functional networks for associating distal regulatory regions to disease

Chen X, Zhou J, Zhang R, Wong AK, Park CY, Theesfeld CL, Troyanskaya OG.

Cell Syst. 2021 Mar 10. [Website] [Simons Foundation: Press]

Rationale and design of the Kidney Precision Medicine Project

de Boer IH, Alpers CE, Azeloglu EU, Balis UGJ, Barasch JM, Barisoni L, Blank KN, Bomback AS, Brown K, Dagher PC, ..., Troyanskaya OG, Tuttle KR, Vazquez MA, Waikar SS, Williams K, Wilson FP, Zhang K, Iyengar R, Kretzler M, Himmelfarb J; Kidney Precision Medicine Project.

Kidney Int. 2021 Feb 27.

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

Park CY, Zhou J, Wong AK, Chen KM, Theesfeld CL, Darnell RB, Troyanskaya OG.

Nature Genetics. 2021 Jan 19.


Modeling molecular development of breast cancer in canine mammary tumors

Graim K, Gorenshteyn D, Robinson DG, Carriero NJ, Cahill JA, Chakrabarti R, Goldschmidt MH, Durham AC, Funk J, Storey J, Kristensen VN, Theesfeld CL, Sorenmo KU, Troyanskaya OG.

Genome Res. 2020 Dec 28.

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, Jungreis I, Fritch EJ, Hou YJ, Ekena J, Weidmann CA, Theesfeld CL, Kellis M, Troyanskaya OG, Baric RS, Sheahan TP, Weeks KM, Gladfelter AS.

Mol Cell. 2020 Dec 8.

A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project

El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, ..., Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, ... Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin B, Dagher PC, Sharma K, Sarwal M, Hodgin JB, Alpers CE, Kretzer M, Jain S, The Kidney Precision Medicine Project F.

Physiol Genomics. 2020 Nov 16.

SARS-CoV-2 Transmission among Marine Recruits during Quarantine

Letizia AG, Ramos I, Obla A, Goforth C, Weir DL, Ge Y, Bamman MM, Dutta J, Ellis E, Estrella L, ..., Rachel S.G. Sealfon, Sebra R, Simons MP, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya OG, van Bakel H, Sealfon SC.

N Engl J Med. 2020 Nov 11.

SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease

Menon R, Otto EA, Sealfon R, Nair V, Wong AK, Theesfeld CL, Chen X, Wang Y, Boppana A, Luo J ,..., Looker HC, Harder JL, Mariani LH, Hodgin JB, Sexton JZ, Wobus CE, Naik AS, Nelson RG, Troyanskaya OG, Kretzler M.

Kidney International. 2020 Oct 7.

Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies

Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA.

Cell Syst. 2020 Sep 11. [Website] [Computing empowers immune cells to kill cancer]

Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development

Ledo JH, Zhang R, Mesin L, Mourão-Sá D, Azevedo EP, Troyanskaya OG, Bustos V, Greengard P.

PLoS One. 2020 Aug 22.

Presenilin 1 phosphorylation regulates amyloid-β degradation by microglia

Ledo JH, Liebmann T, Zhang R, Chang JC, Azevedo EP, Wong E, Silva HM, Troyanskaya OG, Bustos V, Greengard P.

Mol Psychiatry. 2020 Aug 15.

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares

Orange DE*, Yao V*, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB.

N Engl J Med. 2020 Jul 16.

Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis

Roussarie JP*, Yao V*, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt EF, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof PR, Heiman M, Dolinski K, Flajolet M, Troyanskaya OG, Greengard P.

Neuron. 2020 Jul 1. [Website] [Rockefeller University: Press] [Simons Foundation: Press] [Rice University: Press]

Genomic analyses implicate noncoding de novo variants in congenital heart disease

Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, ..., Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD.

Nature Genetics. 2020 Jul 1.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

Iserman C, Roden C, Boerneke M, Sealfon R, McLaughlin G, Jungreis I, Park C, Boppana A, Fritch E, Hou YJ, Theesfeld C, Troyanskaya OG, Baric RS, Sheahan TP, Weeks K, Gladfelter AS.

bioRxiv. 2020 Jun 27.

Machine learning, the kidney, and genotype-phenotype analysis

Sealfon RSG, Mariani LH, Kretzler M, Troyanskaya OG.

Kidney Int. 2020 May 4.

Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.

Menon R, Otto EA, Hoover P, Eddy S, Mariani L, Godfrey B, Berthier CC, Eichinger F, Subramanian L, Harder J, ..., Naik AS, Luo J, Jain S, Sealfon R, Troyanskaya O, Hacohen N, Hodgin JB, Kretzler M, Kpmp KPMP, Nephrotic Syndrome Study Network (NEPTUNE).

JCI Insight. 2020 Mar 26.


Voices in methods development.

Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, ..., Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.

Nature Methods. 2019 Oct.

Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations.

Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN.

Bioinformatics. 2019 Sep 16.

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.

Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG.

PLoS Genetics. 2019 Sep. [Website]

Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.

Sargin D, Chottekalapanda RU, Perit KE, Yao V, Chu D, Sparks DW, Kalik S, Power SK, Troyanskaya OG, Schmidt EF, Greengard P, Lambe EK.

Molecular Psychiatry. 2019 Aug 20.

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

Zhou J*, Park CY*, Theesfeld CL*, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG.

Nature Genetics. 2019 Jun. [Simons Foundation: Press] [Princeton University: Press] [Scientific American] [SciShow]

Selene: a PyTorch-based deep learning library for sequence data.

Chen KM*, Cofer EM*, Zhou J, Troyanskaya OG.

Nature Methods. 2019 Apr. [Website] [Code]

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, ..., Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV.

Nature Genetics. 2019 Mar.

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG.

Cell Systems. 2019 Feb 27. [Website]

Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.

Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD.

mSystems. 2019 Feb 26.

Organoid single cell profiling identifies a transcriptional signature of glomerular disease.

Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M, European Renal cDNA Bank (ERCB), Nephrotic Syndrome Study Network (NEPTUNE).

JCI Insight. 2019 Jan 10.


Interpretation of an individual functional genomics experiment guided by massive public data.

Lee YS, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, Ramos I, Zaslavsky E, Sealfon SC, Troyanskaya OG.

Nature Methods. 2018 Dec 15. [Website]

An integrative tissue-network approach to identify and test human disease genes.

Yao V*, Kaletsky R*, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG.

Nature Biotechnology. 2018 Oct 22. [Website] [Code]

Enabling Precision Medicine through Integrative Network Models.

Yao V*, Wong AK*, Troyanskaya OG.

Journal of Molecular Biology. 2018 Sep 14.

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.

Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen YC, Troyanskaya O, Spence JR, Kretzler M, Cebrián C.

Development. 2018 Aug 30.

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.

Kaletsky R*, Yao V*, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT.

PLoS Genetics. 2018 Aug 10. [Website]

Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.

Jabeen S, Zucknick M, Nome M, Dannenfelser R, Fleischer T, Kumar S, Lüders T, von der Lippe Gythfeldt H, Troyanskaya O, Kyte JA, Børresen-Dale AL, Naume B, Tekpli X, Engebraaten O, Kristensen V.

Oncoimmunology. 2018 Aug 6.

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG.

Nature Genetics. 2018 Jul 16. [Website] [Code] [Simons Foundation: Press]

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.

Wong AK, Krishnan A, Troyanskaya OG.

Nucleic Acids Research. 2018 May 25. [Website]

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.

Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M, Bipolar Disorders Working Group of the Psychiatric Genomics Consortium.

PLoS Computational Biology. 2018 May 14.


Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.

Clancy T, Dannenfelser R, Troyanskaya O, Malmberg KJ, Hovig E, Kristensen V.

Current Pharmaceutical Design. 2017 Jul 10.

Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.

Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Moen Vollan HK, Haakensen VD, Helland Å, Naume B, Caldas C, Børresen-Dale AL, Kristensen VN, Troyanskaya OG.

Oncotarget. 2017 Jul 7.

