Missing value estimation methods for DNA microarrays. - Olga G. Troyanskaya; Michael N. Cantor; Gavin Sherlock; Patrick O. Brown; Trevor Hastie; Robert Tibshirani; David Botstein; Russ B. Altman (Bioinform., 2001)

Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity. - Olga G. Troyanskaya; Ora Arbell; Yair Koren; Gad M. Landau; Alexander Bolshoy (Bioinform., 2002)

Nonparametric methods for identifying differentially expressed genes in microarray data. - Olga G. Troyanskaya; Mitchell E. Garber; Patrick O. Brown; David Botstein; Russ B. Altman (Bioinform., 2002)

Accurate detection of aneuploidies in array CGH and gene expression microarray data. - Chad L. Myers; Maitreya J. Dunham; Sun-Yuan Kung; Olga G. Troyanskaya (Bioinform., 2004)

Computational functional genomics. - Mike P. Liang; Olga G. Troyanskaya; Alain Laederach; Douglas L. Brutlag; Russ B. Altman (IEEE Signal Process. Mag., 2004)

Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery. - Olga G. Troyanskaya (Data Analysis and Visualization in Genomics and Proteomics, 2005)

A General Methodology for Integration of Microarray Data. - Curtis Huttenhower; Olga G. Troyanskaya (CSB Workshops, 2005)

Dynamic Scalable Visualization for Collaborative Scientific Applications. - Kai Li 001; Matthew A. Hibbs; Grant Wallace; Olga G. Troyanskaya (IPDPS, 2005)

Putting microarrays in a context: Integrated analysis of diverse biological data. - Olga G. Troyanskaya (Briefings Bioinform., 2005)

Visualization methods for statistical analysis of microarray clusters. - Matthew A. Hibbs; Nathaniel C. Dirksen; Kai Li 001; Olga G. Troyanskaya (BMC Bioinform., 2005)

Visualization-based discovery and analysis of genomic aberrations in microarray data. - Chad L. Myers; Xing Chen; Olga G. Troyanskaya (BMC Bioinform., 2005)

Tools and Applications for Large-Scale Display Walls. - Grant Wallace; Otto J. Anshus; Peng Bi; Han Chen; Yuqun Chen; Douglas W. Clark; Perry R. Cook; Adam Finkelstein; Thomas A. Funkhouser; Anoop Gupta; Matthew A. Hibbs; Kai Li 001; et al. (IEEE Computer Graphics and Applications, 2005)

Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. - Lars Ailo Bongo; Grant Wallace; Tore Larsen; Kai Li 001; Olga G. Troyanskaya (GCCB, 2006)

Hierarchical multi-label prediction of gene function. - Zafer Barutçuoglu; Robert E. Schapire; Olga G. Troyanskaya (Bioinform., 2006)

A scalable method for integration and functional analysis of multiple microarray datasets. - Curtis Huttenhower; Matthew A. Hibbs; Chad L. Myers; Olga G. Troyanskaya (Bioinform., 2006)

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. - Rachel S. G. Sealfon; Matthew A. Hibbs; Curtis Huttenhower; Chad L. Myers; Olga G. Troyanskaya (BMC Bioinform., 2006)

Scalable, Dynamic Analysis and Visualization for Genomic Datasets. - Grant Wallace; Matthew A. Hibbs; Maitreya J. Dunham; Rachel S. G. Sealfon; Olga G. Troyanskaya; Kai Li 001 (IPDPS, 2007)

Nested effects models for high-dimensional phenotyping screens. - Florian Markowetz; Dennis Kostka; Olga G. Troyanskaya; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Viewing the Larger Context of Genomic Data through Horizontal Integration. - Matthew A. Hibbs; Grant Wallace; Maitreya J. Dunham; Kai Li 001; Olga G. Troyanskaya (IV, 2007)

Exploring the functional landscape of gene expression: directed search of large microarray compendia. - Matthew A. Hibbs; David C. Hess; Chad L. Myers; Curtis Huttenhower; Kai Li 001; Olga G. Troyanskaya (Bioinform., 2007)

Context-sensitive data integration and prediction of biological networks. - Chad L. Myers; Olga G. Troyanskaya (Bioinform., 2007)

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. - Curtis Huttenhower; Avi I. Flamholz; Jessica N. Landis; Sauhard Sahi; Chad L. Myers; Kellen L. Olszewski; Matthew A. Hibbs; Nathan O. Siemers; Olga G. Troyanskaya; Hilary A. Coller (BMC Bioinform., 2007)

