2021
Attenuated activation of pulmonary immune cells in mRNA-1273 vaccinated hamsters after SARS-CoV-2 infection
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.
Spatial transcriptional mapping of the human nephrogenic program
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.
Decoding disease: from genomes to networks to phenotypes
Decoding disease: from genomes to networks to phenotypes
Wong AK, Sealfon RS, Theesfeld CL, Troyanskaya OG
Machine learning methods to model multicellular complexity and tissue specificity
Machine learning methods to model multicellular complexity and tissue specificity
Sealfon RS, Wong AK, Troyanskaya OG
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes
Li VR, Zhang Z, Troyanskaya OG.
Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures
Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures
Roden CA, Dai Y, 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.
Single nucleus multi-omics regulatory landscape of the murine pituitary
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.
Viable virus shedding during SARS-CoV-2 reinfection
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
Modeling transcriptional regulation of model species with deep learning
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.
An automated framework for efficiently designing deep convolutional neural networks in genomics
An automated framework for efficiently designing deep convolutional neural networks in genomics
Zhang Z*, Park CY, Theesfeld CL, Troyanskaya OG.
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease
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.
Rationale and design of the Kidney Precision Medicine Project
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.
mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge
mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge
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.
Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk
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.
2020
Modeling molecular development of breast cancer in canine mammary tumors
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.
Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid
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.
A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project
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.
SARS-CoV-2 Transmission among Marine Recruits during Quarantine
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.
SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease
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 AS, Luo J, ..., Looker HC, Harder JL, Mariani LH, Hodgin JB, Sexton JZ, Wobus CE, Naik AS, Nelson RG, Troyanskaya OG, Kretzler M.
SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease
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.
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies
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.
Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development
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.
Presenilin 1 phosphorylation regulates amyloid-β degradation by microglia
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.
RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares
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.
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis
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.
Genomic analyses implicate noncoding de novo variants in congenital heart disease
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.
Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
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.
Machine learning, the kidney, and genotype-phenotype analysis
Machine learning, the kidney, and genotype-phenotype analysis
Sealfon RSG, Mariani LH, Kretzler M, Troyanskaya OG.
Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.
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).
2019
Voices in methods development.
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.
Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations.
Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations.
Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN.
Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.
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.
Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.
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.
Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.
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.
Selene: a PyTorch-based deep learning library for sequence data.
Selene: a PyTorch-based deep learning library for sequence data.
Chen KM*, Cofer EM*, Zhou J, Troyanskaya OG.
New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.
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.
A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.
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.
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.
Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD.
Organoid single cell profiling identifies a transcriptional signature of glomerular disease.
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).
2018
Interpretation of an individual functional genomics experiment guided by massive public data.
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.
An integrative tissue-network approach to identify and test human disease genes.
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.
Enabling Precision Medicine through Integrative Network Models.
Enabling Precision Medicine through Integrative Network Models.
Yao V*, Wong AK*, Troyanskaya OG.
Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.
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.
Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.
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.
Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.
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.
Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.
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.
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.
Wong AK, Krishnan A, Troyanskaya OG.
A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.
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.
2017
Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.
Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.
Clancy T, Dannenfelser R, Troyanskaya O, Malmberg KJ, Hovig E, Kristensen V.
Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.
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.
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.
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.
2016
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.
Krishnan A*, Zhang R*, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG.
A global genetic interaction network maps a wiring diagram of cellular function.
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.
GIANT API: an application programming interface for functional genomics.
GIANT API: an application programming interface for functional genomics.
Roberts AM*, Wong AK*, Fisk I, Troyanskaya OG.
Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.
Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.
Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ.
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.
Zhou J, Troyanskaya OG.
2015
Predicting effects of noncoding variants with deep learning-based sequence model.
Predicting effects of noncoding variants with deep learning-based sequence model.
Zhou J, Troyanskaya OG.
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.
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.
Implications of Big Data for cell biology.
Implications of Big Data for cell biology.
Dolinski K, Troyanskaya OG.
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG.
FNTM: a server for predicting functional networks of tissues in mouse.
FNTM: a server for predicting functional networks of tissues in mouse.