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.

Nirschl CJ, Suárez-Fariñas M, Izar B, Prakadan S, Dannenfelser R, Tirosh I, Liu Y, Zhu Q, Devi KSP, Carroll SL, ..., Quintana FJ, Lee YS, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya O, Anandasabapathy N.

Cell. 2017 Jun 29.


A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M*, VanderSluis B*, Koch EN*, Baryshnikova A*, Pons C*, Tan G*, Wang W, Usaj M, Hanchard J, Lee SD, ..., Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23.

GIANT API: an application programming interface for functional genomics.

Roberts AM*, Wong AK*, Fisk I, Troyanskaya OG.

Nucleic Acids Research. 2016 Jul 8. [Website] [Code]


Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.

Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC.

Immunity. 2015 Sep 15. [Website]

Implications of Big Data for cell biology.

Dolinski K, Troyanskaya OG.

Molecular Biology of the Cell. 2015 Jul 15.

FNTM: a server for predicting functional networks of tissues in mouse.

Goya J*, Wong AK*, Yao V*, Krishnan A, Homilius M, Troyanskaya OG.

Nucleic Acids Research. 2015 Jul 1. [Website]

Understanding multicellular function and disease with human tissue-specific networks.

Greene CS*, Krishnan A*, Wong AK*, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG.

Nature Genetics. 2015 Jun. [Website] [Nature Biotechnology: News and Views]

Low-variance RNAs identify Parkinson's disease molecular signature in blood.

Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, Wong AK, Krishnan A, Troyanskaya OG, Raymond D, Saunders-Pullman R, Bressman SB, Yue Z, Sealfon SC.

Movement Disorders. 2015 May.

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.

Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG.

Bioinformatics. 2015 Apr 1.

Targeted exploration and analysis of large cross-platform human transcriptomic compendia.

Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG.

Nature Methods. 2015 Mar. [Website]

Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.

Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HK, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V.

Molecular Cancer Research. 2015 Mar.


Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction

Zhou JTroyanskaya OG.

Proceedings of the International Conference of Machine Learning (ICML 2014), JMLR W&CP. 2014 Jun 21.

Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection.

VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA.

Genome Biology. 2014 Apr 10.

Global quantitative modeling of chromatin factor interactions.

Zhou J, Troyanskaya OG.

PLoS Computational Biology. 2014 Mar.


Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.

Aure MR, Leivonen SK, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GI, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale AL, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN.

Genome Biology. 2013 Nov 20.

Defining cell-type specificity at the transcriptional level in human disease.

Ju W*, Greene CS*, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee YS, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M.

Genome Research. 2013 Nov. [Website]

A new system for comparative functional genomics of Saccharomyces yeasts.

Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, ..., Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep.

Comparative gene expression between two yeast species.

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA.

BMC Genomics. 2013 Jan 16.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

Park CY*, Wong AK*, Greene CS*, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG.

PLoS Computational Biology. 2013.


Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.

Nair VD, Ge Y, Balasubramaniyan N, Kim J, Okawa Y, Chikina M, Troyanskaya O, Sealfon SC.

Molecular and Cellular Biology. 2012 Dec.

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.

Nucleic Acids Research. 2012 Jul.

Accurate evaluation and analysis of functional genomics data and methods.

Greene CS, Troyanskaya OG.

Annals of the New York Academy of Sciences. 2012 Jul.

An effective statistical evaluation of ChIPseq dataset similarity.

Chikina MD, Troyanskaya OG.

Bioinformatics. 2012 Mar 1.

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.

Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL.

Proceedings of the National Academy of Sciences of the United States of America. 2012 Feb 21.

Chapter 2: Data-driven view of disease biology.

Greene CS, Troyanskaya OG.

PLoS Computational Biology. 2012.

Tissue-specific functional networks for prioritizing phenotype and disease genes.

Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG.

PLoS Computational Biology. 2012.


Nucleosome-coupled expression differences in closely-related species.

Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG.

BMC Genomics. 2011 Sep 26.

PILGRM: an interactive data-driven discovery platform for expert biologists.