"Getting Started In...": A Series Not to Miss. - Olga G. Troyanskaya (PLoS Comput. Biol., 2007)

Assessing the functional structure of genomic data. - Curtis Huttenhower; Olga G. Troyanskaya (ISMB, 2008)

The Sleipnir library for computational functional genomics. - Curtis Huttenhower; Mark Schroeder; Maria D. Chikina; Olga G. Troyanskaya (Bioinform., 2008)

A Genomewide Functional Network for the Laboratory Mouse. - Yuanfang Guan; Chad L. Myers; Rong Lu; Ihor Lemischka; Carol J. Bult; Olga G. Troyanskaya (PLoS Comput. Biol., 2008)

Tech-note: Device-free interaction spaces. - Daniel Stødle; Olga G. Troyanskaya; Kai Li 001; Otto J. Anshus (3DUI, 2009)

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. - Zafer Barutçuoglu; Edoardo M. Airoldi; Vanessa Dumeaux; Robert E. Schapire; Olga G. Troyanskaya (Bioinform., 2009)

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. - Curtis Huttenhower; Matthew A. Hibbs; Chad L. Myers; Amy A. Caudy; David C. Hess; Olga G. Troyanskaya (Bioinform., 2009)

Detailing regulatory networks through large scale data integration. - Curtis Huttenhower; K. Tsheko Mutungu; Natasha Indik; Woongcheol Yang; Mark Schroeder; Joshua J. Forman; Olga G. Troyanskaya; Hilary A. Coller (Bioinform., 2009)

Papers on normalization, variable selection, classification or clustering of microarray data. - David M. Rocke; Trey Ideker; Olga G. Troyanskaya; John Quackenbush; Joaquín Dopazo (Bioinform., 2009)

Selected proceedings of the First Summit on Translational Bioinformatics 2008. - Atul J. Butte; Indra Neil Sarkar; Marco Ramoni; Yves A. Lussier; Olga G. Troyanskaya (BMC Bioinform., 2009)

Graphle: Interactive exploration of large, dense graphs. - Curtis Huttenhower; Sajid O. Mehmood; Olga G. Troyanskaya (BMC Bioinform., 2009)

Predicting Cellular Growth from Gene Expression Signatures. - Edoardo M. Airoldi; Curtis Huttenhower; David Gresham; Charles Lu 004; Amy A. Caudy; Maitreya J. Dunham; James R. Broach; David Botstein; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. - Patrick H. Bradley; Matthew J. Brauer; Joshua D. Rabinowitz; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans. - Maria D. Chikina; Curtis Huttenhower; Coleen T. Murphy; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis. - Matthew A. Hibbs; Chad L. Myers; Curtis Huttenhower; David C. Hess; Kai Li 001; Amy A. Caudy; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. - Ana Pop; Curtis Huttenhower; Anjali Iyer-Pascuzzi; Philip N. Benfey; Olga G. Troyanskaya (BMC Syst. Biol., 2010)

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations. - Yuanfang Guan; Cheryl L. Ackert-Bicknell; Braden Kell; Olga G. Troyanskaya; Matthew A. Hibbs (PLoS Comput. Biol., 2010)

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species. - Yuanfang Guan; Maitreya J. Dunham; Amy A. Caudy; Olga G. Troyanskaya (PLoS Comput. Biol., 2010)

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells. - Florian Markowetz; Klaas W. Mulder; Edoardo M. Airoldi; Ihor Lemischka; Olga G. Troyanskaya (PLoS Comput. Biol., 2010)

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components. - Christopher Y. Park; David C. Hess; Curtis Huttenhower; Olga G. Troyanskaya (PLoS Comput. Biol., 2010)

An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. - Chris Mungall; David Anderson; Anita E. Bandrowski; Brian A. Canada; Andrew Chatr-aryamontri; Keith C. Cheng; P. Michael Conn; Kara Dolinski; Mark H. Ellisman; Janan T. Eppig; Jeffrey S. Grethe; Joseph W. Kemnitz; et al. (ICBO, 2011)

PILGRM: an interactive data-driven discovery platform for expert biologists. - Casey S. Greene; Olga G. Troyanskaya (Nucleic Acids Res., 2011)

Accurate Quantification of Functional Analogy among Close Homologs. - Maria D. Chikina; Olga G. Troyanskaya (PLoS Comput. Biol., 2011)

