Mark Gerstein

Mark Gerstein

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Mark Gerstein

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Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.

Structure 2019 Sep 3;27(9):1469-1481.e3. Epub 2019 Jul 3.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.06.001DOI Listing
September 2019

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
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

Pollen-derived RNAs Are Found in the Human Circulation.

iScience 2019 Sep 24;19:916-926. Epub 2019 Aug 24.

Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, 368 Plantation St., AS7-1051, Worcester, MA 01605, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S25890042193031
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http://dx.doi.org/10.1016/j.isci.2019.08.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742912PMC
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

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.

PLoS Genet 2019 Aug 30;15(8):e1007860. Epub 2019 Aug 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.1007860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742416PMC
August 2019

Genomics and data science: an application within an umbrella.

Genome Biol 2019 05 29;20(1):109. Epub 2019 May 29.

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/10.1186/s13059-019-1724-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540394PMC
May 2019

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Cell Syst 2019 Apr 4;8(4):352-357.e3. Epub 2019 Apr 4.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.03.004DOI Listing
April 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

MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis.

Nat Cell Biol 2019 03 11;21(3):348-358. Epub 2019 Feb 11.

Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1038/s41556-019-0272-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528464PMC
March 2019

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing.

Brief Bioinform 2019 Mar 20. Epub 2019 Mar 20.

Department of Biomedical Engineering.

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http://dx.doi.org/10.1093/bib/bbz030DOI Listing
March 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

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Nat Biotechnol 2018 07;36(7):566-569

Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

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http://dx.doi.org/10.1038/nbt.4163DOI Listing
July 2018

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.

Nat Commun 2018 06 22;9(1):2453. Epub 2018 Jun 22.

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

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http://dx.doi.org/10.1038/s41467-018-04875-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015012PMC
June 2018

A comprehensive catalog of predicted functional upstream open reading frames in humans.

Nucleic Acids Res 2018 04;46(7):3326-3338

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

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http://dx.doi.org/10.1093/nar/gky188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283423PMC
April 2018

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Bioinformatics 2018 01;34(1):1-8

Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859991PMC
January 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

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.

Nat Genet 2017 Oct 4;49(10):1428-1436. Epub 2017 Sep 4.

Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.

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http://dx.doi.org/10.1038/ng.3950DOI Listing
October 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

Cancer genomics: Less is more in the hunt for driver mutations.

Nature 2017 07 28;547(7661):40-41. Epub 2017 Jun 28.

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

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http://dx.doi.org/10.1038/nature23085DOI Listing
July 2017

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

PLoS Comput Biol 2017 Jul 24;13(7):e1005647. Epub 2017 Jul 24.

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

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http://dx.doi.org/10.1371/journal.pcbi.1005647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546724PMC
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

Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.

Curr Protoc Bioinformatics 2017 05 2;57:15.11.1-15.11.17. Epub 2017 May 2.

Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York.

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http://dx.doi.org/10.1002/cpbi.23DOI Listing
May 2017

Stroke and Circulating Extracellular RNAs.

Stroke 2017 04 13;48(4):828-834. Epub 2017 Mar 13.

From the Department of Quantitative Health Sciences (E.M.) and Department of Medicine (K.T., J.E.F.), University of Massachusetts Medical School, Worcester; Department of Cardiology, Massachusetts General Hospital, Boston (R.S.); Department of Cardiology, University of Michigan, Ann Arbor (V.M.); Yale University Medical School, Computational Biology, New Haven, CT (M.G., J.R., R.K.); The NHLBI's and Boston University's Framingham Heart Study, MA (M.G.L.); Biostatistics Department, Boston University School of Public Health, MA (M.G.L.); and The Framingham Heart Study, Population Sciences Branch, NHLBI, Bethesda, MD (D.L.).

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http://dx.doi.org/10.1161/STROKEAHA.116.015140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373984PMC
April 2017

Structuring supplemental materials in support of reproducibility.

Genome Biol 2017 04 5;18(1):64. Epub 2017 Apr 5.

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

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http://dx.doi.org/10.1186/s13059-017-1205-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382465PMC
April 2017

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.

Dev Cell 2017 03;40(6):552-565.e5

Section of Cardiology, Department of Internal Medicine, Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404386PMC
March 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

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

PLoS One 2016 28;11(4):e0153691. Epub 2016 Apr 28.

