Olga G. Troyanskaya

68 papers A* 1A 3C 1Journal 57Unranked 5

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. Xi Chen, Yuan Wang, 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, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
2023	J	`jnl`	Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions. Nat. Comput. Sci. Zijun Zhang, Adam R. Lamson, Michael J. Shelley, Olga G. Troyanskaya
2023	J	`jnl`	Interpretable neural architecture search and transfer learning for understanding sequence dependent enzymatic reactions. CoRR Zijun Zhang, Adam R. Lamson, Michael J. Shelley, Olga G. Troyanskaya
2023	J	`jnl`	Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. Xi Chen, Yuan Wang, 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, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
2021	J	`jnl`	An automated framework for efficiently designing deep convolutional neural networks in genomics. Nat. Mach. Intell. Zijun Zhang, Christopher Y. Park, Chandra L. Theesfeld, Olga G. Troyanskaya
2021	J	`jnl`	CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinform. Victoria R. Li, Zijun Zhang, Olga G. Troyanskaya
2020	J	`jnl`	Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. Bioinform. Qian Zhu, Xavier Tekpli, Olga G. Troyanskaya, Vessela N. Kristensen
2018	J	`jnl`	A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. PLoS Comput. Biol. Aaditya V. Rangan, Caroline C. McGrouther, John Kelsoe, Nicholas J. Schork, Eli Stahl, Qian Zhu, Arjun Krishnan, Vicky Yao, Olga G. Troyanskaya, Seda Bilaloglu, Preeti Raghavan, Sarah Bergen, Anders Juréus, Mikael Landen
2018	J	`jnl`	GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. Aaron K. Wong, Arjun Krishnan, Olga G. Troyanskaya
2016	J	`jnl`	GIANT API: an application programming interface for functional genomics. Nucleic Acids Res. Andrew M. Roberts, Aaron K. Wong, Ian Fisk, Olga G. Troyanskaya
2015	J	`jnl`	FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. Jonathan Goya, Aaron K. Wong, Victoria Yao, Arjun Krishnan, Max Homilius, Olga G. Troyanskaya
2015	J	`jnl`	IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. Aaron K. Wong, Arjun Krishnan, Victoria Yao, Alicja Tadych, Olga G. Troyanskaya
2015	J	`jnl`	Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinform. Christopher Y. Park, Arjun Krishnan, Qian Zhu, Aaron K. Wong, Young-Suk Lee, Olga G. Troyanskaya
2014	A*	`conf`	Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. ICML Jian Zhou, Olga G. Troyanskaya
2014	J	`jnl`	Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. CoRR Jian Zhou, Olga G. Troyanskaya
2014	J	`jnl`	Global Quantitative Modeling of Chromatin Factor Interactions. PLoS Comput. Biol. Jian Zhou, Olga G. Troyanskaya
2014	J	`jnl`	ISCB/SPRINGER series in computational biology. Bioinform. Andreas W. M. Dress, Michal Linial, Olga G. Troyanskaya, Martin Vingron
2013	J	`jnl`	Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
2013	J	`jnl`	Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinform. Young-Suk Lee, Arjun Krishnan, Qian Zhu, Olga G. Troyanskaya
2012	J	`jnl`	An effective statistical evaluation of ChIPseq dataset similarity. Bioinform. Maria D. Chikina, Olga G. Troyanskaya
2012	J	`jnl`	Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. Casey S. Greene, Olga G. Troyanskaya
2012	J	`jnl`	IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
2012	J	`jnl`	Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes. PLoS Comput. Biol. Yuanfang Guan, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K. Wong, John C. Schimenti, Mary Ann Handel, Carol J. Bult, Matthew A. Hibbs, Olga G. Troyanskaya
2011	J	`jnl`	Accurate Quantification of Functional Analogy among Close Homologs. PLoS Comput. Biol. Maria D. Chikina, Olga G. Troyanskaya
2011	—	`conf`	An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. ICBO 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, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone, Mike Tyers, Carlo Torniai, Olga G. Troyanskaya, Judith Turner, Monte Westerfield, Melissa A. Haendel
2011	J	`jnl`	PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. Casey S. Greene, Olga G. Troyanskaya
2010	J	`jnl`	Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations. PLoS Comput. Biol. Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
2010	J	`jnl`	Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst. Biol. Ana Pop, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N. Benfey, Olga G. Troyanskaya
2010	J	`jnl`	Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells. PLoS Comput. Biol. Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor Lemischka, Olga G. Troyanskaya
2010	J	`jnl`	Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components. PLoS Comput. Biol. Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya
2010	J	`jnl`	Systematic Planning of Genome-Scale Experiments in Poorly Studied Species. PLoS Comput. Biol. Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya
2009	J	`jnl`	Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinform. Zafer Barutçuoglu, Edoardo M. Airoldi, Vanessa Dumeaux, Robert E. Schapire, Olga G. Troyanskaya
2009	J	`jnl`	Coordinated Concentration Changes of Transcripts and Metabolites in PLoS Comput. Biol. Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya
2009	J	`jnl`	Detailing regulatory networks through large scale data integration. Bioinform. Curtis Huttenhower, K. Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J. Forman, Olga G. Troyanskaya, Hilary A. Coller
2009	J	`jnl`	Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis. PLoS Comput. Biol. Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya
2009	J	`jnl`	Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in PLoS Comput. Biol. Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya
2009	J	`jnl`	Graphle: Interactive exploration of large, dense graphs. BMC Bioinform. Curtis Huttenhower, Sajid O. Mehmood, Olga G. Troyanskaya
2009	J	`jnl`	Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
2009	J	`jnl`	Predicting Cellular Growth from Gene Expression Signatures. PLoS Comput. Biol. Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya
2009	J	`jnl`	Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinform. Atul J. Butte, Indra Neil Sarkar, Marco Ramoni, Yves A. Lussier, Olga G. Troyanskaya
2009	—	`conf`	Tech-note: Device-free interaction spaces. 3DUI Daniel Stødle, Olga G. Troyanskaya, Kai Li, Otto J. Anshus
2009	J	`jnl`	The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinform. Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, Olga G. Troyanskaya
2008	J	`jnl`	A Genomewide Functional Network for the Laboratory Mouse. PLoS Comput. Biol. Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya
2008	A	`conf`	Assessing the functional structure of genomic data. ISMB Curtis Huttenhower, Olga G. Troyanskaya
2008	J	`jnl`	The Sleipnir library for computational functional genomics. Bioinform. Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya
2007	J	`jnl`	"Getting Started In...": A Series Not to Miss. PLoS Comput. Biol. Olga G. Troyanskaya
2007	J	`jnl`	Context-sensitive data integration and prediction of biological networks. Bioinform. Chad L. Myers, Olga G. Troyanskaya
2007	J	`jnl`	Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinform. Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, Olga G. Troyanskaya
2007	J	`jnl`	Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinform. 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
2007	—	`conf`	Nested effects models for high-dimensional phenotyping screens. ISMB/ECCB (Supplement of Bioinformatics) Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang
2007	A	`conf`	Scalable, Dynamic Analysis and Visualization for Genomic Datasets. IPDPS Grant Wallace, Matthew A. Hibbs, Maitreya J. Dunham, Rachel S. G. Sealfon, Olga G. Troyanskaya, Kai Li
2007	C	`conf`	Viewing the Larger Context of Genomic Data through Horizontal Integration. IV Matthew A. Hibbs, Grant Wallace, Maitreya J. Dunham, Kai Li, Olga G. Troyanskaya
2006	J	`jnl`	A scalable method for integration and functional analysis of multiple microarray datasets. Bioinform. Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Olga G. Troyanskaya
2006	J	`jnl`	GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinform. Rachel S. G. Sealfon, Matthew A. Hibbs, Curtis Huttenhower, Chad L. Myers, Olga G. Troyanskaya
2006	J	`jnl`	Hierarchical multi-label prediction of gene function. Bioinform. Zafer Barutçuoglu, Robert E. Schapire, Olga G. Troyanskaya
2006	—	`conf`	Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. GCCB Lars Ailo Bongo, Grant Wallace, Tore Larsen, Kai Li, Olga G. Troyanskaya
2005	—	`conf`	A General Methodology for Integration of Microarray Data. CSB Workshops Curtis Huttenhower, Olga G. Troyanskaya
2005	A	`conf`	Dynamic Scalable Visualization for Collaborative Scientific Applications. IPDPS Kai Li, Matthew A. Hibbs, Grant Wallace, Olga G. Troyanskaya
2005	J	`jnl`	Putting microarrays in a context: Integrated analysis of diverse biological data. Briefings Bioinform. Olga G. Troyanskaya
2005	J	`jnl`	Tools and Applications for Large-Scale Display Walls. IEEE Computer Graphics and Applications 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, Zhiyan Liu, Rudrajit Samanta, Rahul Sukthankar, Olga G. Troyanskaya
2005	—	`ch.`	Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery. Data Analysis and Visualization in Genomics and Proteomics Olga G. Troyanskaya
2005	J	`jnl`	Visualization methods for statistical analysis of microarray clusters. BMC Bioinform. Matthew A. Hibbs, Nathaniel C. Dirksen, Kai Li, Olga G. Troyanskaya
2005	J	`jnl`	Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinform. Chad L. Myers, Xing Chen, Olga G. Troyanskaya
2004	J	`jnl`	Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinform. Chad L. Myers, Maitreya J. Dunham, Sun-Yuan Kung, Olga G. Troyanskaya
2004	J	`jnl`	Computational functional genomics. IEEE Signal Process. Mag. Mike P. Liang, Olga G. Troyanskaya, Alain Laederach, Douglas L. Brutlag, Russ B. Altman
2002	J	`jnl`	Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinform. Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman
2002	J	`jnl`	Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity. Bioinform. Olga G. Troyanskaya, Ora Arbell, Yair Koren, Gad M. Landau, Alexander Bolshoy
2001	J	`jnl`	Missing value estimation methods for DNA microarrays. Bioinform. Olga G. Troyanskaya, Michael N. Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman