William Fairbrother

William Fairbrother

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William Fairbrother

William Fairbrother

Publications by authors named "William Fairbrother"

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Future directions for high-throughput splicing assays in precision medicine.

Hum Mutat 2019 Sep 17;40(9):1225-1234. Epub 2019 Aug 17.

Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.

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http://dx.doi.org/10.1002/humu.23866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744296PMC
September 2019

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing.

Genome Biol 2019 03 1;20(1):48. Epub 2019 Mar 1.

Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany.

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http://dx.doi.org/10.1186/s13059-019-1653-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396468PMC
March 2019

ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data.

Quant Biol 2018 Sep 25;6(3):267-274. Epub 2018 Jul 25.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1007/s40484-018-0141-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688498PMC
September 2018

Hereditary cancer genes are highly susceptible to splicing mutations.

PLoS Genet 2018 03 5;14(3):e1007231. Epub 2018 Mar 5.

Molecular and Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854443PMC
March 2018

Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection.

Cell 2018 02;172(5):952-965.e18

St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA; Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris 75015, France.

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http://dx.doi.org/10.1016/j.cell.2018.02.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886375PMC
February 2018

Defective splicing of the RB1 transcript is the dominant cause of retinoblastomas.

Hum Genet 2017 09 5;136(9):1303-1312. Epub 2017 Aug 5.

Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1007/s00439-017-1833-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699175PMC
September 2017

Spliceman2: a computational web server that predicts defects in pre-mRNA splicing.

Bioinformatics 2017 Sep;33(18):2943-2945

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870721PMC
September 2017

Widespread intra-dependencies in the removal of introns from human transcripts.

Nucleic Acids Res 2017 Sep;45(16):9503-9513

Department of Molecular and Cellular Biology, Brown University, Providence, RI 02903, USA.

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http://dx.doi.org/10.1093/nar/gkx661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766209PMC
September 2017

The effects of structure on pre-mRNA processing and stability.

Methods 2017 08 6;125:36-44. Epub 2017 Jun 6.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737760PMC
August 2017

Pathogenic variants that alter protein code often disrupt splicing.

Nat Genet 2017 Jun 17;49(6):848-855. Epub 2017 Apr 17.

Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA.

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http://dx.doi.org/10.1038/ng.3837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679692PMC
June 2017

Large-scale analysis of branchpoint usage across species and cell lines.

Genome Res 2017 04 24;27(4):639-649. Epub 2017 Jan 24.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1101/gr.202820.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378181PMC
April 2017

Soluble programmed cell death receptor-1 (sPD-1): a potential biomarker with anti-inflammatory properties in human and experimental acute respiratory distress syndrome (ARDS).

J Transl Med 2016 11 11;14(1):312. Epub 2016 Nov 11.

Division of Surgical Research, Department of Surgery, Alpert School of Medicine at Brown University and Rhode Island Hospital, 593 Eddy Street, Providence, RI, 02903, USA.

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http://dx.doi.org/10.1186/s12967-016-1071-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106799PMC
November 2016

RNA structure in splicing: An evolutionary perspective.

RNA Biol 2016 09 25;13(9):766-71. Epub 2016 Jul 25.

a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA.

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http://dx.doi.org/10.1080/15476286.2016.1208893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014005PMC
September 2016

RNA structure replaces the need for U2AF2 in splicing.

Genome Res 2016 Jan 13;26(1):12-23. Epub 2015 Nov 13.

Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA;

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http://dx.doi.org/10.1101/gr.181008.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691745PMC
January 2016

RNA-Binding Proteins: Splicing Factors and Disease.

Biomolecules 2015 May 13;5(2):893-909. Epub 2015 May 13.

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.

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http://dx.doi.org/10.3390/biom5020893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496701PMC
May 2015

Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms.

