Publications by authors named "Mark Gerstein"

100Publications

Transcriptional activity and strain-specific history of mouse pseudogenes.

Nat Commun 2020 Jul 29;11(1):3695. Epub 2020 Jul 29.

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

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http://dx.doi.org/10.1038/s41467-020-17157-wDOI Listing
July 2020

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.

Genome Biol 2020 Jul 30;21(1):151. Epub 2020 Jul 30.

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

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http://dx.doi.org/10.1186/s13059-020-01979-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391703PMC
July 2020

FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data.

Bioinformatics 2020 Jul 29. Epub 2020 Jul 29.

Computational Biology and Bioinformatics, Yale University, New Haven, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa661DOI Listing
July 2020

Using blockchain to log genome dataset access: efficient storage and query.

BMC Med Genomics 2020 Jul 21;13(Suppl 7):78. Epub 2020 Jul 21.

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

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http://dx.doi.org/10.1186/s12920-020-0716-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372787PMC
July 2020

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.

Nat Commun 2020 Jul 17;11(1):3575. Epub 2020 Jul 17.

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

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http://dx.doi.org/10.1038/s41467-020-17388-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368050PMC
July 2020

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring.

BMC Bioinformatics 2020 Jul 2;21(1):281. Epub 2020 Jul 2.

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

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http://dx.doi.org/10.1186/s12859-020-03605-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333332PMC
July 2020

Epigenome-based splicing prediction using a recurrent neural network.

PLoS Comput Biol 2020 06 25;16(6):e1008006. Epub 2020 Jun 25.

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.1008006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343189PMC
June 2020

Origins and characterization of variants shared between databases of somatic and germline human mutations.

BMC Bioinformatics 2020 Jun 4;21(1):227. Epub 2020 Jun 4.

Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA.

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http://dx.doi.org/10.1186/s12859-020-3508-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273669PMC
June 2020

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts.

BMC Med Genomics 2020 Jun 1;13(1):74. Epub 2020 Jun 1.

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

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http://dx.doi.org/10.1186/s12920-020-00732-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268467PMC
June 2020

The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.

BMC Bioinformatics 2020 May 29;21(1):222. Epub 2020 May 29.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA.

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http://dx.doi.org/10.1186/s12859-020-03545-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260828PMC
May 2020

Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer.

Cancer 2020 Aug 15;126(16):3657-3666. Epub 2020 May 15.

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

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http://dx.doi.org/10.1002/cncr.32914DOI Listing
August 2020

Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair.

Cell Stem Cell 2020 Jun 16;26(6):880-895.e6. Epub 2020 Apr 16.

Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Dermatology, Yale University, New Haven, CT 06511, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2020.03.013DOI Listing
June 2020

Comparing Technological Development and Biological Evolution from a Network Perspective.

Cell Syst 2020 Mar;10(3):219-222

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

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http://dx.doi.org/10.1016/j.cels.2020.02.004DOI Listing
March 2020

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Cell 2020 03 20;180(5):915-927.e16. Epub 2020 Feb 20.

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 06511, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210002PMC
March 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

Estimating growth patterns and driver effects in tumor evolution from individual samples.

Nat Commun 2020 02 5;11(1):732. Epub 2020 Feb 5.

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

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http://dx.doi.org/10.1038/s41467-020-14407-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002450PMC
February 2020

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

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

PLoS Genet 2019 08 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

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

Proc Natl Acad Sci U S A 2019 09 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 08 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

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

Neuron 2019 09 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

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

Structure 2019 09 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

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

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

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Cell Syst 2019 04 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079576PMC
April 2019

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

Brief Bioinform 2020 May;21(3):836-850

Department of Biomedical Engineering.

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http://dx.doi.org/10.1093/bib/bbz030DOI Listing
May 2020

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

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6870991PMC
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

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

Gene names can confound most-searched listings.

Nature 2018 Jan;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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834871PMC
March 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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February 2016

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