Olga G. Troyanskaya

发表

An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases

Kara Dolinski, Mike Tyers, Chris Mungall, 2011, ICBO.

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Olga G. Troyanskaya, Curtis Huttenhower, Christopher Y. Park, 2010, PLoS Comput. Biol..

PILGRM: an interactive data-driven discovery platform for expert biologists

Casey S. Greene, Olga G. Troyanskaya, O. Troyanskaya, 2011, Nucleic Acids Res..

Tech-note: Device-free interaction spaces

Kai Li, Olga G. Troyanskaya, Otto J. Anshus, 2009, 2009 IEEE Symposium on 3D User Interfaces.

FNTM: a server for predicting functional networks of tissues in mouse

Olga G. Troyanskaya, Arjun Krishnan, Jonathan Goya, 2015, Nucleic Acids Res..

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields

Edoardo M. Airoldi, Robert E. Schapire, Olga G. Troyanskaya, 2008, Bioinform..

The Sleipnir library for computational functional genomics

Olga G. Troyanskaya, Curtis Huttenhower, Mark Schroeder, 2008, Bioinform..

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

Kai Li, Olga G. Troyanskaya, Curtis Huttenhower, 2009, PLoS Comput. Biol..

Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes

Yuanfang Guan, Olga G. Troyanskaya, Margit Burmeister, 2012, PLoS Comput. Biol..

“Getting Started In…”: A Series Not to Miss

Olga G. Troyanskaya, 2007, PLoS Comput. Biol..

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction

Olga G. Troyanskaya, Curtis Huttenhower, David C. Hess, 2009, Bioinform..

Experimental validation of bioPIXIE prediction for the biological role of YPL017C

Kara Dolinski, Olga G. Troyanskaya, Chad L. Myers, 2011 .

Dynamic scalable visualization for collaborative scientific applications

Kai Li, Olga G. Troyanskaya, Grant Wallace, 2005, 19th IEEE International Parallel and Distributed Processing Symposium.

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

Qian Zhu, Olga G. Troyanskaya, Arjun Krishnan, 2013, Bioinform..

Exploring the functional landscape of gene expression: directed search of large microarray compendia

Kai Li, Olga G. Troyanskaya, Curtis Huttenhower, 2007, Bioinform..

Visualization-based discovery and analysis of genomic aberrations in microarray data

Xing Chen, Olga G. Troyanskaya, Chad L. Myers, 2005, BMC Bioinformatics.

Detailing regulatory networks through large scale data integration

Olga G. Troyanskaya, Curtis Huttenhower, Mark Schroeder, 2009, Bioinform..

A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project

Jian Zhou, Ravi Iyengar, Olga G. Troyanskaya, 2019, bioRxiv.

Assessing the functional structure of genomic data

Olga G. Troyanskaya, Curtis Huttenhower, C. Huttenhower, 2008, ISMB.

GIANT API: an application programming interface for functional genomics

Olga G. Troyanskaya, Aaron K. Wong, Ian Fisk, 2016, Nucleic Acids Res..

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

Yuanfang Guan, Olga G. Troyanskaya, Matthew A. Hibbs, 2010, PLoS Comput. Biol..

Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks

Kai Li, Olga G. Troyanskaya, Grant Wallace, 2007, GCCB.

Scalable, Dynamic Analysis and Visualization for Genomic Datasets

Kai Li, Olga G. Troyanskaya, Grant Wallace, 2007, 2007 IEEE International Parallel and Distributed Processing Symposium.

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

Olga G. Troyanskaya, Curtis Huttenhower, Philip N. Benfey, 2010, BMC Systems Biology.

Hierarchical multi-label prediction of gene function

Robert E. Schapire, Olga G. Troyanskaya, Zafer Barutçuoglu, 2006, Bioinform..

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

Casey S. Greene, Yuanfang Guan, Olga G. Troyanskaya, 2013, PLoS Comput. Biol..

Chapter 2: Data-Driven View of Disease Biology

Casey S. Greene, Olga G. Troyanskaya, O. Troyanskaya, 2012, PLoS Comput. Biol..