Goya J*, Wong AK*, Yao V*, Krishnan A, Homilius M, Troyanskaya OG.
Understanding multicellular function and disease with human tissue-specific networks.
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.
Low-variance RNAs identify Parkinson's disease molecular signature in blood.
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.
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.
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.
Targeted exploration and analysis of large cross-platform human transcriptomic compendia.
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.
Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.
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.
2014
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction
Zhou J, Troyanskaya OG.
Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection.
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.
Global quantitative modeling of chromatin factor interactions.
Global quantitative modeling of chromatin factor interactions.
Zhou J, Troyanskaya OG.
2013
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.
Lee YS, Krishnan A, Zhu Q, Troyanskaya OG.
Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.
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.
Defining cell-type specificity at the transcriptional level in human disease.
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.
A new system for comparative functional genomics of Saccharomyces yeasts.
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.
Comparative gene expression between two yeast species.
Comparative gene expression between two yeast species.
Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA.
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.
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.
2012
Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.
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.
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
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.
Accurate evaluation and analysis of functional genomics data and methods.
Accurate evaluation and analysis of functional genomics data and methods.
Greene CS, Troyanskaya OG.
An effective statistical evaluation of ChIPseq dataset similarity.
An effective statistical evaluation of ChIPseq dataset similarity.
Chikina MD, Troyanskaya OG.
Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.
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.
Chapter 2: Data-driven view of disease biology.
Chapter 2: Data-driven view of disease biology.
Greene CS, Troyanskaya OG.
Tissue-specific functional networks for prioritizing phenotype and disease genes.
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.
2011
Nucleosome-coupled expression differences in closely-related species.
Nucleosome-coupled expression differences in closely-related species.
Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG.
PILGRM: an interactive data-driven discovery platform for expert biologists.
PILGRM: an interactive data-driven discovery platform for expert biologists.
Greene CS, Troyanskaya OG.
Accurate quantification of functional analogy among close homologs.
Accurate quantification of functional analogy among close homologs.
Chikina MD, Troyanskaya OG.
2010
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.
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.
Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.
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.
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.
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.
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.
Park CY, Hess DC, Huttenhower C, Troyanskaya OG.
Functional genomics complements quantitative genetics in identifying disease-gene associations.
Functional genomics complements quantitative genetics in identifying disease-gene associations.
Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA.
Integrative systems biology for data-driven knowledge discovery.
Integrative systems biology for data-driven knowledge discovery.
Greene CS, Troyanskaya OG.
Systematic planning of genome-scale experiments in poorly studied species.
Systematic planning of genome-scale experiments in poorly studied species.
Guan Y, Dunham M, Caudy A, Troyanskaya O.
The genetic landscape of a cell.
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.
2009
Detailing regulatory networks through large scale data integration.
Detailing regulatory networks through large scale data integration.
Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA.
Graphle: Interactive exploration of large, dense graphs.
Graphle: Interactive exploration of large, dense graphs.
Huttenhower C, Mehmood SO, Troyanskaya OG.
Systems-level dynamic analyses of fate change in murine embryonic stem cells.
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.
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.
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.
Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.
Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.
Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.
Exploring the human genome with functional maps.
Exploring the human genome with functional maps.
Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG.
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.
Directing experimental biology: a case study in mitochondrial biogenesis.
Directing experimental biology: a case study in mitochondrial biogenesis.
Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.
Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.
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.
Selected proceedings of the First Summit on Translational Bioinformatics 2008.
Selected proceedings of the First Summit on Translational Bioinformatics 2008.
Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O.
Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.
Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.
Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG.
Predicting cellular growth from gene expression signatures.
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.
Discovering biological networks from diverse functional genomic data.
Discovering biological networks from diverse functional genomic data.
Myers CL, Chiriac C, Troyanskaya OG.
Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.
Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.
Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG.
2008
A genomewide functional network for the laboratory mouse.
A genomewide functional network for the laboratory mouse.
Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG.
The Sleipnir library for computational functional genomics.
The Sleipnir library for computational functional genomics.
Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.
Assessing the functional structure of genomic data.
Assessing the functional structure of genomic data.
Huttenhower C, Troyanskaya OG.
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.
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.
Predicting gene function in a hierarchical context with an ensemble of classifiers.
