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Items: 15

1.

Does conservation account for splicing patterns?

Wainberg M, Alipanahi B, Frey B.

BMC Genomics. 2016 Oct 7;17(1):787.

2.

Genome-wide characteristics of de novo mutations in autism.

Yuen RK, Merico D, Cao H, Pellecchia G, Alipanahi B, Thiruvahindrapuram B, Tong X, Sun Y, Cao D, Zhang T, Wu X, Jin X, Zhou Z, Liu X, Nalpathamkalam T, Walker S, Howe JL, Wang Z, MacDonald JR, Chan A, D'Abate L, Deneault E, Siu MT, Tammimies K, Uddin M, Zarrei M, Wang M, Li Y, Wang J, Wang J, Yang H, Bookman M, Bingham J, Gross SS, Loy D, Pletcher M, Marshall CR, Anagnostou E, Zwaigenbaum L, Weksberg R, Fernandez BA, Roberts W, Szatmari P, Glazer D, Frey BJ, Ring RH, Xu X, Scherer SW.

NPJ Genom Med. 2016 Aug 3;1:160271-1602710.

3.

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

Stavropoulos DJ, Merico D, Jobling R, Bowdin S, Monfared N, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Yuen RKC, Szego MJ, Hayeems RZ, Shaul RZ, Brudno M, Girdea M, Frey B, Alipanahi B, Ahmed S, Babul-Hirji R, Porras RB, Carter MT, Chad L, Chaudhry A, Chitayat D, Doust SJ, Cytrynbaum C, Dupuis L, Ejaz R, Fishman L, Guerin A, Hashemi B, Helal M, Hewson S, Inbar-Feigenberg M, Kannu P, Karp N, Kim R, Kronick J, Liston E, MacDonald H, Mercimek-Mahmutoglu S, Mendoza-Londono R, Nasr E, Nimmo G, Parkinson N, Quercia N, Raiman J, Roifman M, Schulze A, Shugar A, Shuman C, Sinajon P, Siriwardena K, Weksberg R, Yoon G, Carew C, Erickson R, Leach RA, Klein R, Ray PN, Meyn MS, Scherer SW, Cohn RD, Marshall CR.

NPJ Genom Med. 2016 Jan 13;1. pii: 15012. doi: 10.1038/npjgenmed.2015.12.

4.

Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome.

Merico D, Zarrei M, Costain G, Ogura L, Alipanahi B, Gazzellone MJ, Butcher NJ, Thiruvahindrapuram B, Nalpathamkalam T, Chow EW, Andrade DM, Frey BJ, Marshall CR, Scherer SW, Bassett AS.

G3 (Bethesda). 2015 Sep 16;5(11):2453-61. doi: 10.1534/g3.115.021345.

5.

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
6.

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.

7.

Widespread intron retention in mammals functionally tunes transcriptomes.

Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ.

Genome Res. 2014 Nov;24(11):1774-86. doi: 10.1101/gr.177790.114. Epub 2014 Sep 25.

8.

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
9.

Network cleanup.

Alipanahi B, Frey BJ.

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

PMID:
23929347
10.

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.

11.

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

Cui X, Li SC, Bu D, Alipanahi B, Li M.

Algorithms Mol Biol. 2013 Feb 25;8(1):5. doi: 10.1186/1748-7188-8-5.

12.

Determining protein structures from NOESY distance constraints by semidefinite programming.

Alipanahi B, Krislock N, Ghodsi A, Wolkowicz H, Donaldson L, Li M.

J Comput Biol. 2013 Apr;20(4):296-310. doi: 10.1089/cmb.2012.0089. Epub 2012 Oct 31.

13.

Error tolerant NMR backbone resonance assignment and automated structure generation.

Alipanahi B, Gao X, Karakoc E, Li SC, Balbach F, Feng G, Donaldson L, Li M.

J Bioinform Comput Biol. 2011 Feb;9(1):15-41.

PMID:
21328705
14.

Protein secondary structure prediction using NMR chemical shift data.

Zhao Y, Alipanahi B, Li SC, Li M.

J Bioinform Comput Biol. 2010 Oct;8(5):867-84.

PMID:
20981892
15.

PICKY: a novel SVD-based NMR spectra peak picking method.

Alipanahi B, Gao X, Karakoc E, Donaldson L, Li M.

Bioinformatics. 2009 Jun 15;25(12):i268-75. doi: 10.1093/bioinformatics/btp225.

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