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ORCIDOlga G. Troyanskaya
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2020 – today
- 2023
[j55]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): 644-657 (2023)- [j54]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): 805 (2023) - [j53]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): 1056-1066 (2023) - [i2]Zijun Zhang, Adam R. Lamson, Michael J. Shelley, Olga G. Troyanskaya:
Interpretable neural architecture search and transfer learning for understanding sequence dependent enzymatic reactions. CoRR abs/2305.11917 (2023) - 2021
- [j52]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): 342-348 (2021) - [j51]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): 392-400 (2021) - 2020
- [j50]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): 994-999 (2020)
2010 – 2019
- 2018
- [j49]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): W65-W70 (2018) - [j48]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) - 2016
- [j47]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): W587-W592 (2016) - 2015
- [j46]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): 1093-1101 (2015) - [j45]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): W128-W133 (2015) - [j44]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): W182-W187 (2015) - 2014
- [j43]Andreas W. M. Dress, Michal Linial, Olga G. Troyanskaya, Martin Vingron:
ISCB/SPRINGER series in computational biology. Bioinform. 30(1): 146-147 (2014) - [j42]Jian Zhou, Olga G. Troyanskaya:
Global Quantitative Modeling of Chromatin Factor Interactions. PLoS Comput. Biol. 10(3) (2014) - [c10]Jian Zhou, Olga G. Troyanskaya:
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. ICML 2014: 745-753 - [i1]Jian Zhou, Olga G. Troyanskaya:
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction. CoRR abs/1403.1347 (2014) - 2013
- [j41]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): 3036-3044 (2013) - [j40]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) - 2012
- [j39]Maria D. Chikina, Olga G. Troyanskaya:
An effective statistical evaluation of ChIPseq dataset similarity. Bioinform. 28(5): 607-613 (2012) - [j38]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): 484-490 (2012) - [j37]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) - [j36]Casey S. Greene, Olga G. Troyanskaya:
Chapter 2: Data-Driven View of Disease Biology. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j35]Casey S. Greene, Olga G. Troyanskaya:
PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 39(Web-Server-Issue): 368-374 (2011) - [j34]Maria D. Chikina, Olga G. Troyanskaya:
Accurate Quantification of Functional Analogy among Close Homologs. PLoS Comput. Biol. 7(2) (2011) - [c9]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 - 2010
- [j33]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: 180 (2010) - [j32]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) - [j31]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) - [j30]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) - [j29]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)
2000 – 2009
- 2009
- [j28]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): 701-702 (2009) - [j27]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): 1307-1313 (2009) - [j26]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): 2404-2410 (2009) - [j25]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): 3267-3274 (2009) - [j24]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) - [j23]Curtis Huttenhower, Sajid O. Mehmood, Olga G. Troyanskaya:
Graphle: Interactive exploration of large, dense graphs. BMC Bioinform. 10: 417 (2009) - [j22]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) - [j21]Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya:
Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. PLoS Comput. Biol. 5(1) (2009) - [j20]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) - [j19]Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya:
Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans. PLoS Comput. Biol. 5(6) (2009) - [c8]Daniel Stødle, Olga G. Troyanskaya, Kai Li, Otto J. Anshus:
Tech-note: Device-free interaction spaces. 3DUI 2009: 39-42 - 2008
- [j18]Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya:
The Sleipnir library for computational functional genomics. Bioinform. 24(13): 1559-1561 (2008) - [j17]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) - [c7]Curtis Huttenhower, Olga G. Troyanskaya:
Assessing the functional structure of genomic data. ISMB 2008: 330-338 - 2007
- [j16]Chad L. Myers, Olga G. Troyanskaya:
Context-sensitive data integration and prediction of biological networks. Bioinform. 23(17): 2322-2330 (2007) - [j15]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): 2692-2699 (2007) - [j14]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) - [j13]Olga G. Troyanskaya:
"Getting Started In...": A Series Not to Miss. PLoS Comput. Biol. 3(10) (2007) - [c6]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: 1-6 - [c5]Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang:
Nested effects models for high-dimensional phenotyping screens. ISMB/ECCB (Supplement of Bioinformatics) 2007: 305-312 - [c4]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: 326-334 - 2006
- [j12]Zafer Barutçuoglu, Robert E. Schapire, Olga G. Troyanskaya:
Hierarchical multi-label prediction of gene function. Bioinform. 22(7): 830-836 (2006) - [j11]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): 2890-2897 (2006) - [j10]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: 443 (2006) - [c3]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: 157-174 - 2005
- [j9]Olga G. Troyanskaya:
Putting microarrays in a context: Integrated analysis of diverse biological data. Briefings Bioinform. 6(1): 34-43 (2005) - [j8]Matthew A. Hibbs, Nathaniel C. Dirksen, Kai Li, Olga G. Troyanskaya:
Visualization methods for statistical analysis of microarray clusters. BMC Bioinform. 6: 115 (2005) - [j7]Chad L. Myers, Xing Chen, Olga G. Troyanskaya:
Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinform. 6: 146 (2005) - [j6]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): 24-33 (2005) - [c2]Curtis Huttenhower, Olga G. Troyanskaya:
A General Methodology for Integration of Microarray Data. CSB Workshops 2005: 109 - [c1]Kai Li, Matthew A. Hibbs, Grant Wallace, Olga G. Troyanskaya:
Dynamic Scalable Visualization for Collaborative Scientific Applications. IPDPS 2005 - [p1]Olga G. Troyanskaya:
Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery. Data Analysis and Visualization in Genomics and Proteomics 2005: 175-192 - 2004
- [j5]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): 3533-3543 (2004) - [j4]Mike P. Liang, Olga G. Troyanskaya, Alain Laederach, Douglas L. Brutlag, Russ B. Altman:
Computational functional genomics. IEEE Signal Process. Mag. 21(6): 62-69 (2004) - 2002
- [j3]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): 679-688 (2002) - [j2]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): 1454-1461 (2002) - 2001
- [j1]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): 520-525 (2001)
Coauthor Index
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