Adv Exp Med Biol 2014 ;825:227-66

Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1007/978-1-4939-1221-6_7DOI Listing
December 2014

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Authors:
Catherine A Brownstein Alan H Beggs Nils Homer Barry Merriman Timothy W Yu Katherine C Flannery Elizabeth T DeChene Meghan C Towne Sarah K Savage Emily N Price Ingrid A Holm Lovelace J Luquette Elaine Lyon Joseph Majzoub Peter Neupert David McCallie Peter Szolovits Huntington F Willard Nancy J Mendelsohn Renee Temme Richard S Finkel Sabrina W Yum Livija Medne Shamil R Sunyaev Ivan Adzhubey Christopher A Cassa Paul I W de Bakker Hatice Duzkale Piotr Dworzyński William Fairbrother Laurent Francioli Birgit H Funke Monica A Giovanni Robert E Handsaker Kasper Lage Matthew S Lebo Monkol Lek Ignaty Leshchiner Daniel G MacArthur Heather M McLaughlin Michael F Murray Tune H Pers Paz P Polak Soumya Raychaudhuri Heidi L Rehm Rachel Soemedi Nathan O Stitziel Sara Vestecka Jochen Supper Claudia Gugenmus Bernward Klocke Alexander Hahn Max Schubach Mortiz Menzel Saskia Biskup Peter Freisinger Mario Deng Martin Braun Sven Perner Richard J H Smith Janeen L Andorf Jian Huang Kelli Ryckman Val C Sheffield Edwin M Stone Thomas Bair E Ann Black-Ziegelbein Terry A Braun Benjamin Darbro Adam P DeLuca Diana L Kolbe Todd E Scheetz Aiden E Shearer Rama Sompallae Kai Wang Alexander G Bassuk Erik Edens Katherine Mathews Steven A Moore Oleg A Shchelochkov Pamela Trapane Aaron Bossler Colleen A Campbell Jonathan W Heusel Anne Kwitek Tara Maga Karin Panzer Thomas Wassink Douglas Van Daele Hela Azaiez Kevin Booth Nic Meyer Michael M Segal Marc S Williams Gerard Tromp Peter White Donald Corsmeier Sara Fitzgerald-Butt Gail Herman Devon Lamb-Thrush Kim L McBride David Newsom Christopher R Pierson Alexander T Rakowsky Aleš Maver Luca Lovrečić Anja Palandačić Borut Peterlin Ali Torkamani Anna Wedell Mikael Huss Andrey Alexeyenko Jessica M Lindvall Måns Magnusson Daniel Nilsson Henrik Stranneheim Fulya Taylan Christian Gilissen Alexander Hoischen Bregje van Bon Helger Yntema Marcel Nelen Weidong Zhang Jason Sager Lu Zhang Kathryn Blair Deniz Kural Michael Cariaso Greg G Lennon Asif Javed Saloni Agrawal Pauline C Ng Komal S Sandhu Shuba Krishna Vamsi Veeramachaneni Ofer Isakov Eran Halperin Eitan Friedman Noam Shomron Gustavo Glusman Jared C Roach Juan Caballero Hannah C Cox Denise Mauldin Seth A Ament Lee Rowen Daniel R Richards F Anthony San Lucas Manuel L Gonzalez-Garay C Thomas Caskey Yu Bai Ying Huang Fang Fang Yan Zhang Zhengyuan Wang Jorge Barrera Juan M Garcia-Lobo Domingo González-Lamuño Javier Llorca Maria C Rodriguez Ignacio Varela Martin G Reese Francisco M De La Vega Edward Kiruluta Michele Cargill Reece K Hart Jon M Sorenson Gholson J Lyon David A Stevenson Bruce E Bray Barry M Moore Karen Eilbeck Mark Yandell Hongyu Zhao Lin Hou Xiaowei Chen Xiting Yan Mengjie Chen Cong Li Can Yang Murat Gunel Peining Li Yong Kong Austin C Alexander Zayed I Albertyn Kym M Boycott Dennis E Bulman Paul M K Gordon A Micheil Innes Bartha M Knoppers Jacek Majewski Christian R Marshall Jillian S Parboosingh Sarah L Sawyer Mark E Samuels Jeremy Schwartzentruber Isaac S Kohane David M Margulies

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

Recessive truncating titin gene, TTN, mutations presenting as centronuclear myopathy.

