Mark B Gerstein

Mark B Gerstein

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Mark B Gerstein

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A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.

Neuron 2019 Sep 11;103(5):785-801.e8. Epub 2019 Jul 11.

Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08966273193056
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http://dx.doi.org/10.1016/j.neuron.2019.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6831089PMC
September 2019

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures.

Proc Natl Acad Sci U S A 2019 Sep 28;116(38):18962-18970. Epub 2019 Aug 28.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520;

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http://dx.doi.org/10.1073/pnas.1901156116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754584PMC
September 2019

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.

PLoS Comput Biol 2019 Aug 19;15(8):e1007293. Epub 2019 Aug 19.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715295PMC
August 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Next-Generation Sequencing to Diagnose Suspected Genetic Disorders.

N Engl J Med 2019 01;380(2):200

Yale University, New Haven, CT

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http://dx.doi.org/10.1056/NEJMc1814955DOI Listing
January 2019

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

J Proteome Res 2018 10 6;17(10):3431-3444. Epub 2018 Sep 6.

Department of Psychiatry , Yale School of Medicine, Connecticut Mental Health Center , 34 Park Street , New Haven , Connecticut 06519 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392456PMC
October 2018

Gene names can confound most-searched listings.

Nature 2018 01;553(7689):405

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http://dx.doi.org/10.1038/d41586-018-01077-3DOI Listing
January 2018

A multiregional proteomic survey of the postnatal human brain.

Nat Neurosci 2017 Dec 13;20(12):1787-1795. Epub 2017 Nov 13.

Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1038/s41593-017-0011-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894337PMC
December 2017

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.

Genome Res 2017 07 5;27(7):1184-1194. Epub 2017 Apr 5.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.215954.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495070PMC
July 2017

Landscape and variation of novel retroduplications in 26 human populations.

PLoS Comput Biol 2017 Jun 29;13(6):e1005567. Epub 2017 Jun 29.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510864PMC
June 2017

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.

PLoS Genet 2017 03 30;13(3):e1006685. Epub 2017 Mar 30.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391127PMC
March 2017

Understanding genome structural variations.

Oncotarget 2016 Feb;7(7):7370-1

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.18632/oncotarget.6485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884923PMC
February 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.

Mol Cell 2015 Sep;59(5):858-66

Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560836PMC
September 2015

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Nat Commun 2015 Jun 1;6:7256. Epub 2015 Jun 1.

1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/ncomms8256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451611PMC
June 2015

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Bioinformatics 2015 May 17;31(9):1469-71. Epub 2014 Dec 17.

Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410653PMC
May 2015

Loregic: a method to characterize the cooperative logic of regulatory factors.

PLoS Comput Biol 2015 Apr 17;11(4):e1004132. Epub 2015 Apr 17.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America; Department of Computer Science, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401777PMC
April 2015

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Plant J 2014 Dec 21;80(5):848-61. Epub 2014 Oct 21.

MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.

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http://dx.doi.org/10.1111/tpj.12679DOI Listing
December 2014

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Nat Neurosci 2014 Nov 28;17(11):1491-9. Epub 2014 Oct 28.

Division of Molecular Psychiatry, Abraham Ribicoff Research Facilities, Connecticut Mental Health Center, Yale University School of Medicine, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.3829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737617PMC
November 2014

Comparative analysis of pseudogenes across three phyla.

Proc Natl Acad Sci U S A 2014 Sep 25;111(37):13361-6. Epub 2014 Aug 25.

Program in Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Department of Computer Science, Yale University, New Haven, CT 06511

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http://dx.doi.org/10.1073/pnas.1407293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169933PMC
September 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Transcriptional landscape of the prenatal human brain.

Nature 2014 Apr 2;508(7495):199-206. Epub 2014 Apr 2.

Allen Institute for Brain Science, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1038/nature13185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105188PMC
April 2014

Novel insights through the integration of structural and functional genomics data with protein networks.

J Struct Biol 2012 Sep 11;179(3):320-6. Epub 2012 Feb 11.

Department of Chemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.jsb.2012.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830681PMC
September 2012

The GENCODE pseudogene resource.

Genome Biol 2012 Sep 26;13(9):R51. Epub 2012 Sep 26.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395PMC
September 2012

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Genome Res 2012 Jun 15;22(6):1069-80. Epub 2012 Mar 15.

Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1101/gr.129817.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371702PMC
June 2012

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.

Genome Biol 2011 31;12(3):R32. Epub 2011 Mar 31.

Department of Genetics, 77 Ave. of Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-r32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129682PMC
January 2012

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.

Genome Biol 2011 Nov 7;12(11):R111. Epub 2011 Nov 7.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2011-12-11-r111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334597PMC
November 2011

Predicting protein ligand binding motions with the conformation explorer.

BMC Bioinformatics 2011 Oct 27;12:417. Epub 2011 Oct 27.

Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1186/1471-2105-12-417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354956PMC
October 2011

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

Nucleic Acids Res 2011 Sep 19;39(16):7058-76. Epub 2011 May 19.

Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520, USA.

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http://nar.oxfordjournals.org/content/early/2011/05/19/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkr342
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http://dx.doi.org/10.1093/nar/gkr342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167619PMC
September 2011

The real cost of sequencing: higher than you think!

Genome Biol 2011 Aug 25;12(8):125. Epub 2011 Aug 25.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2011-12-8-125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245608PMC
August 2011

Measuring the evolutionary rewiring of biological networks.

