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Items: 37

1.

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

Taggart AJ, Fairbrother WG.

Quant Biol. 2018 Sep;6(3):267-274. doi: 10.1007/s40484-018-0141-x. Epub 2018 Jul 25.

2.

Assessing predictions of the impact of variants on splicing in CAGI5.

Mount SM, Avsec Ž, Carmel L, Casadio R, Çelik MH, Chen K, Cheng J, Cohen NE, Fairbrother WG, Fenesh T, Gagneur J, Gotea V, Holzer T, Lin CF, Martelli PL, Naito T, Nguyen TYD, Savojardo C, Unger R, Wang R, Yang Y, Zhao H.

Hum Mutat. 2019 Sep;40(9):1215-1224. doi: 10.1002/humu.23869. Epub 2019 Aug 19.

PMID:
31301154
3.

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

Rhine CL, Neil C, Glidden DT, Cygan KJ, Fredericks AM, Wang J, Walton NA, Fairbrother WG.

Hum Mutat. 2019 Sep;40(9):1225-1234. doi: 10.1002/humu.23866. Epub 2019 Aug 17.

PMID:
31297895
4.

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

Cheng J, Nguyen TYD, Cygan KJ, Çelik MH, Fairbrother WG, Avsec Ž, Gagneur J.

Genome Biol. 2019 Mar 1;20(1):48. doi: 10.1186/s13059-019-1653-z.

5.

Changes in the process of alternative RNA splicing results in soluble B and T lymphocyte attenuator with biological and clinical implications in critical illness.

Monaghan SF, Banerjee D, Chung CS, Lomas-Neira J, Cygan KJ, Rhine CL, Fairbrother WG, Heffernan DS, Levy MM, Cioffi WG, Ayala A.

Mol Med. 2018 Jun 18;24(1):32. doi: 10.1186/s10020-018-0036-3.

6.

Hereditary cancer genes are highly susceptible to splicing mutations.

Rhine CL, Cygan KJ, Soemedi R, Maguire S, Murray MF, Monaghan SF, Fairbrother WG.

PLoS Genet. 2018 Mar 5;14(3):e1007231. doi: 10.1371/journal.pgen.1007231. eCollection 2018 Mar.

7.

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

Zhang SY, Clark NE, Freije CA, Pauwels E, Taggart AJ, Okada S, Mandel H, Garcia P, Ciancanelli MJ, Biran A, Lafaille FG, Tsumura M, Cobat A, Luo J, Volpi S, Zimmer B, Sakata S, Dinis A, Ohara O, Garcia Reino EJ, Dobbs K, Hasek M, Holloway SP, McCammon K, Hussong SA, DeRosa N, Van Skike CE, Katolik A, Lorenzo L, Hyodo M, Faria E, Halwani R, Fukuhara R, Smith GA, Galvan V, Damha MJ, Al-Muhsen S, Itan Y, Boeke JD, Notarangelo LD, Studer L, Kobayashi M, Diogo L, Fairbrother WG, Abel L, Rosenberg BR, Hart PJ, Etzioni A, Casanova JL.

Cell. 2018 Feb 22;172(5):952-965.e18. doi: 10.1016/j.cell.2018.02.019.

8.

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

Kim SW, Taggart AJ, Heintzelman C, Cygan KJ, Hull CG, Wang J, Shrestha B, Fairbrother WG.

Nucleic Acids Res. 2017 Sep 19;45(16):9503-9513. doi: 10.1093/nar/gkx661.

9.

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

Cygan KJ, Sanford CH, Fairbrother WG.

Bioinformatics. 2017 Sep 15;33(18):2943-2945. doi: 10.1093/bioinformatics/btx343.

10.

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

Cygan KJ, Soemedi R, Rhine CL, Profeta A, Murphy EL, Murray MF, Fairbrother WG.

Hum Genet. 2017 Sep;136(9):1303-1312. doi: 10.1007/s00439-017-1833-4. Epub 2017 Aug 5.

11.

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

Soemedi R, Cygan KJ, Rhine CL, Glidden DT, Taggart AJ, Lin CL, Fredericks AM, Fairbrother WG.

Methods. 2017 Aug 1;125:36-44. doi: 10.1016/j.ymeth.2017.06.001. Epub 2017 Jun 6. Review.

12.

Pathogenic variants that alter protein code often disrupt splicing.

Soemedi R, Cygan KJ, Rhine CL, Wang J, Bulacan C, Yang J, Bayrak-Toydemir P, McDonald J, Fairbrother WG.

Nat Genet. 2017 Jun;49(6):848-855. doi: 10.1038/ng.3837. Epub 2017 Apr 17.

13.

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

Taggart AJ, Lin CL, Shrestha B, Heintzelman C, Kim S, Fairbrother WG.

Genome Res. 2017 Apr;27(4):639-649. doi: 10.1101/gr.202820.115. Epub 2017 Jan 24.

14.

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

Monaghan SF, Chung CS, Chen Y, Lomas-Neira J, Fairbrother WG, Heffernan DS, Cioffi WG, Ayala A.

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

15.

RNA structure in splicing: An evolutionary perspective.

Lin CL, Taggart AJ, Fairbrother WG.

RNA Biol. 2016 Sep;13(9):766-71. doi: 10.1080/15476286.2016.1208893. Epub 2016 Jul 25. Review.

16.

The importance of p53 pathway genetics in inherited and somatic cancer genomes.

Stracquadanio G, Wang X, Wallace MD, Grawenda AM, Zhang P, Hewitt J, Zeron-Medina J, Castro-Giner F, Tomlinson IP, Goding CR, Cygan KJ, Fairbrother WG, Thomas LF, Sætrom P, Gemignani F, Landi S, Schuster-Böckler B, Bell DA, Bond GL.

Nat Rev Cancer. 2016 Apr;16(4):251-65. doi: 10.1038/nrc.2016.15. Review.

PMID:
27009395
17.

RNA structure replaces the need for U2AF2 in splicing.

Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG.

Genome Res. 2016 Jan;26(1):12-23. doi: 10.1101/gr.181008.114. Epub 2015 Nov 13.

18.

RNA-Binding Proteins: Splicing Factors and Disease.

Fredericks AM, Cygan KJ, Brown BA, Fairbrother WG.

Biomolecules. 2015 May 13;5(2):893-909. doi: 10.3390/biom5020893. Review.

19.

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

Soemedi R, Vega H, Belmont JM, Ramachandran S, Fairbrother WG.

Adv Exp Med Biol. 2014;825:227-66. doi: 10.1007/978-1-4939-1221-6_7. Review.

PMID:
25201108
20.

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

Ceyhan-Birsoy O, Agrawal PB, Hidalgo C, Schmitz-Abe K, DeChene ET, Swanson LC, Soemedi R, Vasli N, Iannaccone ST, Shieh PB, Shur N, Dennison JM, Lawlor MW, Laporte J, Markianos K, Fairbrother WG, Granzier H, Beggs AH.

Neurology. 2013 Oct 1;81(14):1205-14. doi: 10.1212/WNL.0b013e3182a6ca62. Epub 2013 Aug 23.

21.

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

Yajima M, Fairbrother WG, Wessel GM.

Development. 2012 Oct;139(19):3613-22. doi: 10.1242/dev.081828.

22.

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

Taggart AJ, DeSimone AM, Shih JS, Filloux ME, Fairbrother WG.

Nat Struct Mol Biol. 2012 Jun 17;19(7):719-21. doi: 10.1038/nsmb.2327.

23.

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

Lim KH, Fairbrother WG.

Bioinformatics. 2012 Apr 1;28(7):1031-2. doi: 10.1093/bioinformatics/bts074. Epub 2012 Feb 10.

24.

Association between regulator of G protein signaling 9-2 and body weight.

Waugh JL, Celver J, Sharma M, Dufresne RL, Terzi D, Risch SC, Fairbrother WG, Neve RL, Kane JP, Malloy MJ, Pullinger CR, Gu HF, Tsatsanis C, Hamilton SP, Gold SJ, Zachariou V, Kovoor A.

PLoS One. 2011;6(11):e27984. doi: 10.1371/journal.pone.0027984. Epub 2011 Nov 23.

25.

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

Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11093-8. doi: 10.1073/pnas.1101135108. Epub 2011 Jun 17.

26.

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

Ferraris L, Stewart AP, Kang J, DeSimone AM, Gemberling M, Tantin D, Fairbrother WG.

Genome Res. 2011 Jul;21(7):1055-64. doi: 10.1101/gr.115824.110. Epub 2011 Apr 28.

27.

High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach.

Ferraris L, Stewart AP, Gemberling MP, Reid DC, Lapadula MJ, Thompson WA, Fairbrother WG.

Nucleic Acids Res. 2011 Mar;39(6):e33. doi: 10.1093/nar/gkq1213. Epub 2010 Dec 17.

28.

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

Chang B, Levin J, Thompson WA, Fairbrother WG.

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

29.

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

Reid DC, Chang BL, Gunderson SI, Alpert L, Thompson WA, Fairbrother WG.

RNA. 2009 Dec;15(12):2385-97. doi: 10.1261/rna.1821809. Epub 2009 Oct 27.

30.

A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress.

Kang J, Gemberling M, Nakamura M, Whitby FG, Handa H, Fairbrother WG, Tantin D.

Genes Dev. 2009 Jan 15;23(2):208-22. doi: 10.1101/gad.1750709.

31.

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

Tantin D, Gemberling M, Callister C, Fairbrother WG.

Genome Res. 2008 Apr;18(4):631-9. doi: 10.1101/gr.072942.107. Epub 2008 Jan 22. Erratum in: Genome Res. 2009 Apr;19(4):690. Fairbrother, William [corrected to Fairbrother, William G].

32.

Repressing the neuron within.

Fairbrother WG, Lipscombe D.

Bioessays. 2008 Jan;30(1):1-4. Review. Erratum in: Bioessays. 2009 Apr;31(4):487. Fairbrother, Will [corrected to Fairbrother, William G].

33.

Linking C5 deficiency to an exonic splicing enhancer mutation.

Pfarr N, Prawitt D, Kirschfink M, Schroff C, Knuf M, Habermehl P, Mannhardt W, Zepp F, Fairbrother WG, Loos M, Burge CB, Pohlenz J.

J Immunol. 2005 Apr 1;174(7):4172-7. Erratum in: J Immunol. 2009 Apr 15;182(8):5152. Fairbrother, William [corrected to Fairbrother, William G].

34.

Single nucleotide polymorphism-based validation of exonic splicing enhancers.

Fairbrother WG, Holste D, Burge CB, Sharp PA.

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

35.

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

Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W187-90.

36.

Predictive identification of exonic splicing enhancers in human genes.

Fairbrother WG, Yeh RF, Sharp PA, Burge CB.

Science. 2002 Aug 9;297(5583):1007-13. Epub 2002 Jul 11.

37.

Human genomic sequences that inhibit splicing.

Fairbrother WG, Chasin LA.

Mol Cell Biol. 2000 Sep;20(18):6816-25.

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