Neurology 2013 Oct 23;81(14):1205-14. Epub 2013 Aug 23.

From the Division of Genetics and Program in Genomics, The Manton Center for Orphan Disease Research (O.C.-B., P.B.A., K.S.-A., E.T.D., L.C.S., K.M., A.H.B.), and Division of Newborn Medicine (P.B.A.), Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Physiology and Sarver Molecular Cardiovascular Research Program (C.H., H.G.), University of Arizona, Tucson; Center for Computational Molecular Biology and Department of Molecular and Cellular Biology and Biochemistry (R.S., W.G.F.), Brown University, Providence, RI; Department of Translational Medicine (N.V., J.L.), IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France; Departments of Pediatrics and Neurology and Neurotherapeutics (S.T.I.), University of Texas Southwestern Medical Center, Dallas; Department of Neurology (P.B.S.), University of California, Los Angeles; Division of Human Genetics (N.S.), Department of Pediatrics, Rhode Island Hospital, Providence; Department of Pediatrics, Division of Pediatric Pathology (J.M.D.), and Department of Pathology and Laboratory Medicine (M.W.L), Medical College of Wisconsin, Milwaukee; Hasbro Children's Hospital (J.M.D.), and Center for Biomedical Engineering (W.G.F.), Brown University, Providence, RI.

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http://dx.doi.org/10.1212/WNL.0b013e3182a6ca62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795603PMC
October 2013

ISWI contributes to ArsI insulator function in development of the sea urchin.

Development 2012 Oct;139(19):3613-22

MCB Department, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA.

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http://dx.doi.org/10.1242/dev.081828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436113PMC
October 2012

Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo.

Nat Struct Mol Biol 2012 Jun 17;19(7):719-21. Epub 2012 Jun 17.

Laboratory of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA.

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http://dx.doi.org/10.1038/nsmb.2327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465671PMC
June 2012

Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing.

Bioinformatics 2012 Apr 10;28(7):1031-2. Epub 2012 Feb 10.

Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315715PMC
April 2012

Combinatorial binding of transcription factors in the pluripotency control regions of the genome.

Genome Res 2011 Jul 28;21(7):1055-64. Epub 2011 Apr 28.

Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1101/gr.115824.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129248PMC
July 2011

Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes.

Proc Natl Acad Sci U S A 2011 Jul 17;108(27):11093-8. Epub 2011 Jun 17.

Department of Molecular and Cellular Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.

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http://dx.doi.org/10.1073/pnas.1101135108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131313PMC
July 2011

High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs.

Comb Chem High Throughput Screen 2010 Mar;13(3):242-52

Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427726PMC
http://dx.doi.org/10.2174/138620710790980522DOI Listing
March 2010

Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence.

RNA 2009 Dec 27;15(12):2385-97. Epub 2009 Oct 27.

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1261/rna.1821809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779669PMC
December 2009

A rapid high-throughput method for mapping ribonucleoproteins (RNPs) on human pre-mRNA.

J Vis Exp 2009 Dec 2(34). Epub 2009 Dec 2.

Department of Molecular and Cellular Biology, Brown University, USA.

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http://dx.doi.org/10.3791/1622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152247PMC
December 2009

High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.

Genome Res 2008 Apr 22;18(4):631-9. Epub 2008 Jan 22.

Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1101/gr.072942.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279250PMC
April 2008

Repressing the neuron within.

Bioessays 2008 Jan;30(1):1-4

Department of Molecular Cell Biology and Biochemistry, Brown University, Laboratory of Molecular Medicine, Providence Rhode Island, USA.

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http://dx.doi.org/10.1002/bies.20696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593115PMC
January 2008

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

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

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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http://www.sciencemag.org/cgi/doi/10.1126/science.1073774
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http://dx.doi.org/10.1126/science.1073774DOI Listing
August 2002