Christopher B Burge

Christopher B Burge

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Christopher B Burge

Publications by authors named "Christopher B Burge"

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Widespread PERK-dependent repression of ER targets in response to ER stress.

Sci Rep 2019 Mar 13;9(1):4330. Epub 2019 Mar 13.

Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel.

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http://dx.doi.org/10.1038/s41598-019-38705-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416471PMC
March 2019

Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain.

Cell Rep 2018 11;25(9):2447-2456.e4

Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.10.094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354779PMC
November 2018

Numerous recursive sites contribute to accuracy of splicing in long introns in flies.

PLoS Genet 2018 08 27;14(8):e1007588. Epub 2018 Aug 27.

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1007588
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http://dx.doi.org/10.1371/journal.pgen.1007588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110457PMC
August 2018

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

Mol Cell 2018 06 7;70(5):854-867.e9. Epub 2018 Jun 7.

Department of Biology, MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062212PMC
June 2018

The kinetics of pre-mRNA splicing in the genome and the influence of gene architecture.

Elife 2017 12 27;6. Epub 2017 Dec 27.

Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.

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http://dx.doi.org/10.7554/eLife.32537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762160PMC
December 2017

A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons.

Neuron 2017 Aug 20;95(3):608-622.e5. Epub 2017 Jul 20.

The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2017.06.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5616167PMC
August 2017

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Neuron 2016 Nov 20;92(4):780-795. Epub 2016 Oct 20.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore 138673, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2016.09.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123850PMC
November 2016

Identification of new branch points and unconventional introns in Saccharomyces cerevisiae.

RNA 2016 10 29;22(10):1522-34. Epub 2016 Jul 29.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029451PMC
http://dx.doi.org/10.1261/rna.057216.116DOI Listing
October 2016

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation.

Mol Cell 2016 10 6;64(2):294-306. Epub 2016 Oct 6.

Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.molcel.2016.08.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5107313PMC
October 2016

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

Cell Rep 2016 Apr 7;15(3):666-679. Epub 2016 Apr 7.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92037, USA; Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92037, USA; Molecular Engineering Laboratory, A(∗)STAR, Singapore 1190777, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 1190777, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.03.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839292PMC
April 2016

RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins.

Methods Enzymol 2015 12;558:465-493. Epub 2015 May 12.

Department of Biology, MIT, Cambridge Massachusetts, USA; Program in Computational and Systems Biology, MIT, Cambridge, Massachusetts, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2015.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576890PMC
March 2016

Distal Alternative Last Exons Localize mRNAs to Neural Projections.

Mol Cell 2016 Mar 18;61(6):821-33. Epub 2016 Feb 18.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.01.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798900PMC
March 2016

Meta-analysis of RNA-seq expression data across species, tissues and studies.

Genome Biol 2015 Dec 22;16:287. Epub 2015 Dec 22.

Department of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1186/s13059-015-0853-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699362PMC
December 2015

Genomic analysis of RNA localization.

RNA Biol 2014 ;11(8):1040-50

a Department of Biology; Massachusetts Institute of Technology ; Cambridge , MA USA.

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http://dx.doi.org/10.4161/rna.32146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615561PMC
August 2015

Quantitative visualization of alternative exon expression from RNA-seq data.

Bioinformatics 2015 Jul 22;31(14):2400-2. Epub 2015 Jan 22.

Department of Biology, MIT, Cambridge, MA, Department of Biological Engineering, MIT, Cambridge, MA.

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http://dx.doi.org/10.1093/bioinformatics/btv034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542614PMC
July 2015

Interactome analysis brings splicing into focus.

Genome Biol 2015 Jul 7;16:135. Epub 2015 Jul 7.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1186/s13059-015-0707-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493805PMC
July 2015

Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.

Genome Res 2015 Jun 16;25(6):858-71. Epub 2015 Apr 16.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA;

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http://dx.doi.org/10.1101/gr.184390.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448682PMC
June 2015

Origins and impacts of new mammalian exons.

Cell Rep 2015 Mar 19;10(12):1992-2005. Epub 2015 Mar 19.

Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.02.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715653PMC
March 2015

MicroRNA target finding by comparative genomics.

Methods Mol Biol 2014 ;1097:457-76

Institut Pasteur, Paris, France.

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http://dx.doi.org/10.1007/978-1-62703-709-9_21DOI Listing
November 2014

Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis.

Blood 2014 Jul 28;124(4):598-610. Epub 2014 May 28.

Whitehead Institute for Biomedical Research, Cambridge, MA; Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and.

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http://dx.doi.org/10.1182/blood-2013-12-542209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4110662PMC
July 2014

RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.

Mol Cell 2014 Jun 15;54(5):887-900. Epub 2014 May 15.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765140032
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http://dx.doi.org/10.1016/j.molcel.2014.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142047PMC
June 2014

Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock.

Cell Rep 2014 Jun 22;7(5):1362-1370. Epub 2014 May 22.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.04.044DOI Listing
June 2014

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.

Bioinformatics 2014 Jun;30(12):i113-20

Department of Information and Computer Science, Aalto University, FI-00076 Aalto, Finland, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, FinlandDepartment of Information and Computer Science, Aalto University, FI-00076 Aalto, Finland, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btu274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058923PMC
June 2014

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development.

Nat Commun 2014 Apr 22;5:3603. Epub 2014 Apr 22.

1] Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [3] Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms4603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018662PMC
April 2014

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts.

Genome Res 2013 Dec 26;23(12):2078-90. Epub 2013 Sep 26.

Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;

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http://dx.doi.org/10.1101/gr.156919.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847777PMC
December 2013

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay.

Genome Res 2013 Oct 13;23(10):1636-50. Epub 2013 Jun 13.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.157354.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787261PMC
October 2013

Promoter directionality is controlled by U1 snRNP and polyadenylation signals.

Nature 2013 Jul 23;499(7458):360-3. Epub 2013 Jun 23.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature12349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720719PMC
July 2013

SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase.

Cell 2013 May;153(4):855-68

State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.

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http://dx.doi.org/10.1016/j.cell.2013.04.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103662PMC
May 2013

Widespread regulation of translation by elongation pausing in heat shock.

Mol Cell 2013 Feb 3;49(3):439-52. Epub 2013 Jan 3.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.11.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570722PMC
February 2013

A complex network of factors with overlapping affinities represses splicing through intronic elements.

Nat Struct Mol Biol 2013 Jan 16;20(1):36-45. Epub 2012 Dec 16.

Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1038/nsmb.2459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537874PMC
January 2013

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

Science 2012 Dec;338(6114):1593-9

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1228186
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http://dx.doi.org/10.1126/science.1228186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568499PMC
December 2012

The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.

RNA 2012 May 28;18(5):1041-9. Epub 2012 Mar 28.

Molecular Biology Interdepartmental Graduate Program, University of California, Los Angeles, California 90095, USA.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.032912.112
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http://dx.doi.org/10.1261/rna.032912.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334691PMC
May 2012

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.

PLoS Biol 2012 Jan 3;10(1):e1001229. Epub 2012 Jan 3.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250501PMC
January 2012

Genome-wide impact of a recently expanded microRNA cluster in mouse.

Proc Natl Acad Sci U S A 2011 Sep 12;108(38):15804-9. Epub 2011 Sep 12.

MIT Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.1112772108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179086PMC
September 2011

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype.

PLoS Genet 2011 Aug 18;7(8):e1002218. Epub 2011 Aug 18.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158048PMC
August 2011

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.

Nat Biotechnol 2011 Jun 26;29(7):659-64. Epub 2011 Jun 26.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.1882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134637PMC
June 2011

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Nat Methods 2010 Dec 7;7(12):1009-15. Epub 2010 Nov 7.

