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Items: 1 to 50 of 59

1.

Inference of the Human Polyadenylation Code.

Leung MKK, Delong A, Frey BJ.

Bioinformatics. 2018 Apr 10. doi: 10.1093/bioinformatics/bty211. [Epub ahead of print]

PMID:
29648582
2.

Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism.

Kemaladewi DU, Maino E, Hyatt E, Hou H, Ding M, Place KM, Zhu X, Bassi P, Baghestani Z, Deshwar AG, Merico D, Xiong HY, Frey BJ, Wilson MD, Ivakine EA, Cohn RD.

Nat Med. 2017 Aug;23(8):984-989. doi: 10.1038/nm.4367. Epub 2017 Jul 17.

PMID:
28714989
3.

Effectively infinite optical path-length created using a simple cubic photonic crystal for extreme light trapping.

Frey BJ, Kuang P, Hsieh ML, Jiang JH, John S, Lin SY.

Sci Rep. 2017 Jun 23;7(1):4171. doi: 10.1038/s41598-017-03800-y.

4.

Automated analysis of high-content microscopy data with deep learning.

Kraus OZ, Grys BT, Ba J, Chong Y, Frey BJ, Boone C, Andrews BJ.

Mol Syst Biol. 2017 Apr 18;13(4):924. doi: 10.15252/msb.20177551.

5.

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.

C Yuen RK, Merico D, Bookman M, L Howe J, Thiruvahindrapuram B, Patel RV, Whitney J, Deflaux N, Bingham J, Wang Z, Pellecchia G, Buchanan JA, Walker S, Marshall CR, Uddin M, Zarrei M, Deneault E, D'Abate L, Chan AJ, Koyanagi S, Paton T, Pereira SL, Hoang N, Engchuan W, Higginbotham EJ, Ho K, Lamoureux S, Li W, MacDonald JR, Nalpathamkalam T, Sung WW, Tsoi FJ, Wei J, Xu L, Tasse AM, Kirby E, Van Etten W, Twigger S, Roberts W, Drmic I, Jilderda S, Modi BM, Kellam B, Szego M, Cytrynbaum C, Weksberg R, Zwaigenbaum L, Woodbury-Smith M, Brian J, Senman L, Iaboni A, Doyle-Thomas K, Thompson A, Chrysler C, Leef J, Savion-Lemieux T, Smith IM, Liu X, Nicolson R, Seifer V, Fedele A, Cook EH, Dager S, Estes A, Gallagher L, Malow BA, Parr JR, Spence SJ, Vorstman J, Frey BJ, Robinson JT, Strug LJ, Fernandez BA, Elsabbagh M, Carter MT, Hallmayer J, Knoppers BM, Anagnostou E, Szatmari P, Ring RH, Glazer D, Pletcher MT, Scherer SW.

Nat Neurosci. 2017 Apr;20(4):602-611. doi: 10.1038/nn.4524. Epub 2017 Mar 6.

6.

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.

7.

Classifying and segmenting microscopy images with deep multiple instance learning.

Kraus OZ, Ba JL, Frey BJ.

Bioinformatics. 2016 Jun 15;32(12):i52-i59. doi: 10.1093/bioinformatics/btw252.

8.

Computer vision for high content screening.

Kraus OZ, Frey BJ.

Crit Rev Biochem Mol Biol. 2016;51(2):102-9. doi: 10.3109/10409238.2015.1135868. Epub 2016 Jan 24. Review.

PMID:
26806341
9.

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.

10.

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
11.

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
12.

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.

13.

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.

14.

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
15.

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.

16.

Network cleanup.

Alipanahi B, Frey BJ.

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

PMID:
23929347
17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

PMID:
23419374
22.

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
23.

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.

24.

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.

25.

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.

26.

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.

PMID:
21803804
27.

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.

28.

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.

29.

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
30.

Varicose veins. Today's treatment tools.

Frey BJ.

Adv Nurse Pract. 2009 Jun;17(6):49-51. No abstract available.

