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Items: 37

1.

Similarity regression predicts evolution of transcription factor sequence specificity.

Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR.

Nat Genet. 2019 Jun;51(6):981-989. doi: 10.1038/s41588-019-0411-1. Epub 2019 May 27.

PMID:
31133749
2.

ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development.

Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL.

Nucleic Acids Res. 2019 Apr 8;47(6):2856-2870. doi: 10.1093/nar/gkz010.

3.

The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.

Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR.

Elife. 2018 Dec 21;7. pii: e35478. doi: 10.7554/eLife.35478.

4.

Neutral tumor evolution?

Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F; PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P.

Nat Genet. 2018 Dec;50(12):1630-1633. doi: 10.1038/s41588-018-0258-x. No abstract available.

5.

Motif models for RNA-binding proteins.

Sasse A, Laverty KU, Hughes TR, Morris QD.

Curr Opin Struct Biol. 2018 Dec;53:115-123. doi: 10.1016/j.sbi.2018.08.001. Epub 2018 Aug 29. Review.

PMID:
30172081
6.

A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B).

François-Moutal L, Jahanbakhsh S, Nelson ADL, Ray D, Scott DD, Hennefarth MR, Moutal A, Perez-Miller S, Ambrose AJ, Al-Shamari A, Coursodon P, Meechoovet B, Reiman R, Lyons E, Beilstein M, Chapman E, Morris QD, Van Keuren-Jensen K, Hughes TR, Khanna R, Koehler C, Jen J, Gokhale V, Khanna M.

ACS Chem Biol. 2018 Oct 19;13(10):3000-3010. doi: 10.1021/acschembio.8b00745. Epub 2018 Sep 6.

7.

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.

Espiritu SMG, Liu LY, Rubanova Y, Bhandari V, Holgersen EM, Szyca LM, Fox NS, Chua MLK, Yamaguchi TN, Heisler LE, Livingstone J, Wintersinger J, Yousif F, Lalonde E, Rouette A, Salcedo A, Houlahan KE, Li CH, Huang V, Fraser M, van der Kwast T, Morris QD, Bristow RG, Boutros PC.

Cell. 2018 May 3;173(4):1003-1013.e15. doi: 10.1016/j.cell.2018.03.029. Epub 2018 Apr 19.

8.

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma.

Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW.

Cancer Cell. 2017 Jul 10;32(1):101-114.e8. doi: 10.1016/j.ccell.2017.06.002.

9.

RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.

Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD.

Methods. 2017 Aug 15;126:18-28. doi: 10.1016/j.ymeth.2017.06.024. Epub 2017 Jun 24.

PMID:
28651966
10.

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.

Ray D, Ha KCH, Nie K, Zheng H, Hughes TR, Morris QD.

Methods. 2017 Apr 15;118-119:3-15. doi: 10.1016/j.ymeth.2016.12.003. Epub 2016 Dec 10.

11.

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.

12.

High-throughput characterization of protein-RNA interactions.

Cook KB, Hughes TR, Morris QD.

Brief Funct Genomics. 2015 Jan;14(1):74-89. doi: 10.1093/bfgp/elu047. Epub 2014 Dec 13. Review.

13.

Staufen2 regulates neuronal target RNAs.

Heraud-Farlow JE, Sharangdhar T, Li X, Pfeifer P, Tauber S, Orozco D, Hörmann A, Thomas S, Bakosova A, Farlow AR, Edbauer D, Lipshitz HD, Morris QD, Bilban M, Doyle M, Kiebler MA.

Cell Rep. 2013 Dec 26;5(6):1511-8. doi: 10.1016/j.celrep.2013.11.039. Epub 2013 Dec 19.

14.

Finding the target sites of RNA-binding proteins.

Li X, Kazan H, Lipshitz HD, Morris QD.

Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):111-30. doi: 10.1002/wrna.1201. Epub 2013 Nov 11. Review.

15.

A unified model for yeast transcript definition.

de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR.

Genome Res. 2014 Jan;24(1):154-66. doi: 10.1101/gr.164327.113. Epub 2013 Oct 29.

16.

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity.

Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD.

Nucleic Acids Res. 2013 Nov;41(20):9438-60. doi: 10.1093/nar/gkt702. Epub 2013 Aug 13.

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.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.

19.

Unsupervised detection of genes of influence in lung cancer using biological networks.

Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD.

Bioinformatics. 2011 Nov 15;27(22):3166-72. doi: 10.1093/bioinformatics/btr533. Epub 2011 Sep 28.

PMID:
21965819
20.

Predicting the target genes of intronic microRNAs using large-scale gene expression data.

Radfar M, Wong W, Morris QD.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:791-4. doi: 10.1109/IEMBS.2010.5626505.

PMID:
21096111
21.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.

22.

Conservation of core gene expression in vertebrate tissues.

Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR.

J Biol. 2009;8(3):33. doi: 10.1186/jbiol130. Epub 2009 Apr 16.

23.

Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.

Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16.

24.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

25.

Comparing sequence and expression for predicting microRNA targets using GenMiR3.

Huang JC, Frey BJ, Morris QD.

Pac Symp Biocomput. 2008:52-63.

26.

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
27.

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
28.

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.

29.

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
30.

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
31.

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
32.

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
33.

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
34.

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.

35.

Detection and discovery of RNA modifications using microarrays.

Hiley SL, Jackman J, Babak T, Trochesset M, Morris QD, Phizicky E, Hughes TR.

Nucleic Acids Res. 2005 Jan 7;33(1):e2.

36.

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.

Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ.

Mol Cell. 2004 Dec 22;16(6):929-41.

37.

The functional landscape of mouse gene expression.

Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR.

J Biol. 2004;3(5):21. doi: 10.1186/jbiol16. Epub 2004 Dec 6.

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