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Papers authored by Hughes TR

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Establishing legitimacy and function in the new transcriptome.

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van Bakel H and Hughes TR

Briefings in functional genomics & proteomics 8(6):424-36, 2009 Nov - Who cited this? | PubMed ID: 19833698 | Fulltext

Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression.

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Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, and Andrews BJ

Molecular cell 35(3):340-51, 2009 Aug 14 - Who cited this? | PubMed ID: 19683497 | 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

Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast.

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Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, and Andrews B

Methods (San Diego, Calif.) 48(3):258-64, 2009 Jul - Who cited this? | PubMed ID: 19269327 | 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

Identification of the high affinity binding site in the Streptococcus intermedius toxin intermedilysin for its membrane receptor, the human complement regulator CD59.

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Hughes TR, Ross KS, Cowan GJ, Sivasankar B, Harris CL, Mitchell TJ, and Morgan BP

Molecular immunology 46(7):1561-7, 2009 Apr - Who cited this? | PubMed ID: 19200600 | Fulltext

The DNA-encoded nucleosome organization of a eukaryotic genome.

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Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, and Segal E

Nature 458(7236):362-6, 2009 Mar 19 - Who cited this? | PubMed ID: 19092803 | Fulltext

Crry deficiency in complement sufficient mice: C3 consumption occurs without associated renal injury.

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Ruseva MM, Hughes TR, Donev RM, Sivasankar B, Pickering MC, Wu X, Harris CL, and Morgan BP

Molecular immunology 46(5):803-11, 2009 Feb - Who cited this? | PubMed ID: 18947875 | Fulltext

'Validation' in genome-scale research.

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Hughes TR

Journal of biology 8(1):3, 2009 - Who cited this? | PubMed ID: 19222867 | Fulltext

TFCat: the curated catalog of mouse and human transcription factors.

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Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, and Sladek R

Genome biology 10(3):R29, 2009 - Who cited this? | PubMed ID: 19284633 | 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

Prediction and verification of mouse tRNA gene families.

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Coughlin DJ, Babak T, Nihranz C, Hughes TR, and Engelke DR

RNA biology 6(2):195-202, 2009 - Who cited this? | PubMed ID: 19246989 | Fulltext

A library of yeast transcription factor motifs reveals a widespread function for rsc3 in targeting nucleosome exclusion at promoters.

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Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D,

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Molecular cell 32(6):878-87, 2008 Dec 26 - Who cited this? | PubMed ID: 19111667 | Fulltext

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome.

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Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, and Winston F

PLoS biology 6(11):e277, 2008 Nov 11 - Who cited this? | PubMed ID: 18998772 | Fulltext

The interferon-gamma-mediated inhibition of lipoprotein lipase gene transcription in macrophages involves casein kinase 2- and phosphoinositide-3-kinase-mediated regulation of transcription factors Sp1 and Sp3.

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Harris SM, Harvey EJ, Hughes TR, and Ramji DP

Cellular signalling, 2008 Aug 28 - Who cited this? | PubMed ID: 18793716 | Fulltext

Modulation of CD59 expression by restrictive silencer factor-derived peptides in cancer immunotherapy for neuroblastoma.

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Donev RM, Gray LC, Sivasankar B, Hughes TR, van den Berg CW, and Morgan BP

Cancer research 68(14):5979, 2008 Jul 15 - Who cited this? | PubMed ID: 18632654 | Fulltext

Plasmodium falciparum shows transcriptional versatility within the human host.

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Lovegrove FE, Peña-Castillo L, Liles WC, Hughes TR, and Kain KC

Trends in parasitology 24(7):288-91, 2008 Jul - Who cited this? | PubMed ID: 18538633 | Fulltext

Genetic Interactions of MAF1 Identify a Role for Med20 in Transcriptional Repression of Ribosomal Protein Genes.

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Willis IM, Chua G, Tong AH, Brost RL, Hughes TR, Boone C, and Moir RD

PLoS genetics 4(7):e1000112, 2008 Jul - Who cited this? | PubMed ID: 18604275 | 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

Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model.

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Lovegrove FE, Gharib SA, Peña-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, and Kain KC

PLoS pathogens 4(5):e1000068, 2008 May - Who cited this? | PubMed ID: 18483551 | Fulltext

Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer.

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Sandhu C, Hewel JA, Badis G, Talukder S, Liu J, Hughes TR, and Emili A

Journal of proteome research 7(4):1529-41, 2008 Apr - Who cited this? | PubMed ID: 18311902 | Fulltext

Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation.

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Zhao R, Kakihara Y, Gribun A, Huen J, Yang G, Khanna M, Costanzo M, Brost RL, Boone C, Hughes TR, Yip CM, and Houry WA

The Journal of cell biology 180(3):563, 2008 Feb 11 - Who cited this? | PubMed ID: 18268103 | 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

A race through the maze of genomic evidence.