University of Massachusetts Medical School, Department of Medicine, Division of Cardiovascular Medicine, Worcester, MA, 01605, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849639PMC
February 2017

Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats.

J Mol Biol 2017 02 7;429(3):435-445. Epub 2016 Dec 7.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420328PMC
February 2017

Localized structural frustration for evaluating the impact of sequence variants.

Nucleic Acids Res 2016 12 18;44(21):10062-10073. Epub 2016 Oct 18.

Program in Computational Biology and Bioinformatics, Yale University, 260/266 Whitney Avenue PO Box 208114, New Haven, CT 06520, USA

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http://dx.doi.org/10.1093/nar/gkw927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137452PMC
December 2016

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.

PLoS Comput Biol 2016 Oct 19;12(10):e1005146. Epub 2016 Oct 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.1005146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5070849PMC
October 2016

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

BMC Genomics 2016 08 12;17(1):632. Epub 2016 Aug 12.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.

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http://dx.doi.org/10.1186/s12864-016-2963-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983039PMC
August 2016

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

Plant J 2016 06;86(6):472-80

Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.

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http://dx.doi.org/10.1111/tpj.13175DOI Listing
June 2016

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Trends Genet 2016 05 20;32(5):251-253. Epub 2016 Mar 20.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.02.006DOI Listing
May 2016

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.

Structure 2016 05 7;24(5):826-837. Epub 2016 Apr 7.

Program in Computational Biology and Bioinformatics, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA; Department of Computer Science, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA. Electronic address:

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http://www.cell.com/structure/pdf/S0969-2126(16)00086-1.pdf
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http://dx.doi.org/10.1016/j.str.2016.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883016PMC
May 2016

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Nat Commun 2016 Apr 18;7:11101. Epub 2016 Apr 18.

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

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http://dx.doi.org/10.1038/ncomms11101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837449PMC
April 2016

Quantification of private information leakage from phenotype-genotype data: linking attacks.

Nat Methods 2016 Mar 1;13(3):251-6. Epub 2016 Feb 1.

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

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http://www.nature.com/articles/nmeth.3746
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http://dx.doi.org/10.1038/nmeth.3746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834871PMC
March 2016

The real cost of sequencing: scaling computation to keep pace with data generation.

Genome Biol 2016 Mar 23;17:53. Epub 2016 Mar 23.

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

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http://dx.doi.org/10.1186/s13059-016-0917-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806511PMC
March 2016

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.

Cell Syst 2016 Mar;2(3):147-157

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

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http://dx.doi.org/10.1016/j.cels.2016.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817108PMC
March 2016

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

Role of non-coding sequence variants in cancer.

Nat Rev Genet 2016 Feb 19;17(2):93-108. Epub 2016 Jan 19.

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

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http://www.nature.com/articles/nrg.2015.17
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http://dx.doi.org/10.1038/nrg.2015.17DOI Listing
February 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

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

Reads meet rotamers: structural biology in the age of deep sequencing.

Curr Opin Struct Biol 2015 Dec 1;35:125-34. Epub 2015 Dec 1.

Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2015.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751031PMC
December 2015

High-order neural networks and kernel methods for peptide-MHC binding prediction.

Bioinformatics 2015 Nov 23;31(22):3600-7. Epub 2015 Jul 23.

Program of Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry and Department of Computer Science, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv371DOI Listing
November 2015

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Genome Biol 2014 ;15(10):480

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

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http://dx.doi.org/10.1186/s13059-014-0480-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203974PMC
October 2015

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

Genome Biol 2014 ;15(10):474

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

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http://dx.doi.org/10.1186/s13059-014-0474-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234855PMC
October 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

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

Nucleic Acids Res 2015 Sep 24;43(17):8123-34. Epub 2015 Aug 24.

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

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787796PMC
September 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

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.

Cell 2015 Jul;162(2):375-390

Program in Neurodevelopment and Regeneration, Yale University, New Haven, CT 06520, USA; Child Study Center, Yale University, New Haven, CT 06520, USA; Department of Neurobiology, Yale University, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519016PMC
July 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

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.

Genome Biol 2015 Mar 31;16:63. Epub 2015 Mar 31.

Program in Computational Biology and Bioinformatics, Yale University, 260 Whitney Avenue, New Haven, CT, 06520, USA.

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http://dx.doi.org/10.1186/s13059-015-0624-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404648PMC
March 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