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Results: 1 to 20 of 50

1.

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.

Alipanahi B, Delong A, Weirauch MT, Frey BJ.

Nat Biotechnol. 2015 Aug;33(8):831-8. doi: 10.1038/nbt.3300. Epub 2015 Jul 27.

PMID:
26213851
2.

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR.

Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18.

PMID:
25690854
3.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.

PMID:
25525159
4.

Deep learning of the tissue-regulated splicing code.

Leung MK, Xiong HY, Lee LJ, Frey BJ.

Bioinformatics. 2014 Jun 15;30(12):i121-9. doi: 10.1093/bioinformatics/btu277.

5.

Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder.

Uddin M, Tammimies K, Pellecchia G, Alipanahi B, Hu P, Wang Z, Pinto D, Lau L, Nalpathamkalam T, Marshall CR, Blencowe BJ, Frey BJ, Merico D, Yuen RK, Scherer SW.

Nat Genet. 2014 Jul;46(7):742-7. doi: 10.1038/ng.2980. Epub 2014 May 25.

PMID:
24859339
6.

AVISPA: a web tool for the prediction and analysis of alternative splicing.

Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ.

Genome Biol. 2013;14(10):R114.

7.

Network cleanup.

Alipanahi B, Frey BJ.

Nat Biotechnol. 2013 Aug;31(8):714-5. doi: 10.1038/nbt.2657. No abstract available.

PMID:
23929347
8.

A compendium of RNA-binding motifs for decoding gene regulation.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

9.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ.

Nature. 2013 Jun 13;498(7453):241-5. doi: 10.1038/nature12270. Epub 2013 Jun 5.

10.

Prevention of root caries: a literature review of primary and secondary preventive agents.

Gluzman R, Katz RV, Frey BJ, McGowan R.

Spec Care Dentist. 2013 May-Jun;33(3):133-40. doi: 10.1111/j.1754-4505.2012.00318.x. Epub 2012 Dec 10. Review.

11.

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome.

McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, Carter MT, Lee LJ, Clericuzio CL, Graham JM Jr, Morris-Rosendahl DJ, Polster T, Acsadi G, Townshend S, Williams S, Halbert A, Isidor B, David A, Smyser CD, Paciorkowski AR, Willing M, Woulfe J, Das S, Beaulieu CL, Marcadier J; FORGE Canada Consortium, Geraghty MT, Frey BJ, Majewski J, Bulman DE, Dobyns WB, O'Driscoll M, Boycott KM.

Nat Genet. 2013 May;45(5):556-62. doi: 10.1038/ng.2602. Epub 2013 Mar 31.

12.

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.

Chung C, Emili A, Frey BJ.

Bioinformatics. 2013 Apr 1;29(7):821-9. doi: 10.1093/bioinformatics/btt056. Epub 2013 Feb 17.

13.

The evolutionary landscape of alternative splicing in vertebrate species.

Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ.

Science. 2012 Dec 21;338(6114):1587-93. doi: 10.1126/science.1230612.

PMID:
23258890
14.

A generalizable pre-clinical research approach for orphan disease therapy.

Beaulieu CL, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, Hicks GG, Frey BJ, Boycott KM, Mackenzie AE.

Orphanet J Rare Dis. 2012 Jun 15;7:39. Review.

15.

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.

Kakaradov B, Xiong HY, Lee LJ, Jojic N, Frey BJ.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S11. doi: 10.1186/1471-2105-13-S6-S11.

16.

Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.

Lahiry P, Lee LJ, Frey BJ, Rupar CA, Siu VM, Blencowe BJ, Hegele RA.

PLoS One. 2011;6(9):e25400. doi: 10.1371/journal.pone.0025400. Epub 2011 Sep 27.

17.

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.

Xiong HY, Barash Y, Frey BJ.

Bioinformatics. 2011 Sep 15;27(18):2554-62. doi: 10.1093/bioinformatics/btr444. Epub 2011 Jul 29.

18.

Computational refinement of post-translational modifications predicted from tandem mass spectrometry.

Chung C, Liu J, Emili A, Frey BJ.

Bioinformatics. 2011 Mar 15;27(6):797-806. doi: 10.1093/bioinformatics/btr017. Epub 2011 Jan 22.

19.

Model-based detection of alternative splicing signals.

Barash Y, Blencowe BJ, Frey BJ.

Bioinformatics. 2010 Jun 15;26(12):i325-33. doi: 10.1093/bioinformatics/btq200.

20.

Deciphering the splicing code.

Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ.

Nature. 2010 May 6;465(7294):53-9. doi: 10.1038/nature09000.

PMID:
20445623
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