PLoS Comput Biol 2011 Jan 6;7(1):e1001050. Epub 2011 Jan 6.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017101PMC
January 2011

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

Segmental duplications in the human genome reveal details of pseudogene formation.

Nucleic Acids Res 2010 Nov 8;38(20):6997-7007. Epub 2010 Jul 8.

Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/nar/gkq587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978362PMC
November 2010

Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators.

Sci Signal 2010 Nov 2;3(146):ra79. Epub 2010 Nov 2.

Program in Computational Biology and Bioinformatics, Yale University, Bass 426, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/scisignal.2001014DOI Listing
November 2010

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.

BMC Bioinformatics 2010 Oct 31;11:539. Epub 2010 Oct 31.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1186/1471-2105-11-539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992546PMC
October 2010

Annotating non-coding regions of the genome.

Nat Rev Genet 2010 Aug 13;11(8):559-71. Epub 2010 Jul 13.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/nrg2814DOI Listing
August 2010

Structured digital tables on the Semantic Web: toward a structured digital literature.

Mol Syst Biol 2010 Aug;6:403

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1038/msb.2010.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950080PMC
August 2010

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.

Genome Res 2010 Jul 29;20(7):960-71. Epub 2010 Apr 29.

Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.102814.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892097PMC
July 2010

MOTIPS: automated motif analysis for predicting targets of modular protein domains.

BMC Bioinformatics 2010 May 11;11:243. Epub 2010 May 11.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/1471-2105-11-243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882932PMC
May 2010

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.

PLoS Comput Biol 2010 May 27;6(5):e1000755. Epub 2010 May 27.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877725PMC
May 2010

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.

Proc Natl Acad Sci U S A 2010 Apr 29;107(15):6841-6. Epub 2010 Mar 29.

Program in Computational Biology and Bioinformatics, Yale University, Bass 426, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1073/pnas.0910867107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872381PMC
April 2010

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.

PLoS Comput Biol 2010 Apr 1;6(4):e1000730. Epub 2010 Apr 1.

Section of Genetic Medicine and Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1000730
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http://dx.doi.org/10.1371/journal.pcbi.1000730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848541PMC
April 2010

Getting started in gene orthology and functional analysis.

PLoS Comput Biol 2010 Mar 26;6(3):e1000703. Epub 2010 Mar 26.

Department of Molecular Biophysics and Biophysics, Medical School, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845645PMC
March 2010

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Nat Biotechnol 2010 Jan 27;28(1):47-55. Epub 2009 Dec 27.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://www.nature.com/articles/nbt.1600
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http://dx.doi.org/10.1038/nbt.1600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951730PMC
January 2010

Computational analysis of membrane proteins: the largest class of drug targets.

Drug Discov Today 2009 Dec 3;14(23-24):1130-5. Epub 2009 Sep 3.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

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http://dx.doi.org/10.1016/j.drudis.2009.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796609PMC
December 2009

Robust-linear-model normalization to reduce technical variability in functional protein microarrays.

J Proteome Res 2009 Dec;8(12):5451-64

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1021/pr900412kDOI Listing
December 2009

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

PLoS Comput Biol 2009 Jul 10;5(7):e1000432. Epub 2009 Jul 10.

Department of Computer Science, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700963PMC
July 2009

Understanding modularity in molecular networks requires dynamics.

Sci Signal 2009 Jul 28;2(81):pe44. Epub 2009 Jul 28.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/scisignal.281pe44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243459PMC
July 2009

Small RNAs originated from pseudogenes: cis- or trans-acting?

PLoS Comput Biol 2009 Jul 31;5(7):e1000449. Epub 2009 Jul 31.

Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Albert Einstein College of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708354PMC
July 2009

Getting started in text mining: part two.

PLoS Comput Biol 2009 Jul 31;5(7):e1000411. Epub 2009 Jul 31.

University of Chicago, Chicago, Illinois, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1000411
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http://dx.doi.org/10.1371/journal.pcbi.1000411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709911PMC
July 2009

Dynamic and complex transcription factor binding during an inducible response in yeast.

Genes Dev 2009 Jun;23(11):1351-63

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gad.1781909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701586PMC
June 2009

Integrated assessment of genomic correlates of protein evolutionary rate.

PLoS Comput Biol 2009 Jun 12;5(6):e1000413. Epub 2009 Jun 12.

Bioinformatics Program, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688033PMC
June 2009

Quantifying environmental adaptation of metabolic pathways in metagenomics.

Proc Natl Acad Sci U S A 2009 Feb 22;106(5):1374-9. Epub 2009 Jan 22.

Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry, Computer Science, and Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1073/pnas.0808022106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629784PMC
February 2009

StoneHinge: hinge prediction by network analysis of individual protein structures.

Protein Sci 2009 Feb;18(2):359-71

Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1002/pro.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708048PMC
February 2009

Pseudofam: the pseudogene families database.

Nucleic Acids Res 2009 Jan 28;37(Database issue):D738-43. Epub 2008 Oct 28.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/nar/gkn758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686518PMC
January 2009

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Nat Biotechnol 2009 Jan 4;27(1):66-75. Epub 2009 Jan 4.

Molecular Biophysics & Biochemistry Dept., Yale University, PO Box 208114, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1038/nbt.1518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924752PMC
January 2009