Olga G. Troyanskaya

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 10

Top Topics

Transfer Learning

Neural Architecture

Protein Secondary Structure Prediction

Data Integration

Top Venues

Nucleic Acids Res.

Nat. Comput. Sci.

Publications

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
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. 3 (9) (2023)
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
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat. Comput. Sci. 3 (7) (2023)
Zijun Zhang, Adam R. Lamson, Michael Shelley, Olga G. Troyanskaya
Interpretable neural architecture search and transfer learning for understanding sequence dependent enzymatic reactions. CoRR (2023)
Zijun Zhang, Adam R. Lamson, Michael J. Shelley, Olga G. Troyanskaya
Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions. Nat. Comput. Sci. 3 (12) (2023)
Victoria R. Li, Zijun Zhang, Olga G. Troyanskaya
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinform. 37 (Supplement) (2021)
Zijun Zhang, Christopher Y. Park, Chandra L. Theesfeld, Olga G. Troyanskaya
An automated framework for efficiently designing deep convolutional neural networks in genomics. Nat. Mach. Intell. 3 (5) (2021)
Qian Zhu, Xavier Tekpli, Olga G. Troyanskaya, Vessela N. Kristensen
Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. Bioinform. 36 (4) (2020)
Aaron K. Wong, Arjun Krishnan, Olga G. Troyanskaya
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
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
A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. PLoS Comput. Biol. 14 (5) (2018)
Andrew M. Roberts, Aaron K. Wong, Ian Fisk, Olga G. Troyanskaya
GIANT API: an application programming interface for functional genomics. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Jonathan Goya, Aaron K. Wong, Victoria Yao, Arjun Krishnan, Max Homilius, Olga G. Troyanskaya
FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Christopher Y. Park, Arjun Krishnan, Qian Zhu, Aaron K. Wong, Young-Suk Lee, Olga G. Troyanskaya
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinform. 31 (7) (2015)
Aaron K. Wong, Arjun Krishnan, Victoria Yao, Alicja Tadych, Olga G. Troyanskaya
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Jian Zhou, Olga G. Troyanskaya
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. CoRR (2014)
Jian Zhou, Olga G. Troyanskaya
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. ICML (2014)
Jian Zhou, Olga G. Troyanskaya
Global Quantitative Modeling of Chromatin Factor Interactions. PLoS Comput. Biol. 10 (3) (2014)
Young-Suk Lee, Arjun Krishnan, Qian Zhu, Olga G. Troyanskaya
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinform. 29 (23) (2013)
Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Comput. Biol. 9 (3) (2013)
Maria D. Chikina, Olga G. Troyanskaya
An effective statistical evaluation of ChIPseq dataset similarity. Bioinform. 28 (5) (2012)
Casey S. Greene, Olga G. Troyanskaya
Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. 8 (12) (2012)
Yuanfang Guan, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K. Wong, John C. Schimenti, Mary Ann Handel, Carol J. Bult, Matthew A. Hibbs, Olga G. Troyanskaya
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes. PLoS Comput. Biol. 8 (9) (2012)
Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
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
An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. ICBO (2011)
Casey S. Greene, Olga G. Troyanskaya
PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Maria D. Chikina, Olga G. Troyanskaya
Accurate Quantification of Functional Analogy among Close Homologs. PLoS Comput. Biol. 7 (2) (2011)
Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya
Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components. PLoS Comput. Biol. 6 (11) (2010)
Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species. PLoS Comput. Biol. 6 (3) (2010)
Ana Pop, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N. Benfey, Olga G. Troyanskaya
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst. Biol. 4 (2010)
Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor Lemischka, Olga G. Troyanskaya
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells. PLoS Comput. Biol. 6 (12) (2010)
Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations. PLoS Comput. Biol. 6 (11) (2010)
Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya
Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis. PLoS Comput. Biol. 5 (3) (2009)
Curtis Huttenhower, Sajid O. Mehmood, Olga G. Troyanskaya
Graphle: Interactive exploration of large, dense graphs. BMC Bioinform. 10 (2009)
Zafer Barutçuoglu, Edoardo M. Airoldi, Vanessa Dumeaux, Robert E. Schapire, Olga G. Troyanskaya
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinform. 25 (10) (2009)
Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya
Predicting Cellular Growth from Gene Expression Signatures. PLoS Comput. Biol. 5 (1) (2009)
Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya
. PLoS Comput. Biol. 5 (1) (2009)
Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, Olga G. Troyanskaya
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinform. 25 (18) (2009)
David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. 25 (6) (2009)
Atul J. Butte, Indra Neil Sarkar, Marco Ramoni, Yves A. Lussier, Olga G. Troyanskaya
Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinform. 10 (S-2) (2009)
Daniel Stødle, Olga G. Troyanskaya, Kai Li, Otto J. Anshus
Tech-note: Device-free interaction spaces. 3DUI (2009)
Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya
. PLoS Comput. Biol. 5 (6) (2009)
Curtis Huttenhower, K. Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J. Forman, Olga G. Troyanskaya, Hilary A. Coller
Detailing regulatory networks through large scale data integration. Bioinform. 25 (24) (2009)
Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya
The Sleipnir library for computational functional genomics. Bioinform. 24 (13) (2008)
Curtis Huttenhower, Olga G. Troyanskaya
Assessing the functional structure of genomic data. ISMB (2008)
Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya
A Genomewide Functional Network for the Laboratory Mouse. PLoS Comput. Biol. 4 (9) (2008)
Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, Olga G. Troyanskaya
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinform. 23 (20) (2007)
Olga G. Troyanskaya
"Getting Started In...": A Series Not to Miss. PLoS Comput. Biol. 3 (10) (2007)
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
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinform. 8 (2007)
Chad L. Myers, Olga G. Troyanskaya
Context-sensitive data integration and prediction of biological networks. Bioinform. 23 (17) (2007)
Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang
Nested effects models for high-dimensional phenotyping screens. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Grant Wallace, Matthew A. Hibbs, Maitreya J. Dunham, Rachel S. G. Sealfon, Olga G. Troyanskaya, Kai Li
Scalable, Dynamic Analysis and Visualization for Genomic Datasets. IPDPS (2007)
Matthew A. Hibbs, Grant Wallace, Maitreya J. Dunham, Kai Li, Olga G. Troyanskaya
Viewing the Larger Context of Genomic Data through Horizontal Integration. IV (2007)
Zafer Barutçuoglu, Robert E. Schapire, Olga G. Troyanskaya
Hierarchical multi-label prediction of gene function. Bioinform. 22 (7) (2006)
Lars Ailo Bongo, Grant Wallace, Tore Larsen, Kai Li, Olga G. Troyanskaya
Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. GCCB (2006)
Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Olga G. Troyanskaya
A scalable method for integration and functional analysis of multiple microarray datasets. Bioinform. 22 (23) (2006)
Rachel S. G. Sealfon, Matthew A. Hibbs, Curtis Huttenhower, Chad L. Myers, Olga G. Troyanskaya
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinform. 7 (2006)
Olga G. Troyanskaya
Putting microarrays in a context: Integrated analysis of diverse biological data. Briefings Bioinform. 6 (1) (2005)
Kai Li, Matthew A. Hibbs, Grant Wallace, Olga G. Troyanskaya
Dynamic Scalable Visualization for Collaborative Scientific Applications. IPDPS (2005)
Matthew A. Hibbs, Nathaniel C. Dirksen, Kai Li, Olga G. Troyanskaya
Visualization methods for statistical analysis of microarray clusters. BMC Bioinform. 6 (2005)
Curtis Huttenhower, Olga G. Troyanskaya
A General Methodology for Integration of Microarray Data. CSB Workshops (2005)
Chad L. Myers, Xing Chen, Olga G. Troyanskaya
Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinform. 6 (2005)
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
Tools and Applications for Large-Scale Display Walls. IEEE Computer Graphics and Applications 25 (4) (2005)
Mike P. Liang, Olga G. Troyanskaya, Alain Laederach, Douglas L. Brutlag, Russ B. Altman
Computational functional genomics. IEEE Signal Process. Mag. 21 (6) (2004)
Chad L. Myers, Maitreya J. Dunham, Sun-Yuan Kung, Olga G. Troyanskaya
Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinform. 20 (18) (2004)
Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinform. 18 (11) (2002)
Olga G. Troyanskaya, Ora Arbell, Yair Koren, Gad M. Landau, Alexander Bolshoy
Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity. Bioinform. 18 (5) (2002)
Olga G. Troyanskaya, Michael N. Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman
Missing value estimation methods for DNA microarrays. Bioinform. 17 (6) (2001)