Olga G Troyanskaya

Olga G Troyanskaya

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Olga G Troyanskaya

Publications by authors named "Olga G Troyanskaya"

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100Publications

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Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations.

Bioinformatics 2019 Sep 16. Epub 2019 Sep 16.

Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.

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http://dx.doi.org/10.1093/bioinformatics/btz709DOI Listing
September 2019

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.

PLoS Genet 2019 Sep 25;15(9):e1008382. Epub 2019 Sep 25.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779412PMC
September 2019

Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Authors:
Nick Shrine Anna L Guyatt A Mesut Erzurumluoglu Victoria E Jackson Brian D Hobbs Carl A Melbourne Chiara Batini Katherine A Fawcett Kijoung Song Phuwanat Sakornsakolpat Xingnan Li Ruth Boxall Nicola F Reeve Ma'en Obeidat Jing Hua Zhao Matthias Wielscher Stefan Weiss Katherine A Kentistou James P Cook Benjamin B Sun Jian Zhou Jennie Hui Stefan Karrasch Medea Imboden Sarah E Harris Jonathan Marten Stefan Enroth Shona M Kerr Ida Surakka Veronique Vitart Terho Lehtimäki Richard J Allen Per S Bakke Terri H Beaty Eugene R Bleecker Yohan Bossé Corry-Anke Brandsma Zhengming Chen James D Crapo John Danesh Dawn L DeMeo Frank Dudbridge Ralf Ewert Christian Gieger Amund Gulsvik Anna L Hansell Ke Hao Joshua D Hoffman John E Hokanson Georg Homuth Peter K Joshi Philippe Joubert Claudia Langenberg Xuan Li Liming Li Kuang Lin Lars Lind Nicholas Locantore Jian'an Luan Anubha Mahajan Joseph C Maranville Alison Murray David C Nickle Richard Packer Margaret M Parker Megan L Paynton David J Porteous Dmitry Prokopenko Dandi Qiao Rajesh Rawal Heiko Runz Ian Sayers Don D Sin Blair H Smith María Soler Artigas David Sparrow Ruth Tal-Singer Paul R H J Timmers Maarten Van den Berge John C Whittaker Prescott G Woodruff Laura M Yerges-Armstrong Olga G Troyanskaya Olli T Raitakari Mika Kähönen Ozren Polašek Ulf Gyllensten Igor Rudan Ian J Deary Nicole M Probst-Hensch Holger Schulz Alan L James James F Wilson Beate Stubbe Eleftheria Zeggini Marjo-Riitta Jarvelin Nick Wareham Edwin K Silverman Caroline Hayward Andrew P Morris Adam S Butterworth Robert A Scott Robin G Walters Deborah A Meyers Michael H Cho David P Strachan Ian P Hall Martin D Tobin Louise V Wain

Nat Genet 2019 Jun;51(6):1067

Department of Health Sciences, University of Leicester, Leicester, UK.

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http://dx.doi.org/10.1038/s41588-019-0438-3DOI Listing
June 2019

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

Nat Methods 2019 04 28;16(4):315-318. Epub 2019 Mar 28.

Flatiron Institute, Simons Foundation, New York, NY, USA.

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http://dx.doi.org/10.1038/s41592-019-0360-8DOI Listing
April 2019