PMID:
20000185
31.

A binary variable model for affinity propagation.

Givoni IE, Frey BJ.

Neural Comput. 2009 Jun;21(6):1589-600. doi: 10.1162/neco.2009.05-08-785.

PMID:
19191593
32.

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.

Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ.

Nat Genet. 2008 Dec;40(12):1413-5. doi: 10.1038/ng.259. Epub 2008 Nov 2. Erratum in: Nat Genet. 2009 Jun;41(6):762.

PMID:
18978789
33.

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation.

Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ.

Genome Res. 2008 Aug;18(8):1247-58. doi: 10.1101/gr.073155.107. Epub 2008 May 2.

34.

Comparing sequence and expression for predicting microRNA targets using GenMiR3.

Huang JC, Frey BJ, Morris QD.

Pac Symp Biocomput. 2008:52-63.

35.

Using expression profiling data to identify human microRNA targets.

Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD.

Nat Methods. 2007 Dec;4(12):1045-9. Epub 2007 Nov 18.

PMID:
18026111
36.

Bayesian inference of MicroRNA targets from sequence and expression data.

Huang JC, Morris QD, Frey BJ.

J Comput Biol. 2007 Jun;14(5):550-63. Review.

PMID:
17683260
37.

Functional coordination of alternative splicing in the mammalian central nervous system.

Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, Frey BJ, Blencowe BJ.

Genome Biol. 2007;8(6):R108.

38.

Clustering by passing messages between data points.

Frey BJ, Dueck D.

Science. 2007 Feb 16;315(5814):972-6. Epub 2007 Jan 11.

39.

Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.

Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, Graham TR, Andersen RJ, Boone C.

Cell. 2006 Aug 11;126(3):611-25.

40.

Identifying transcription factor functions and targets by phenotypic activation.

Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12045-50. Epub 2006 Jul 31.

41.

GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data.

Frey BJ, Morris QD, Hughes TR.

J Comput Biol. 2006 Mar;13(2):200-14.

PMID:
16597235
42.

How many new genes are there?

Lee LJ, Hughes TR, Frey BJ.

Science. 2006 Mar 24;311(5768):1709-11; author reply 1709-11. No abstract available.

PMID:
16556823
43.

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression.

Pan Q, Saltzman AL, Kim YK, Misquitta C, Shai O, Maquat LE, Frey BJ, Blencowe BJ.

Genes Dev. 2006 Jan 15;20(2):153-8.

44.

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.

Shai O, Morris QD, Blencowe BJ, Frey BJ.

Bioinformatics. 2006 Mar 1;22(5):606-13. Epub 2006 Jan 10.

PMID:
16403798
45.

Unwrapping of MR phase images using a Markov random field model.

Ying L, Liang ZP, Munson DC Jr, Koetter R, Frey BJ.

IEEE Trans Med Imaging. 2006 Jan;25(1):128-36.

PMID:
16398421
46.

A comparison of algorithms for inference and learning in probabilistic graphical models.

Frey BJ, Jojic N.

IEEE Trans Pattern Anal Mach Intell. 2005 Sep;27(9):1392-416.

PMID:
16173184
47.

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs.

Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR.

Nat Genet. 2005 Sep;37(9):991-6. Epub 2005 Aug 28.

PMID:
16127451
48.

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.

Huang JC, Morris QD, Hughes TR, Frey BJ.

Bioinformatics. 2005 Jun;21 Suppl 1:i222-31.

PMID:
15961461
49.

Multi-way clustering of microarray data using probabilistic sparse matrix factorization.

Dueck D, Morris QD, Frey BJ.

Bioinformatics. 2005 Jun;21 Suppl 1:i144-51.

PMID:
15961451
50.

Genrate: a generative model that finds and scores new genes and exons in genomic microarray data.

Frey BJ, Morris QD, Zhang W, Mohammad N, Hughes TR.

Pac Symp Biocomput. 2005:495-506.

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