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA

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http://www.nature.com/articles/nmeth.1528
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http://dx.doi.org/10.1038/nmeth.1528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037023PMC
December 2010

Global regulation of alternative splicing during myogenic differentiation.

Nucleic Acids Res 2010 Nov 15;38(21):7651-64. Epub 2010 Jul 15.

Department of Pathology and Immunology, Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkq614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995044PMC
November 2010

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.

PLoS Comput Biol 2009 Dec 11;5(12):e1000598. Epub 2009 Dec 11.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1000598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781110PMC
December 2009

Splice site strength-dependent activity and genetic buffering by poly-G runs.

Nat Struct Mol Biol 2009 Oct 13;16(10):1094-100. Epub 2009 Sep 13.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.nature.com/articles/nsmb.1661
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http://dx.doi.org/10.1038/nsmb.1661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766517PMC
October 2009

Biased chromatin signatures around polyadenylation sites and exons.

Mol Cell 2009 Oct;36(2):245-54

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10972765090074
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http://dx.doi.org/10.1016/j.molcel.2009.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786773PMC
October 2009

Most mammalian mRNAs are conserved targets of microRNAs.

Genome Res 2009 Jan 27;19(1):92-105. Epub 2008 Oct 27.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.082701.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612969PMC
January 2009

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart.

Proc Natl Acad Sci U S A 2008 Dec 15;105(51):20333-8. Epub 2008 Dec 15.

Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.0809045105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629332PMC
December 2008

Alternative isoform regulation in human tissue transcriptomes.

Nature 2008 Nov;456(7221):470-6

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature07509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593745PMC
November 2008

Ab initio identification of functionally interacting pairs of cis-regulatory elements.

Genome Res 2008 Oct 17;18(10):1643-51. Epub 2008 Sep 17.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.080085.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556269PMC
October 2008

Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites.

Science 2008 Jun;320(5883):1643-7

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.1155390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587246PMC
June 2008

Splicing regulation: from a parts list of regulatory elements to an integrated splicing code.

RNA 2008 May 27;14(5):802-13. Epub 2008 Mar 27.

Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://www.rnajournal.org/cgi/doi/10.1261/rna.876308
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http://dx.doi.org/10.1261/rna.876308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2327353PMC
May 2008

Identification of let-7-regulated oncofetal genes.

Cancer Res 2008 Apr;68(8):2587-91

The Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-08-0264DOI Listing
April 2008

Coevolutionary networks of splicing cis-regulatory elements.

Proc Natl Acad Sci U S A 2007 Nov 12;104(47):18583-8. Epub 2007 Nov 12.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0707349104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2141820PMC
November 2007

Dynamic regulation of miRNA expression in ordered stages of cellular development.

Genes Dev 2007 Mar;21(5):578-89

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gad.1522907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820899PMC
March 2007

Detection of broadly expressed neuronal genes in C. elegans.

Dev Biol 2007 Feb 15;302(2):617-26. Epub 2006 Sep 15.

Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, 185 Cambridge Street, Simches 7, Boston, MA 02114, USA.

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http://dx.doi.org/10.1016/j.ydbio.2006.09.014DOI Listing
February 2007

Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia.

Hum Mutat 2007 Jan;28(1):41-53

Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1002/humu.20401DOI Listing
January 2007

Inference of splicing regulatory activities by sequence neighborhood analysis.

PLoS Genet 2006 Nov 28;2(11):e191. Epub 2006 Sep 28.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1657047PMC
November 2006

General and specific functions of exonic splicing silencers in splicing control.

Mol Cell 2006 Jul 22;23(1):61-70. Epub 2006 Jun 22.

Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA.

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http://dx.doi.org/10.1016/j.molcel.2006.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839040PMC
July 2006

Untangling influences of hydrophobicity on protein sequences and structures.

Proteins 2006 Mar;62(4):1101-6

Department of Pathology, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1002/prot.20775DOI Listing
March 2006

HOLLYWOOD: a comparative relational database of alternative splicing.

Nucleic Acids Res 2006 Jan;34(Database issue):D56-62

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02319, USA.

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http://dx.doi.org/10.1093/nar/gkj048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347411PMC
January 2006

Gene structure prediction using an orthologous gene of known exon-intron structure.

Appl Bioinformatics 2004 ;3(2-3):81-90

Computer Science and Artificial Intelligence Laboratory, 32-G438, Spoken Language Systems Group, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.

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December 2005

The widespread impact of mammalian MicroRNAs on mRNA repression and evolution.

Science 2005 Dec 24;310(5755):1817-21. Epub 2005 Nov 24.

Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.

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December 2005

A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

Proc Natl Acad Sci U S A 2005 Sep 24;102(36):12932-7. Epub 2005 Aug 24.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.0506174102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1200305PMC
September 2005

Variation in alternative splicing across human tissues.

Genome Biol 2004 13;5(10):R74. Epub 2004 Sep 13.

Department of Biology, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA.

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http://dx.doi.org/10.1186/gb-2004-5-10-r74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545594PMC
July 2005

Recognition of unknown conserved alternatively spliced exons.

PLoS Comput Biol 2005 Jul 8;1(2):113-22. Epub 2005 Jul 8.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0010015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185642PMC
July 2005

A combinatorial code for splicing silencing: UAGG and GGGG motifs.

PLoS Biol 2005 May 19;3(5):e158. Epub 2005 Apr 19.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pbio.0030158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1079783PMC
May 2005

Identification and analysis of alternative splicing events conserved in human and mouse.

Proc Natl Acad Sci U S A 2005 Feb 11;102(8):2850-5. Epub 2005 Feb 11.

Department of Biology and Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA.

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http://dx.doi.org/10.1073/pnas.0409742102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548664PMC
February 2005

Patterns of intron gain and loss in fungi.

PLoS Biol 2004 Dec 30;2(12):e422. Epub 2004 Nov 30.

Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pbio.0020422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532390PMC
December 2004

Systematic identification and analysis of exonic splicing silencers.

Cell 2004 Dec;119(6):831-45

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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December 2004

Variation in sequence and organization of splicing regulatory elements in vertebrate genes.

Proc Natl Acad Sci U S A 2004 Nov 25;101(44):15700-5. Epub 2004 Oct 25.

Departments of Biology and Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue 68-223, Cambridge, MA 02139-4307, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524216PMC
November 2004

Single nucleotide polymorphism-based validation of exonic splicing enhancers.

PLoS Biol 2004 Sep 31;2(9):E268. Epub 2004 Aug 31.

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pbio.0020268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514884PMC
September 2004

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.

J Comput Biol 2004 ;11(2-3):377-94

Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68-223, Cambridge, MA 02319, USA.

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http://dx.doi.org/10.1089/1066527041410418DOI Listing
August 2004

RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W187-90

Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gkh393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441531PMC
July 2004

DNA sequence evolution with neighbor-dependent mutation.

J Comput Biol 2003 ;10(3-4):313-22

Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1089/10665270360688039DOI Listing
March 2004

Prediction of mammalian microRNA targets.

Cell 2003 Dec;115(7):787-98

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/s0092-8674(03)01018-3DOI Listing
December 2003

Widespread selection for local RNA secondary structure in coding regions of bacterial genes.

Genome Res 2003 Sep;13(9):2042-51

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.1257503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403678PMC
September 2003

The microRNAs of Caenorhabditis elegans.

Genes Dev 2003 Apr 2;17(8):991-1008. Epub 2003 Apr 2.

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.

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http://dx.doi.org/10.1101/gad.1074403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196042PMC
April 2003

Vertebrate microRNA genes.

Science 2003 Mar;299(5612):1540

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.1080372DOI Listing
March 2003

Predictive identification of exonic splicing enhancers in human genes.

Science 2002 Aug 11;297(5583):1007-13. Epub 2002 Jul 11.

Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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August 2002

Prediction of plant microRNA targets.

Cell 2002 Aug;110(4):513-20

Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA.

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August 2002