Predicting gene function in a hierarchical context with an ensemble of classifiers.
Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
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.
2007
Exploring the functional landscape of gene expression: directed search of large microarray compendia.
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.
"Getting started in...": a series not to miss.
"Getting started in...": a series not to miss.
Troyanskaya O.
Context-sensitive data integration and prediction of biological networks.
Context-sensitive data integration and prediction of biological networks.
Myers CL, Troyanskaya OG.
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.
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.
Nested effects models for high-dimensional phenotyping screens.
Nested effects models for high-dimensional phenotyping screens.
Markowetz F, Kostka D, Troyanskaya OG, Spang R.
Computational identification of cellular networks and pathways.
Computational identification of cellular networks and pathways.
Markowetz F, Troyanskaya OG.
Viewing the Larger Context of Genomic Data through Horizontal Integration
Viewing the Larger Context of Genomic Data through Horizontal Integration
Hibbs MA, Wallace G, Dunham MJ, Li K, Troyanskaya OG.
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.
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.
Functional analysis of gene duplications in Saccharomyces cerevisiae.
Functional analysis of gene duplications in Saccharomyces cerevisiae.
Guan Y, Dunham MJ, Troyanskaya OG.
Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.
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.
Systems support for remote visualization of genomics applications over wide area networks
Systems support for remote visualization of genomics applications over wide area networks
Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya OG.
Integrated analysis of microarray results.
Integrated analysis of microarray results.
Troyanskaya OG.
2006
A scalable method for integration and functional analysis of multiple microarray datasets.
A scalable method for integration and functional analysis of multiple microarray datasets.
Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.
Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG.
Finding function: evaluation methods for functional genomic data.
Finding function: evaluation methods for functional genomic data.
Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG.
Hierarchical multi-label prediction of gene function.
Hierarchical multi-label prediction of gene function.
Barutcuoglu Z, Schapire RE, Troyanskaya OG.
Bayesian data integration: a functional perspective.
Bayesian data integration: a functional perspective.
Huttenhower C, Troyanskaya OG.
Global analysis of gene function in yeast by quantitative phenotypic profiling.
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.
2005
Tools and applications for large-scale display walls.
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.
A General Methodology for Integration of Microarray Data
A General Methodology for Integration of Microarray Data
Huttenhower C, Troyanskaya OG.
Visualization-based discovery and analysis of genomic aberrations in microarray data.
Visualization-based discovery and analysis of genomic aberrations in microarray data.
Myers CL, Chen X, Troyanskaya OG.
Visualization methods for statistical analysis of microarray clusters.
Visualization methods for statistical analysis of microarray clusters.
Hibbs MA, Dirksen NC, Li K, Troyanskaya OG.
Dynamic Scalable Visualization for Collaborative Scientific Applications
Dynamic Scalable Visualization for Collaborative Scientific Applications
Li K, Hibbs MA, Wallace G, Troyanskaya OG.
Putting microarrays in a context: integrated analysis of diverse biological data.
Putting microarrays in a context: integrated analysis of diverse biological data.
Troyanskaya OG.
Discovery of biological networks from diverse functional genomic data.
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.
Putting the 'bio' into bioinformatics.
Putting the 'bio' into bioinformatics.
Troyanskaya OG.
2004
Accurate detection of aneuploidies in array CGH and gene expression microarray data.
Accurate detection of aneuploidies in array CGH and gene expression microarray data.
Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.
2003
Gene expression patterns in ovarian carcinomas.
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.
Systemic and cell type-specific gene expression patterns in scleroderma skin.
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.
Endothelial cell diversity revealed by global expression profiling.
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.
Variation in gene expression patterns in human gastric cancers.
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.
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).
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.
Variation in gene expression patterns in follicular lymphoma and the response to rituximab.
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.
2002
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.
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.
Nonparametric methods for identifying differentially expressed genes in microarray data.
Nonparametric methods for identifying differentially expressed genes in microarray data.
Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB.
Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.
Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.
Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A.
2001
Diversity of gene expression in adenocarcinoma of the lung.
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.
Missing value estimation methods for DNA microarrays.
Missing value estimation methods for DNA microarrays.
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB.