Casey S Greene

Casey S Greene

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Casey S Greene

Publications by authors named "Casey S Greene"

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Embracing study heterogeneity for finding genetic interactions in large-scale research consortia.

Genet Epidemiol 2019 Oct 4. Epub 2019 Oct 4.

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1002/gepi.22262DOI Listing
October 2019

Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing.

Circ Cardiovasc Qual Outcomes 2019 Jul 9;12(7):e005122. Epub 2019 Jul 9.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia. (C.W., C.S.G.).

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http://dx.doi.org/10.1161/CIRCOUTCOMES.118.005122DOI Listing
July 2019

Show me the models.

Authors:
Casey S Greene

Nat Biotechnol 2019 Jun;37(6):623-625

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1038/s41587-019-0143-xDOI Listing
June 2019

Open collaborative writing with Manubot.

PLoS Comput Biol 2019 Jun 24;15(6):e1007128. Epub 2019 Jun 24.

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611653PMC
June 2019

Text and data mining for biomedical discovery.

Pac Symp Biocomput 2013 ;2013:368-72

Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230431PMC
http://dx.doi.org/10.1142/9789814583220_0030DOI Listing
May 2019

Learning and Imputation for Mass-spec Bias Reduction (LIMBR).

Bioinformatics 2019 May;35(9):1518-1526

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499252PMC
May 2019

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease.

Cell Syst 2019 May;8(5):380-394.e4

Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Childhood Cancer Data Laboratory, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA; Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute of Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538307PMC
May 2019

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Dev Cell 2019 04 28;49(1):10-29. Epub 2019 Mar 28.

Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1016/j.devcel.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616346PMC
April 2019

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.

G3 (Bethesda) 2019 01 9;9(1):251-267. Epub 2019 Jan 9.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA

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http://dx.doi.org/10.1534/g3.118.200867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325913PMC
January 2019

Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics.

Pac Symp Biocomput 2019 ;24:362-373

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417816PMC
January 2019

Bayesian deep learning for single-cell analysis.

Nat Methods 2018 12;15(12):1009-1010

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://www.nature.com/articles/s41592-018-0230-9
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http://dx.doi.org/10.1038/s41592-018-0230-9DOI Listing
December 2018

A parasite's perspective on data sharing.

Gigascience 2018 11 1;7(11). Epub 2018 Nov 1.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, 3400 Civic Blvd SCTR 10-131, Philadelphia, PA 19104, United States.

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http://dx.doi.org/10.1093/gigascience/giy129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258825PMC
November 2018

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

Trends Genet 2018 10 22;34(10):790-805. Epub 2018 Aug 22.

Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309559PMC
October 2018

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders.

Pac Symp Biocomput 2018 ;23:80-91

Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728678PMC
August 2018

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.

Pac Symp Biocomput 2018 ;23:157-167

Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover 03784, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760988PMC
August 2018

Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay.

Crit Care Med 2018 07;46(7):1125-1132

Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.

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http://dx.doi.org/10.1097/CCM.0000000000003148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005735PMC
July 2018

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.

BioData Min 2018 3;11:14. Epub 2018 Jul 3.

1Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA.

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http://dx.doi.org/10.1186/s13040-018-0175-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029133PMC
July 2018

A Multimodal Strategy Used by a Large c-di-GMP Network.

J Bacteriol 2018 04 26;200(8). Epub 2018 Mar 26.

Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA

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http://dx.doi.org/10.1128/JB.00703-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869470PMC
April 2018

Sci-Hub provides access to nearly all scholarly literature.

Elife 2018 03 1;7. Epub 2018 Mar 1.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, United States.

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http://dx.doi.org/10.7554/eLife.32822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410PMC
March 2018

A Pilot Characterization of the Human Chronobiome.

Sci Rep 2017 12 7;7(1):17141. Epub 2017 Dec 7.

Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-017-17362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719427PMC
December 2017

Implicating candidate genes at GWAS signals by leveraging topologically associating domains.

Eur J Hum Genet 2017 11 9;25(11):1286-1289. Epub 2017 Aug 9.

Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1038/ejhg.2017.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643957PMC
November 2017

Machine Learning Analysis Identifies as an Important Learning and Memory Gene Required for Memory Retention and Social Learning.

G3 (Bethesda) 2017 11 6;7(11):3705-3718. Epub 2017 Nov 6.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755

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http://dx.doi.org/10.1534/g3.117.300172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677163PMC
November 2017

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

BMC Bioinformatics 2017 Nov 22;18(1):512. Epub 2017 Nov 22.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12859-017-1905-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700673PMC
November 2017

Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules.

Bioinformatics 2017 Oct;33(20):3250-3257

Department of BioHealth Informatics, Indiana University School of Informatics & Computing, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410887PMC
October 2017

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes.

Curr Epidemiol Rep 2017 Sep 10;4(3):211-220. Epub 2017 Jul 10.

Department of Public Health Sciences, University of Virginia, P.O. Box 800765, Charlottesville, Virginia, 22903.

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http://dx.doi.org/10.1007/s40471-017-0115-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718213PMC
September 2017

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Cell Syst 2017 07 12;5(1):63-71.e6. Epub 2017 Jul 12.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5532071PMC
July 2017

Data-Sharing Models

N Engl J Med 2017 06;376(23):2305

Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

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http://dx.doi.org/10.1056/NEJMc1705477DOI Listing
June 2017

Reproducibility of computational workflows is automated using continuous analysis.

Nat Biotechnol 2017 04 13;35(4):342-346. Epub 2017 Mar 13.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nbt.3780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103790PMC
April 2017

NO-BOUNDARY THINKING IN BIOINFORMATICS.

Pac Symp Biocomput 2017 ;22:646-648

Institute for Biomedical Informatics, University of Pennsylvania Philadelphia, PA 19104, USA,

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http://dx.doi.org/10.1142/9789813207813_0060DOI Listing
March 2017

Celebrating parasites.

Nat Genet 2017 03;49(4):483-484

Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.

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http://dx.doi.org/10.1038/ng.3830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710834PMC
March 2017

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma.

BMC Genomics 2017 02 6;18(1):127. Epub 2017 Feb 6.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s12864-017-3519-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292791PMC
February 2017

Tell me your neighbors, and I will tell you what you are.

Authors:
Casey S Greene

Sci Transl Med 2017 02;9(376)

Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Email:

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http://dx.doi.org/10.1126/scitranslmed.aam6058DOI Listing
February 2017

Semi-supervised learning of the electronic health record for phenotype stratification.

J Biomed Inform 2016 12 12;64:168-178. Epub 2016 Oct 12.

Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.10.007DOI Listing
December 2016

Cheap-seq.

Authors:
Casey S Greene

Sci Transl Med 2016 12;8(370):370ec203

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Email:

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http://stm.sciencemag.org/cgi/doi/10.1126/scitranslmed.aal37
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http://dx.doi.org/10.1126/scitranslmed.aal3701DOI Listing
December 2016

COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.

Pac Symp Biocomput 2016 ;21:557-67

Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA†To whom correspondence should be addressed.,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832978PMC
October 2016

Pathway and network-based strategies to translate genetic discoveries into effective therapies.

Hum Mol Genet 2016 Oct 23;25(R2):R94-R98. Epub 2016 Jun 23.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine Institute for Translational Medicine and Therapeutics, Perelman School of Medicine Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103 USA.

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http://dx.doi.org/10.1093/hmg/ddw160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036870PMC
October 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders.

Pac Symp Biocomput 2015 :132-43

Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299935PMC
April 2016

Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits.

Circ Cardiovasc Genet 2016 Apr;9(2):179-84

From the Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (C.S.G.); and Biological and Medical Informatics, University of California, San Francisco (D.S.H.).

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http://dx.doi.org/10.1161/CIRCGENETICS.115.001181DOI Listing
April 2016

Cross-platform normalization of microarray and RNA-seq data for machine learning applications.

PeerJ 2016 21;4:e1621. Epub 2016 Jan 21.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennslyvania, United States of America.

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http://dx.doi.org/10.7717/peerj.1621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736986PMC
February 2016

Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology.

BioData Min 2016 3;9. Epub 2016 Feb 3.

Department of Genetics, Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756 USA.

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http://dx.doi.org/10.1186/s13040-016-0085-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740998PMC
February 2016

Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts.

BioData Min 2016 19;9. Epub 2016 Jan 19.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire USA ; Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, New Hampshire USA ; Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire USA ; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvnia USA.

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http://dx.doi.org/10.1186/s13040-016-0082-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717572PMC
January 2016

ADAGE-Based Integration of Publicly Available Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions.

mSystems 2016 Jan-Feb;1(1). Epub 2016 Jan 19.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1128/mSystems.00025-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069748PMC
January 2016

Leveraging global gene expression patterns to predict expression of unmeasured genes.

BMC Genomics 2015 Dec 15;16:1065. Epub 2015 Dec 15.

Department of Epidemiology, Geisel School of Medicine at Dartmouth College, One Medical Center Drive, 7927 Rubin Building, Lebanon, NH, 03756, USA.

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http://dx.doi.org/10.1186/s12864-015-2250-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678722PMC
December 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

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

Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.

PLoS Comput Biol 2015 Jan 8;11(1):e1004005. Epub 2015 Jan 8.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hannover, New Hampshire, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288710PMC
January 2015

Big data bioinformatics.

J Cell Physiol 2014 Dec;229(12):1896-900

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire; Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire.

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http://dx.doi.org/10.1002/jcp.24662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604462PMC
December 2014

Computational genetics analysis of grey matter density in Alzheimer's disease.

BioData Min 2014 22;7:17. Epub 2014 Aug 22.

Department of Genetics, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, USA.

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http://dx.doi.org/10.1186/1756-0381-7-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145360PMC
August 2014

Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity.

Genome Med 2014 30;6(4):33. Epub 2014 Apr 30.

Department of Genetics, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA ; Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA.

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http://dx.doi.org/10.1186/gm550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062052PMC
June 2014

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

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

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

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

Evolving hard problems: Generating human genetics datasets with a complex etiology.

BioData Min 2011 Jul 7;4(1):21. Epub 2011 Jul 7.

Department of Genetics, Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA.

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http://dx.doi.org/10.1186/1756-0381-4-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154150PMC
July 2011

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

Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions.

BioData Min 2009 Sep 22;2(1). Epub 2009 Sep 22.

Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA.

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http://dx.doi.org/10.1186/1756-0381-2-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761303PMC
September 2009

Accelerating epistasis analysis in human genetics with consumer graphics hardware.

BMC Res Notes 2009 Jul 24;2:149. Epub 2009 Jul 24.

Computational Genetics Lab, Department of Genetics, Norris-Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA.

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http://dx.doi.org/10.1186/1756-0500-2-149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732631PMC
July 2009

Failure to replicate a genetic association may provide important clues about genetic architecture.

PLoS One 2009 Jun 2;4(6):e5639. Epub 2009 Jun 2.

Department of Genetics, Dartmouth College, Lebanon, New Hampshire, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685469PMC
June 2009

Ability of epistatic interactions of cytokine single-nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients.

Arthritis Rheum 2008 Jul;59(7):974-83

Referral Center for Systemic Autoimmune Diseases, IRCCS Fondazione Policlinico-Mangiagalli-Regina Elena and University of Milan, Milan, Italy.

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http://dx.doi.org/10.1002/art.23836DOI Listing
July 2008

LTR retrotransposon-gene associations in Drosophila melanogaster.

J Mol Evol 2006 Jan 11;62(1):111-20. Epub 2006 Jan 11.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1007/s00239-004-0312-4DOI Listing
January 2006