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Papers authored by Morris Q

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ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing.

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Quon G and Morris Q

Bioinformatics (Oxford, England) 25(21):2882-9, 2009 Nov 1 - Who cited this? | PubMed ID: 19542156 | Fulltext

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

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Ray D, Kazan H, Chan ET, Castillo LP, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, and Hughes TR

Nature biotechnology 27(7):667-70, 2009 Jul - Who cited this? | PubMed ID: 19561594 | Fulltext

Diversity and complexity in DNA recognition by transcription factors.

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Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR,

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Science (New York, N.Y.) 324(5935):1720-3, 2009 Jun 26 - Who cited this? | PubMed ID: 19443739 | Fulltext

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

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

Bioinformatics (Oxford, England) 25(8):1012-8, 2009 Apr 15 - Who cited this? | PubMed ID: 19088121 | Fulltext

Dynamic modularity in protein interaction networks predicts breast cancer outcome.

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Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, and Wrana JL

Nature biotechnology 27(2):199-204, 2009 Feb - Who cited this? | PubMed ID: 19182785 | Fulltext

Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization.

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Blencowe B, Brenner S, Hughes T, and Morris Q

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:545-8, 2009 - Who cited this? | PubMed ID: 19209730 | Fulltext

Conservation of core gene expression in vertebrate tissues.

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

Journal of biology 8(3):33, 2009 - Who cited this? | PubMed ID: 19371447 | Fulltext

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway.

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Miller BW, Lau G, Grouios C, Mollica E, Barrios-Rodiles M, Liu Y, Datti A, Morris Q, Wrana JL, and Attisano L

Molecular systems biology 5:315, 2009 - Who cited this? | PubMed ID: 19888210 | Fulltext

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

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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,

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Cell 133(7):1266, 2008 Jun 27 - Who cited this? | PubMed ID: 18585359 | Fulltext

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

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Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN,

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Genome biology 9 Suppl 1, 2008 - Who cited this? | PubMed ID: 18613946 | Fulltext

Comparing sequence and expression for predicting microRNA targets using GenMiR3.

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Huang JC, Frey BJ, and Morris QD

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:52-63, 2008 - Who cited this? | PubMed ID: 18229676 | Fulltext

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function.

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Mostafavi S, Ray D, Warde-Farley D, Grouios C, and Morris Q

Genome biology 9 Suppl 1:S4, 2008 - Who cited this? | PubMed ID: 18613948 | Fulltext

Using expression profiling data to identify human microRNA targets.

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

Nature methods 4(12):1045-9, 2007 Dec - Who cited this? | PubMed ID: 18026111 | Fulltext

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

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Chen X, Hughes TR, and Morris Q

Bioinformatics (Oxford, England) 23(13):i72-9, 2007 Jul 1 - Who cited this? | PubMed ID: 17646348 | Fulltext

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment.

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Walker E, Ohishi M, Davey RE, Zhang W, Cassar PA, Tanaka TS, Der SD, Morris Q, Hughes TR, Zandstra PW, and Stanford WL

Cell stem cell 1(1):71, 2007 Jun 7 - Who cited this? | PubMed ID: 18371337 | Fulltext

Bayesian inference of MicroRNA targets from sequence and expression data.

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Huang JC, Morris QD, and Frey BJ

Journal of computational biology : a journal of computational molecular cell biology 14(5):550-63, 2007 Jun - Who cited this? | PubMed ID: 17683260 | Fulltext

A genome-wide assessment of adrenocorticotropin action in the Y1 mouse adrenal tumor cell line.

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Schimmer BP, Cordova M, Cheng H, Tsao A, and Morris Q

Molecular and cellular endocrinology 265-266:102-7, 2007 Feb - Who cited this? | PubMed ID: 17207920 | Fulltext

Identifying transcription factor functions and targets by phenotypic activation.

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

Proceedings of the National Academy of Sciences of the United States of America 103(32):12045, 2006 Aug 8 - Who cited this? | PubMed ID: 16880382 | Fulltext

Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells.

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Schimmer BP, Cordova M, Cheng H, Tsao A, Goryachev AB, Schimmer AD, and Morris Q

Endocrinology 147(5):2357, 2006 May - Who cited this? | PubMed ID: 16484322 | Fulltext

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.

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Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, and Emili A

Cell 125(1):173, 2006 Apr 7 - Who cited this? | PubMed ID: 16615898 | Fulltext

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

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

Bioinformatics (Oxford, England) 22(5):606, 2006 Mar 1 - Who cited this? | PubMed ID: 16403798 | Fulltext

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

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Frey BJ, Morris QD, and Hughes TR

Journal of computational biology : a journal of computational molecular cell biology 13(2):200-14, 2006 Mar - Who cited this? | PubMed ID: 16597235 | Fulltext

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

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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, and Hughes TR

Nature genetics 37(9):991, 2005 Sep - Who cited this? | PubMed ID: 16127451 | Fulltext

Network news: functional modules revealed during early embryogenesis in C. elegans.

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Roy PJ and Morris Q

Developmental cell 9(3):307-8, 2005 Sep - Who cited this? | PubMed ID: 16139218 | Fulltext

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

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Dueck D, Morris QD, and Frey BJ

Bioinformatics (Oxford, England) 21 Suppl 1, 2005 Jun - Who cited this? | PubMed ID: 15961451 | Fulltext

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

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

Bioinformatics (Oxford, England) 21 Suppl 1:i222-31, 2005 Jun - Who cited this? | PubMed ID: 15961461 | Fulltext

Alternative splicing of conserved exons is frequently species-specific in human and mouse.

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Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, and Blencowe BJ

Trends in genetics : TIG 21(2):73-7, 2005 Feb - Who cited this? | PubMed ID: 15661351 | Fulltext

Detection and discovery of RNA modifications using microarrays.

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

Nucleic acids research 33(1):e2, 2005 - Who cited this? | PubMed ID: 15640439 | Fulltext

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

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

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:495-506, 2005 - Who cited this? | PubMed ID: 15759654 | Fulltext

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

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

Molecular cell 16(6):929-41, 2004 Dec 22 - Who cited this? | PubMed ID: 15610736 | Fulltext

Transcriptional networks: reverse-engineering gene regulation on a global scale.

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Chua G, Robinson MD, Morris Q, and Hughes TR

Current opinion in microbiology 7(6):638-46, 2004 Dec - Who cited this? | PubMed ID: 15556037 | Fulltext

Probing microRNAs with microarrays: tissue specificity and functional inference.

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Babak T, Zhang W, Morris Q, Blencowe BJ, and Hughes TR

RNA (New York, N.Y.) 10(11):1813-9, 2004 Nov - Who cited this? | PubMed ID: 15496526 | Fulltext

Exploration of essential gene functions via titratable promoter alleles.

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Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q,

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Cell 118(1):31, 2004 Jul 9 - Who cited this? | PubMed ID: 15242642 | Fulltext

The functional landscape of mouse gene expression.

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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,

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Journal of biology 3(5):21, 2004 - Who cited this? | PubMed ID: 15588312 | Fulltext

A panoramic view of yeast noncoding RNA processing.

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Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V,

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Cell 113(7):919-33, 2003 Jun 27 - Who cited this? | PubMed ID: 12837249 | Fulltext

[Editorial: Studies on the biliary clearance of macromolecules].

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Bradley SE, Morris Q, Baker J, and Herz G

Medecine & chirurgie digestives 4 Suppl 1:23-5, 1975 - Who cited this? | PubMed ID: 1230591 | Fulltext

The use of ion exchange resins with flavonoid compounds.

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GAGE TB, MORRIS QL, DETTY WE, and WENDER SH

Science (New York, N.Y.) 113(2940):522-3, 1951 May 4 - Who cited this? | PubMed ID: 14828390 | Fulltext

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