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

Casey S. Greene, Yuanfang Guan, Olga G. Troyanskaya, 2012, Nucleic Acids Res..

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

Olga G. Troyanskaya, Arjun Krishnan, Aaron K. Wong, 2015, Nucleic Acids Res..

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells

Edoardo M. Airoldi, Olga G. Troyanskaya, Florian Markowetz, 2010, PLoS Comput. Biol..

Graphle: Interactive exploration of large, dense graphs

Olga G. Troyanskaya, Curtis Huttenhower, Sajid O. Mehmood, 2009, BMC Bioinformatics.

Selected proceedings of the First Summit on Translational Bioinformatics 2008

Atul J. Butte, Olga G. Troyanskaya, Yves A. Lussier, 2009, BMC Bioinformatics.

An automated framework for efficiently designing deep convolutional neural networks in genomics

Zijun Zhang, Olga G. Troyanskaya, Christopher Y. Park, 2020, Nature Machine Intelligence.

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data

Aaditya V. Rangan, Qian Zhu, Olga G. Troyanskaya, 2018, PLoS Comput. Biol..

Nested effects models for high-dimensional phenotyping screens

Olga G. Troyanskaya, Rainer Spang, Florian Markowetz, 2007, ISMB/ECCB.

A scalable method for integration and functional analysis of multiple microarray datasets

Olga G. Troyanskaya, Curtis Huttenhower, Chad L. Myers, 2006, Bioinform..

ISCB/SPRINGER series in computational biology

Martin Vingron, Michal Linial, Olga G. Troyanskaya, 2013, Bioinform..

Viewing the Larger Context of Genomic Data through Horizontal Integration

Kai Li, Olga G. Troyanskaya, Grant Wallace, 2007, 2007 11th International Conference Information Visualization (IV '07).

Improving The Specificity Of Biological Signal Detection From Microarray Data

David Botstein, Olga G. Troyanskaya, Russ B. Altman, 2003 .

Papers on normalization, variable selection, classification or clustering of microarray data

Joaquín Dopazo, Trey Ideker, Olga G. Troyanskaya, 2009, Bioinform..

Accurate detection of aneuploidies in array CGH and gene expression microarray data

Sun-Yuan Kung, Olga G. Troyanskaya, Chad L. Myers, 2004, Bioinform..

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans

Olga G. Troyanskaya, Curtis Huttenhower, Maria D. Chikina, 2009, PLoS Comput. Biol..

Tools and applications for large-scale display walls

Anoop Gupta, Adam Finkelstein, Thomas A. Funkhouser, 2005, IEEE Computer Graphics and Applications.

Putting microarrays in a context: Integrated analysis of diverse biological data

Olga G. Troyanskaya, O. Troyanskaya, 2005, Briefings Bioinform..

Machine learning, the kidney, and genotype-phenotype analysis.

Olga G. Troyanskaya, Rachel Sealfon, Rachel S. G. Sealfon, 2020, Kidney international.

A general methodology for integration of microarray data

Olga G. Troyanskaya, Curtis Huttenhower, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues

Olga G. Troyanskaya, Arjun Krishnan, Aaron K. Wong, 2018, Nucleic Acids Res..

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm332 Data and text mining

Olga G. Troyanskaya, Chad L. Myers, O. Troyanskaya, 2022 .

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Kai Li, Moses Charikar, Olga G. Troyanskaya, 2015, Nature Methods.

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species

Yuanfang Guan, Olga G. Troyanskaya, Amy A. Caudy, 2010, PLoS Comput. Biol..

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

Olga G. Troyanskaya, Curtis Huttenhower, Nathan O. Siemers, 2007, BMC Bioinformatics.

Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity

Gad M. Landau, Olga G. Troyanskaya, Alexander Bolshoy, 2002, Bioinform..

Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery

Olga G. Troyanskaya, 2005, Data Analysis and Visualization in Genomics and Proteomics.