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Authors:
Nick Shrine Anna L Guyatt A Mesut Erzurumluoglu Victoria E Jackson Brian D Hobbs Carl A Melbourne Chiara Batini Katherine A Fawcett Kijoung Song Phuwanat Sakornsakolpat Xingnan Li Ruth Boxall Nicola F Reeve Ma'en Obeidat Jing Hua Zhao Matthias Wielscher Stefan Weiss Katherine A Kentistou James P Cook Benjamin B Sun Jian Zhou Jennie Hui Stefan Karrasch Medea Imboden Sarah E Harris Jonathan Marten Stefan Enroth Shona M Kerr Ida Surakka Veronique Vitart Terho Lehtimäki Richard J Allen Per S Bakke Terri H Beaty Eugene R Bleecker Yohan Bossé Corry-Anke Brandsma Zhengming Chen James D Crapo John Danesh Dawn L DeMeo Frank Dudbridge Ralf Ewert Christian Gieger Amund Gulsvik Anna L Hansell Ke Hao Joshua D Hoffman John E Hokanson Georg Homuth Peter K Joshi Philippe Joubert Claudia Langenberg Xuan Li Liming Li Kuang Lin Lars Lind Nicholas Locantore Jian'an Luan Anubha Mahajan Joseph C Maranville Alison Murray David C Nickle Richard Packer Margaret M Parker Megan L Paynton David J Porteous Dmitry Prokopenko Dandi Qiao Rajesh Rawal Heiko Runz Ian Sayers Don D Sin Blair H Smith María Soler Artigas David Sparrow Ruth Tal-Singer Paul R H J Timmers Maarten Van den Berge John C Whittaker Prescott G Woodruff Laura M Yerges-Armstrong Olga G Troyanskaya Olli T Raitakari Mika Kähönen Ozren Polašek Ulf Gyllensten Igor Rudan Ian J Deary Nicole M Probst-Hensch Holger Schulz Alan L James James F Wilson Beate Stubbe Eleftheria Zeggini Marjo-Riitta Jarvelin Nick Wareham Edwin K Silverman Caroline Hayward Andrew P Morris Adam S Butterworth Robert A Scott Robin G Walters Deborah A Meyers Michael H Cho David P Strachan Ian P Hall Martin D Tobin Louise V Wain

Nat Genet 2019 03 25;51(3):481-493. Epub 2019 Feb 25.

Department of Health Sciences, University of Leicester, Leicester, UK.

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http://dx.doi.org/10.1038/s41588-018-0321-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397078PMC
March 2019

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Cell Syst 2019 Feb 23;8(2):152-162.e6. Epub 2019 Jan 23.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Flatiron Institute, Simons Foundation, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.12.010DOI Listing
February 2019

Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.

mSystems 2019 Jan-Feb;4(1). Epub 2019 Feb 26.

Department of Chemistry, Princeton University, Princeton, New Jersey, USA.

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http://msystems.asm.org/lookup/doi/10.1128/mSystems.00170-18
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http://dx.doi.org/10.1128/mSystems.00170-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392091PMC
February 2019

Interpretation of an individual functional genomics experiment guided by massive public data.

Nat Methods 2018 12 26;15(12):1049-1052. Epub 2018 Nov 26.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1038/s41592-018-0218-5DOI Listing
December 2018

An integrative tissue-network approach to identify and test human disease genes.

Nat Biotechnol 2018 Oct 22. Epub 2018 Oct 22.

Department of Computer Science, Princeton University, Princeton, New Jersey, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4246
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http://dx.doi.org/10.1038/nbt.4246DOI Listing
October 2018

Enabling Precision Medicine through Integrative Network Models.

J Mol Biol 2018 09 9;430(18 Pt A):2913-2923. Epub 2018 Jul 9.

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.07.004DOI Listing
September 2018

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

Nat Genet 2018 08 16;50(8):1171-1179. Epub 2018 Jul 16.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1038/s41588-018-0160-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6094955PMC
August 2018

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.

PLoS Genet 2018 08 10;14(8):e1007559. Epub 2018 Aug 10.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105014PMC
August 2018

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

Nucleic Acids Res 2018 07;46(W1):W65-W70

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA.

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http://dx.doi.org/10.1093/nar/gky408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030827PMC
July 2018

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.

Nat Neurosci 2016 11 1;19(11):1454-1462. Epub 2016 Aug 1.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1038/nn.4353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803797PMC
November 2016

GIANT API: an application programming interface for functional genomics.

Nucleic Acids Res 2016 Jul 20;44(W1):W587-92. Epub 2016 Apr 20.

Simons Center for Data Analysis, Simons Foundation, New York, NY 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08540, USA Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA

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http://dx.doi.org/10.1093/nar/gkw289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987882PMC
July 2016

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

Nat Commun 2016 Feb 4;7:10528. Epub 2016 Feb 4.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA.

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http://dx.doi.org/10.1038/ncomms10528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742914PMC
February 2016

Predicting effects of noncoding variants with deep learning-based sequence model.