An effective statistical evaluation of ChIPseq dataset similarity. - Maria D. Chikina; Olga G. Troyanskaya (Bioinform., 2012)

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. - Aaron K. Wong; Christopher Y. Park; Casey S. Greene; Lars Ailo Bongo; Yuanfang Guan; Olga G. Troyanskaya (Nucleic Acids Res., 2012)

Chapter 2: Data-Driven View of Disease Biology. - Casey S. Greene; Olga G. Troyanskaya (PLoS Comput. Biol., 2012)

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes. - Yuanfang Guan; Dmitriy Gorenshteyn; Margit Burmeister; Aaron K. Wong; John C. Schimenti; Mary Ann Handel; Carol J. Bult; Matthew A. Hibbs; Olga G. Troyanskaya (PLoS Comput. Biol., 2012)

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. - Young-Suk Lee; Arjun Krishnan; Qian Zhu 005; Olga G. Troyanskaya (Bioinform., 2013)

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. - Christopher Y. Park; Aaron K. Wong; Casey S. Greene; Jessica Rowland; Yuanfang Guan; Lars Ailo Bongo; Rebecca D. Burdine; Olga G. Troyanskaya (PLoS Comput. Biol., 2013)

Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. - Jian Zhou; Olga G. Troyanskaya (ICML, 2014)

Global Quantitative Modeling of Chromatin Factor Interactions. - Jian Zhou; Olga G. Troyanskaya (PLoS Comput. Biol., 2014)

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. - Christopher Y. Park; Arjun Krishnan; Qian Zhu 005; Aaron K. Wong; Young-Suk Lee; Olga G. Troyanskaya (Bioinform., 2015)

FNTM: a server for predicting functional networks of tissues in mouse. - Jonathan Goya; Aaron K. Wong; Victoria Yao; Arjun Krishnan; Max Homilius; Olga G. Troyanskaya (Nucleic Acids Res., 2015)

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. - Aaron K. Wong; Arjun Krishnan; Victoria Yao; Alicja Tadych; Olga G. Troyanskaya (Nucleic Acids Res., 2015)

GIANT API: an application programming interface for functional genomics. - Andrew M. Roberts; Aaron K. Wong; Ian Fisk; Olga G. Troyanskaya (Nucleic Acids Res., 2016)

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. - Aaron K. Wong; Arjun Krishnan; Olga G. Troyanskaya (Nucleic Acids Res., 2018)

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. - Aaditya V. Rangan; Caroline C. McGrouther; John Kelsoe; Nicholas J. Schork; Eli Stahl; Qian Zhu 005; Arjun Krishnan; Vicky Yao; Olga G. Troyanskaya; Seda Bilaloglu; Preeti Raghavan; Sarah Bergen; et al. (PLoS Comput. Biol., 2018)

Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. - Qian Zhu 005; Xavier Tekpli; Olga G. Troyanskaya; Vessela N. Kristensen (Bioinform., 2020)

CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. - Victoria R. Li; Zijun Zhang; Olga G. Troyanskaya (Bioinform., 2021)

An automated framework for efficiently designing deep convolutional neural networks in genomics. - Zijun Zhang; Christopher Y. Park; Chandra L. Theesfeld; Olga G. Troyanskaya (Nat. Mach. Intell., 2021)

Interpretable neural architecture search and transfer learning for understanding sequence dependent enzymatic reactions. - Zijun Zhang; Adam R. Lamson; Michael J. Shelley; Olga G. Troyanskaya (CoRR, 2023)

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; Antonio Cappuccio; Wan-Sze Cheng; Frederique Ruf Zamojski; Venugopalan D. Nair; Clare M. Miller; Aliza B. Rubenstein; German Nudelman; Alicja Tadych; Chandra L. Theesfeld; Alexandria Vornholt; et al. (Nat. Comput. Sci., 2023)

Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. - Xi Chen; Yuan Wang 084; Antonio Cappuccio; Wan-Sze Cheng; Frederique Ruf Zamojski; Venugopalan D. Nair; Clare M. Miller; Aliza B. Rubenstein; German Nudelman; Alicja Tadych; Chandra L. Theesfeld; Alexandria Vornholt; et al. (Nat. Comput. Sci., 2023)

Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions. - Zijun Zhang; Adam R. Lamson; Michael J. Shelley; Olga G. Troyanskaya (Nat. Comput. Sci., 2023)