Greene CS, Troyanskaya OG.

Nucleic Acids Research. 2011 Jul.

Accurate quantification of functional analogy among close homologs.

Chikina MD, Troyanskaya OG.

PLoS Computational Biology. 2011 Feb 3.


Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.

Pop A*, Huttenhower C*, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG.

BMC Systems Biology. 2010 Dec 31.

Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

Markowetz F, Mulder KW, Airoldi EM, Lemischka IR, Troyanskaya OG.

PLoS Computational Biology. 2010 Dec 16.

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL.

Nature Methods. 2010 Dec.

Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.

Park CY, Hess DC, Huttenhower C, Troyanskaya OG.

PLoS Computational Biology. 2010 Nov 24.

Functional genomics complements quantitative genetics in identifying disease-gene associations.

Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA.

PLoS Computational Biology. 2010 Nov 11.

Integrative systems biology for data-driven knowledge discovery.

Greene CS, Troyanskaya OG.

Seminars in Nephrology. 2010 Sep.

Systematic planning of genome-scale experiments in poorly studied species.

Guan Y, Dunham M, Caudy A, Troyanskaya O.

PLoS Computational Biology. 2010 Mar 5.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, ..., Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22.


Detailing regulatory networks through large scale data integration.

Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA.

Bioinformatics. 2009 Dec 15.

Graphle: Interactive exploration of large, dense graphs.

Huttenhower C, Mehmood SO, Troyanskaya OG.

BMC Bioinformatics. 2009 Dec 14.

Systems-level dynamic analyses of fate change in murine embryonic stem cells.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR.

Nature. 2009 Nov 19.

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.

Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG.

Bioinformatics. 2009 Sep 15.

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.

PLoS Computational Biology. 2009 Jun.

Exploring the human genome with functional maps.

Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG.

Genome Research. 2009 Jun.

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.

Bioinformatics. 2009 May 15.

Directing experimental biology: a case study in mitochondrial biogenesis.

Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.

PLoS Computational Biology. 2009 Mar.

Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.

Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA.

PLoS Genetics. 2009 Mar.

Selected proceedings of the First Summit on Translational Bioinformatics 2008.

Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O.

BMC Bioinformatics. 2009 Feb 5.

Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.

Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG.

PLoS Computational Biology. 2009 Jan.

Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Computational Biology. 2009 Jan.

Discovering biological networks from diverse functional genomic data.

Myers CL, Chiriac C, Troyanskaya OG.

Methods in Molecular Biology. 2009.

Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.

Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG.

Methods in Molecular Biology. 2009.


A genomewide functional network for the laboratory mouse.

Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG.

PLoS Computational Biology. 2008 Sep 26.

The Sleipnir library for computational functional genomics.

Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.

Bioinformatics. 2008 Jul 1. [Website] [Code]

Assessing the functional structure of genomic data.

Huttenhower C, Troyanskaya OG.

Bioinformatics. 2008 Jul 1.

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D.

Molecular Biology of the Cell. 2008 Jan.

Predicting gene function in a hierarchical context with an ensemble of classifiers.

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.

Genome Biology. 2008.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, ..., Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biology. 2008.


Exploring the functional landscape of gene expression: directed search of large microarray compendia.

Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG.

Bioinformatics. 2007 Oct 15. [Website]

"Getting started in...": a series not to miss.

Troyanskaya O.

PLoS Computational Biology. 2007 Oct.

Context-sensitive data integration and prediction of biological networks.

Myers CL, Troyanskaya OG.

Bioinformatics. 2007 Sep 1.

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.

Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA.

BMC Bioinformatics. 2007 Jul 12.

Nested effects models for high-dimensional phenotyping screens.

Markowetz F, Kostka D, Troyanskaya OG, Spang R.

Bioinformatics. 2007 Jul 1.

Computational identification of cellular networks and pathways.

Markowetz F, Troyanskaya OG.

Molecular Biosystems. 2007 Jul.

Viewing the Larger Context of Genomic Data through Horizontal Integration

Hibbs MA, Wallace G, Dunham MJ, Li K, Troyanskaya OG.