Nat Methods 2015 Oct 24;12(10):931-4. Epub 2015 Aug 24.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1038/nmeth.3547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768299PMC
October 2015

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

Nucleic Acids Res 2015 Jul 4;43(W1):W182-7. Epub 2015 May 4.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA Simons Center for Data Analysis, Simons Foundation, NY 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08540, USA

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http://dx.doi.org/10.1093/nar/gkv443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489275PMC
July 2015

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

Nucleic Acids Res 2015 Jul 12;43(W1):W128-33. Epub 2015 May 12.

Department of Computer Science, Princeton University, Princeton, NJ 08540, USA Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA Simons Center for Data Analysis, Simons Foundation, NY 10010, USA

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http://dx.doi.org/10.1093/nar/gkv486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489318PMC
July 2015

Implications of Big Data for cell biology.

Mol Biol Cell 2015 Jul;26(14):2575-8

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540 Department of Computer Science, Princeton University, Princeton, NJ 08540 Simons Center for Data Analysis, Simons Foundation, New York, NY 10010

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http://dx.doi.org/10.1091/mbc.E13-12-0756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501356PMC
July 2015

Understanding multicellular function and disease with human tissue-specific networks.

Nat Genet 2015 Jun 27;47(6):569-76. Epub 2015 Apr 27.

1] Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA. [2] Department of Computer Science, Princeton University, Princeton, New Jersey, USA. [3] Simons Center for Data Analysis, Simons Foundation, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828725PMC
June 2015

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

Bioinformatics 2015 Apr 26;31(7):1093-101. Epub 2014 Nov 26.

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA and Simons Center for Data Analysis, Simons Foundation, New York, NY, 10010, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804827PMC
April 2015

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

Nat Methods 2015 Mar 12;12(3):211-4, 3 p following 214. Epub 2015 Jan 12.

1] Department of Computer Science, Princeton University, Princeton, New Jersey, USA. [2] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA. [3] Simons Center for Data Analysis, Simons Foundation, New York, New York, USA.

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http://dx.doi.org/10.1038/nmeth.3249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768301PMC
March 2015

Global quantitative modeling of chromatin factor interactions.

PLoS Comput Biol 2014 Mar 27;10(3):e1003525. Epub 2014 Mar 27.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America; Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967939PMC
March 2014

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

Bioinformatics 2013 Dec 12;29(23):3036-44. Epub 2013 Sep 12.

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834796PMC
December 2013

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

PLoS Comput Biol 2013 14;9(3):e1002957. Epub 2013 Mar 14.

Department of Computer Science, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597527PMC
November 2013

Defining cell-type specificity at the transcriptional level in human disease.

Genome Res 2013 Nov 15;23(11):1862-73. Epub 2013 Aug 15.

Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA;

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http://dx.doi.org/10.1101/gr.155697.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814886PMC
November 2013

A new system for comparative functional genomics of Saccharomyces yeasts.

Genetics 2013 Sep 12;195(1):275-87. Epub 2013 Jul 12.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dunham.gs.washington.edu/Caudy.pdf
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http://www.genetics.org/cgi/doi/10.1534/genetics.113.152918
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http://dx.doi.org/10.1534/genetics.113.152918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761308PMC
September 2013

Chapter 2: Data-driven view of disease biology.

PLoS Comput Biol 2012 27;8(12):e1002816. Epub 2012 Dec 27.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1002816
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http://dx.doi.org/10.1371/journal.pcbi.1002816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531282PMC
May 2013

Tissue-specific functional networks for prioritizing phenotype and disease genes.

PLoS Comput Biol 2012 27;8(9):e1002694. Epub 2012 Sep 27.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

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https://dx.plos.org/10.1371/journal.pcbi.1002694
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http://dx.doi.org/10.1371/journal.pcbi.1002694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459891PMC
January 2013

Comparative gene expression between two yeast species.

BMC Genomics 2013 Jan 16;14:33. Epub 2013 Jan 16.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2164-14-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556494PMC
January 2013

Accurate evaluation and analysis of functional genomics data and methods.

Ann N Y Acad Sci 2012 Jul 23;1260:95-100. Epub 2012 Jan 23.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.

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http://doi.wiley.com/10.1111/j.1749-6632.2011.06383.x
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http://dx.doi.org/10.1111/j.1749-6632.2011.06383.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753770PMC
July 2012

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

Nucleic Acids Res 2012 Jul 7;40(Web Server issue):W484-90. Epub 2012 Jun 7.

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1093/nar/gks458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394282PMC
July 2012

An effective statistical evaluation of ChIPseq dataset similarity.

Bioinformatics 2012 Mar 19;28(5):607-13. Epub 2012 Jan 19.

Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339511PMC
March 2012

Nucleosome-coupled expression differences in closely-related species.

BMC Genomics 2011 Sep 26;12:466. Epub 2011 Sep 26.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2164-12-466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3209474PMC
September 2011

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

Nucleic Acids Res 2011 Jul 7;39(Web Server issue):W368-74. Epub 2011 Jun 7.

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1093/nar/gkr440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125802PMC
July 2011

Accurate quantification of functional analogy among close homologs.

PLoS Comput Biol 2011 Feb 3;7(2):e1001074. Epub 2011 Feb 3.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033368PMC
February 2011

Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

PLoS Comput Biol 2010 Dec 16;6(12):e1001034. Epub 2010 Dec 16.

Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1001034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002996PMC
December 2010

Functional genomics complements quantitative genetics in identifying disease-gene associations.

PLoS Comput Biol 2010 Nov 11;6(11):e1000991. Epub 2010 Nov 11.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978695PMC
November 2010

Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.

PLoS Comput Biol 2010 Nov 24;6(11):e1001009. Epub 2010 Nov 24.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991250PMC
November 2010

Integrative systems biology for data-driven knowledge discovery.

Semin Nephrol 2010 Sep;30(5):443-54

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.semnephrol.2010.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734377PMC
September 2010

Detailing regulatory networks through large scale data integration.

Bioinformatics 2009 Dec 13;25(24):3267-74. Epub 2009 Oct 13.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788929PMC
December 2009

Graphle: Interactive exploration of large, dense graphs.

BMC Bioinformatics 2009 Dec 14;10:417. Epub 2009 Dec 14.

Department of Computer Science, Princeton University, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1186/1471-2105-10-417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803856PMC
December 2009

Discovering biological networks from diverse functional genomic data.

Methods Mol Biol 2009 ;563:157-75

Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.

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http://dx.doi.org/10.1007/978-1-60761-175-2_9DOI Listing
October 2009

Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.

Methods Mol Biol 2009 ;548:273-93

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1007/978-1-59745-540-4_15DOI Listing
July 2009

Exploring the human genome with functional maps.

Genome Res 2009 Jun 26;19(6):1093-106. Epub 2009 Feb 26.

Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.082214.108
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http://dx.doi.org/10.1101/gr.082214.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694471PMC
June 2009

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

PLoS Comput Biol 2009 Jun 19;5(6):e1000417. Epub 2009 Jun 19.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692103PMC
June 2009

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.

Bioinformatics 2009 May 3;25(10):1307-13. Epub 2008 Dec 3.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677736PMC
May 2009

Directing experimental biology: a case study in mitochondrial biogenesis.

PLoS Comput Biol 2009 Mar 20;5(3):e1000322. Epub 2009 Mar 20.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654405PMC
March 2009

Predicting cellular growth from gene expression signatures.

PLoS Comput Biol 2009 Jan 2;5(1):e1000257. Epub 2009 Jan 2.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1000257
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January 2009

Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.

PLoS Comput Biol 2009 Jan 30;5(1):e1000270. Epub 2009 Jan 30.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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January 2009

A genomewide functional network for the laboratory mouse.

PLoS Comput Biol 2008 Sep 26;4(9):e1000165. Epub 2008 Sep 26.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527685PMC
September 2008

Predicting gene function in a hierarchical context with an ensemble of classifiers.

Genome Biol 2008 27;9 Suppl 1:S3. Epub 2008 Jun 27.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447537PMC
August 2008

The Sleipnir library for computational functional genomics.

Bioinformatics 2008 Jul 21;24(13):1559-61. Epub 2008 May 21.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08540, USA.

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July 2008

Integrated analysis of microarray results.

Methods Mol Biol 2007 ;382:429-37

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, NJ, USA.

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March 2008

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Mol Biol Cell 2008 Jan 24;19(1):352-67. Epub 2007 Oct 24.

Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174172PMC
January 2008

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

Bioinformatics 2007 Oct 27;23(20):2692-9. Epub 2007 Aug 27.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

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October 2007

Context-sensitive data integration and prediction of biological networks.

Bioinformatics 2007 Sep 28;23(17):2322-30. Epub 2007 Jun 28.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm332DOI Listing
September 2007

Computational identification of cellular networks and pathways.

Mol Biosyst 2007 Jul 14;3(7):478-82. Epub 2007 May 14.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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July 2007

Nested effects models for high-dimensional phenotyping screens.

Bioinformatics 2007 Jul;23(13):i305-12

Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm178DOI Listing
July 2007

Bayesian data integration: a functional perspective.

Comput Syst Bioinformatics Conf 2006 :341-51

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA.

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June 2007

Functional analysis of gene duplications in Saccharomyces cerevisiae.

Genetics 2007 Feb 6;175(2):933-43. Epub 2006 Dec 6.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, New Jersey, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.106.064329
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800624PMC
February 2007

Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.

Genes Dev 2007 Jan 13;21(2):148-59. Epub 2006 Dec 13.

Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA.

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http://dx.doi.org/10.1101/gad.1477507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1770898PMC
January 2007

Putting the 'bio' into bioinformatics.

Genome Biol 2005 29;6(10):351. Epub 2005 Sep 29.

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1257464PMC
December 2006

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

Bioinformatics 2006 Dec 27;22(23):2890-7. Epub 2006 Sep 27.

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl492DOI Listing
December 2006

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

BMC Bioinformatics 2006 Oct 10;7:443. Epub 2006 Oct 10.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ, USA.

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http://dx.doi.org/10.1186/1471-2105-7-443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618863PMC
October 2006

Global analysis of gene function in yeast by quantitative phenotypic profiling.

Mol Syst Biol 2006 17;2:2006.0001. Epub 2006 Jan 17.

Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305-5152, USA.

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http://dx.doi.org/10.1038/msb4100043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681475PMC
August 2006

Discovery of biological networks from diverse functional genomic data.

Genome Biol 2005 19;6(13):R114. Epub 2005 Dec 19.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1414113PMC
July 2006

Finding function: evaluation methods for functional genomic data.

BMC Genomics 2006 Jul 25;7:187. Epub 2006 Jul 25.

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560386PMC
July 2006

Hierarchical multi-label prediction of gene function.

Bioinformatics 2006 Apr 12;22(7):830-6. Epub 2006 Jan 12.

Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1093/bioinformatics/btk048DOI Listing
April 2006

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

BMC Bioinformatics 2005 Jun 13;6:146. Epub 2005 Jun 13.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2105-6-146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181623PMC
June 2005

Visualization methods for statistical analysis of microarray clusters.

BMC Bioinformatics 2005 May 12;6:115. Epub 2005 May 12.

Computer Science Department, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1471-2105-6-115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156867PMC
May 2005

Putting microarrays in a context: integrated analysis of diverse biological data.

Brief Bioinform 2005 Mar;6(1):34-43

Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ 08544, USA.

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March 2005

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

Bioinformatics 2004 Dec 29;20(18):3533-43. Epub 2004 Jul 29.

Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory.

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http://dx.doi.org/10.1093/bioinformatics/bth440DOI Listing
December 2004

Systemic and cell type-specific gene expression patterns in scleroderma skin.

Proc Natl Acad Sci U S A 2003 Oct 6;100(21):12319-24. Epub 2003 Oct 6.

Department of Dermatology, University of California-San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1073/pnas.1635114100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218756PMC
October 2003

Endothelial cell diversity revealed by global expression profiling.

Proc Natl Acad Sci U S A 2003 Sep 8;100(19):10623-8. Epub 2003 Sep 8.

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.1434429100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196854PMC
September 2003

Variation in gene expression patterns in human gastric cancers.

Mol Biol Cell 2003 Aug 17;14(8):3208-15. Epub 2003 Apr 17.

Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1091/mbc.e02-12-0833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC181561PMC
August 2003

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Proc Natl Acad Sci U S A 2003 Jul 25;100(14):8348-53. Epub 2003 Jun 25.

Department of Genetics, Stanford University School of Medicine, CA 94305, USA.

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http://dx.doi.org/10.1073/pnas.0832373100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166232PMC
July 2003

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

Proc Natl Acad Sci U S A 2003 Feb 5;100(4):1926-30. Epub 2003 Feb 5.

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149935PMC
February 2003