Nonparametric methods for identifying differentially expressed genes in microarray data

Russ B. Altman, David Botstein, Olga G. Troyanskaya, 2002, Bioinform..

An analytical framework for interpretable and generalizable ‘quasilinear’ single-cell data analysis

Olga G. Troyanskaya, Jian Zhou, O. Troyanskaya, 2020, bioRxiv.

An effective statistical evaluation of ChIPseq dataset similarity

Olga G. Troyanskaya, Maria D. Chikina, O. Troyanskaya, 2012, Bioinform..

Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction pdf

Jian Zhou, Olga G. Troyanskaya, O. Troyanskaya, 2014, ICML.

Visualization methods for statistical analysis of microarray clusters

Kai Li, Olga G. Troyanskaya, Matthew A. Hibbs, 2005, BMC Bioinformatics.

Global Quantitative Modeling of Chromatin Factor Interactions

Jian Zhou, Olga G. Troyanskaya, O. Troyanskaya, 2014, PLoS Comput. Biol..

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms

Qian Zhu, Olga G. Troyanskaya, Christopher Y. Park, 2015, Bioinform..

Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project

Jens Hansen, Ravi Iyengar, Olga G. Troyanskaya, 2020 .

Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae

Olga G. Troyanskaya, Joshua D. Rabinowitz, Matthew J. Brauer, 2009, PLoS Comput. Biol..

Missing value estimation methods for DNA microarrays

Russ B. Altman, Robert Tibshirani, David Botstein, 2001, Bioinform..

Predicting Cellular Growth from Gene Expression Signatures

Edoardo M. Airoldi, David Botstein, Olga G. Troyanskaya, 2009, PLoS Comput. Biol..

Accurate Quantification of Functional Analogy among Close Homologs

Olga G. Troyanskaya, Maria D. Chikina, O. Troyanskaya, 2011, PLoS Comput. Biol..

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

Olga G. Troyanskaya, Curtis Huttenhower, Chad L. Myers, 2006, BMC Bioinformatics.

A Genomewide Functional Network for the Laboratory Mouse

Yuanfang Guan, Olga G. Troyanskaya, Carol J. Bult, 2008, PLoS Comput. Biol..

Artificial intelligence and cancer

Anne E Carpenter, Olga G. Troyanskaya, Anne E. Carpenter, 2020, Nature Cancer.

An automated framework for efficiently designing deep convolutional neural networks in genomics

Olga G. Troyanskaya, Christopher Y. Park, Chandra L. Theesfeld, 2021, Nat. Mach. Intell..

Training Data for DeepArk

Olga G. Troyanskaya, Evan M. Cofer, Chandra L. Theesfeld, 2021 .

Variation in gene expression patterns in follicular lymphoma and the response to rituximab

David Botstein, Olga G. Troyanskaya, Patrick O. Brown, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis

Rui Li, David Botstein, Olga G. Troyanskaya, 2002, Proceedings of the National Academy of Sciences of the United States of America.

A New System for Comparative Functional Genomics of Saccharomyces Yeasts

Manuel Llinás, David Botstein, Yuanfang Guan, 2013, Genetics.

Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states

Olga G. Troyanskaya, O. Troyanskaya, Jian Zhou, 2016, Nature Communications.

Selene: a PyTorch-based deep learning library for biological sequence-level data

Olga G. Troyanskaya, Evan M. Cofer, Kathleen M. Chen, 2018, bioRxiv.

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

Olga G. Troyanskaya, A. P. Hayes, Michael Costanzo, 2009, PLoS genetics.

Erratum: Diversity of gene expression in adenocarcinoma of the lung (Proceedings of the National Academy of Sciences of the United States of America (2001) 98 (13784-13789))

Russ B. Altman, David Botstein, Olga G. Troyanskaya, 2002 .

Implications of Big Data for cell biology

Kara Dolinski, Olga G. Troyanskaya, K. Dolinski, 2015, Molecular biology of the cell.

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling

David Haussler, Olga G. Troyanskaya, Charles J. Vaske, 2011, Proceedings of the National Academy of Sciences.