IV '07 Proceedings of the 11th International Conference Information Visualization. 2007 Jul.

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.

Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF.

Proceedings of the National Academy of Sciences of the United States of America. 2007 Feb 13.

Functional analysis of gene duplications in Saccharomyces cerevisiae.

Guan Y, Dunham MJ, Troyanskaya OG.

Genetics. 2007 Feb.

Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.

Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC.

Genes & Development. 2007 Jan 15.

Systems support for remote visualization of genomics applications over wide area networks

Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya OG.

GCCB'06 Proceedings of the 2006 international conference on Distributed, high-performance and grid computing in computational biology. 2007 Jan.

Integrated analysis of microarray results.

Troyanskaya OG.

Methods in Molecular Biology. 2007.


A scalable method for integration and functional analysis of multiple microarray datasets.

Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.

Bioinformatics. 2006 Dec 1.

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.

Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG.

BMC Bioinformatics. 2006 Oct 10.

Finding function: evaluation methods for functional genomic data.

Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG.

BMC Genomics. 2006 Jul 25.

Hierarchical multi-label prediction of gene function.

Barutcuoglu Z, Schapire RE, Troyanskaya OG.

Bioinformatics. 2006 Apr 1.

Bayesian data integration: a functional perspective.

Huttenhower C, Troyanskaya OG.

Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 2006.

Global analysis of gene function in yeast by quantitative phenotypic profiling.

Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM.

Molecular Systems Biology. 2006.


Tools and applications for large-scale display walls.

Wallace G, Anshus OJ, Bi P, Chen H, Chen Y, Clark D, Cook P, Finkelstein A, Funkhouser T, Gupta A, Hibbs M, Li K, Liu Z, Samanta R, Sukthankar R, Troyanskaya O.

IEEE Computer Graphics and Applications. 2005 Aug.

A General Methodology for Integration of Microarray Data

Huttenhower C, Troyanskaya OG.

CSBW '05: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops. 2005 Aug.

Visualization-based discovery and analysis of genomic aberrations in microarray data.

Myers CL, Chen X, Troyanskaya OG.

BMC Bioinformatics. 2005 Jun 13.

Visualization methods for statistical analysis of microarray clusters.

Hibbs MA, Dirksen NC, Li K, Troyanskaya OG.

BMC Bioinformatics. 2005 May 12.

Dynamic Scalable Visualization for Collaborative Scientific Applications

Li K, Hibbs MA, Wallace G, Troyanskaya OG.

IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 10 - Volume 11. 2005 Apr.

Discovery of biological networks from diverse functional genomic data.

Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG.

Genome Biology. 2005.

Putting the 'bio' into bioinformatics.

Troyanskaya OG.

Genome Biology. 2005.


Accurate detection of aneuploidies in array CGH and gene expression microarray data.

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.

Bioinformatics. 2004 Dec 12.


Gene expression patterns in ovarian carcinomas.

Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, ..., Kristensen GB, Borresen-Dale AL, Hastie T, Tibshirani R, van de Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI.

Molecular Biology of the Cell. 2003 Nov.

Systemic and cell type-specific gene expression patterns in scleroderma skin.

Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Oct 14.

Endothelial cell diversity revealed by global expression profiling.

Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Sep 16.

Variation in gene expression patterns in human gastric cancers.

Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO.

Molecular Biology of the Cell. 2003 Aug.

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Jul 8.

Variation in gene expression patterns in follicular lymphoma and the response to rituximab.

Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Feb 18.


Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.

Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan AS, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO.

Proceedings of the National Academy of Sciences of the United States of America. 2002 Dec 10.

Nonparametric methods for identifying differentially expressed genes in microarray data.

Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB.

Bioinformatics. 2002 Nov.

Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.

Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A.

Bioinformatics. 2002 May.


Diversity of gene expression in adenocarcinoma of the lung.

Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I.

Proceedings of the National Academy of Sciences of the United States of America. 2001 Nov 20.

Missing value estimation methods for DNA microarrays.

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB.

Bioinformatics. 2001 Jun. [Code]