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Hughes TR and Roth FP

Genome biology 9 Suppl 1:S1, 2008 - Who cited this? | PubMed ID: 18613945 | 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

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

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Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, and Krause HM

Cell 131(1):174-87, 2007 Oct 5 - Who cited this? | PubMed ID: 17923096 | Fulltext

A high-resolution atlas of nucleosome occupancy in yeast.

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Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, and Nislow C

Nature genetics 39(10):1235-44, 2007 Oct - Who cited this? | PubMed ID: 17873876 | Fulltext

High-resolution structures of bacterially expressed soluble human CD59.

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Leath KJ, Johnson S, Roversi P, Hughes TR, Smith RA, Mackenzie L, Morgan BP, and Lea SM

Acta crystallographica. Section F, Structural biology and crystallization communications 63(Pt 8):648, 2007 Aug 1 - Who cited this? | PubMed ID: 17671359 | Fulltext

Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.

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Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Thérien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, and Coulombe B

Molecular cell 27(2):262, 2007 Jul 20 - Who cited this? | PubMed ID: 17643375 | Fulltext

H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.

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Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, and Berger SL

Molecular cell 27(2):275, 2007 Jul 20 - Who cited this? | PubMed ID: 17643376 | 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

Why are there still over 1000 uncharacterized yeast genes?.

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Peña-Castillo L and Hughes TR

Genetics 176(1):7-14, 2007 May - Who cited this? | PubMed ID: 17435240 | Fulltext

CD59a deficient mice display reduced B cell activity and antibody production in response to T-dependent antigens.

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Sivasankar B, Donev RM, Longhi MP, Hughes TR, Davies R, Cole DS, Morgan BP, and Marchbank KJ

Molecular immunology 44(11):2978, 2007 Apr - Who cited this? | PubMed ID: 17296227 | Fulltext

Considerations in the identification of functional RNA structural elements in genomic alignments.

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Babak T, Blencowe BJ, and Hughes TR

BMC bioinformatics 8:33, 2007 - Who cited this? | PubMed ID: 17263882 | Fulltext

SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase.

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Tadros W, Goldman AL, Babak T, Menzies F, Vardy L, Orr-Weaver T, Hughes TR, Westwood JT, Smibert CA, and Lipshitz HD

Developmental cell 12(1):143, 2007 Jan - Who cited this? | PubMed ID: 17199047 | Fulltext

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

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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,

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Genome biology 8(6):R108, 2007 - Who cited this? | PubMed ID: 17565696 | Fulltext

A survey of essential gene function in the yeast cell division cycle.

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Yu L, Peña Castillo L, Mnaimneh S, Hughes TR, and Brown GW

Molecular biology of the cell 17(11):4736-47, 2006 Nov - Who cited this? | PubMed ID: 16943325 | Fulltext

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

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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,

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Cell 126(3):611, 2006 Aug 11 - Who cited this? | PubMed ID: 16901791 | 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

Complement regulator loss on apoptotic neuronal cells causes increased complement activation and promotes both phagocytosis and cell lysis.

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Cole DS, Hughes TR, Gasque P, and Morgan BP

Molecular immunology 43(12):1953, 2006 May - Who cited this? | PubMed ID: 16406094 | 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

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

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Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD,

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Nature 440(7084):637, 2006 Mar 30 - Who cited this? | PubMed ID: 16554755 | Fulltext

How many new genes are there?.

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Lee LJ, Hughes TR, and Frey BJ

Science (New York, N.Y.) 311(5768):1709-11; author reply 1709-11, 2006 Mar 24 - Who cited this? | PubMed ID: 16556823 | 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

p53 regulates cellular resistance to complement lysis through enhanced expression of CD59.

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Donev RM, Cole DS, Sivasankar B, Hughes TR, and Morgan BP

Cancer research 66(4):2451, 2006 Feb 15 - Who cited this? | PubMed ID: 16489052 | Fulltext

Mapping pathways and phenotypes by systematic gene overexpression.

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Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, and Andrews B

Molecular cell 21(3):319, 2006 Feb 3 - Who cited this? | PubMed ID: 16455487 | Fulltext

Identification of a bacterial type III effector family with G protein mimicry functions.

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Alto NM, Shao F, Lazar CS, Brost RL, Chua G, Mattoo S, McMahon SA, Ghosh P, Hughes TR, Boone C, and Dixon JE

Cell 124(1):133, 2006 Jan 13 - Who cited this? | PubMed ID: 16413487 | Fulltext

Rapid tRNA decay can result from lack of nonessential modifications.

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Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, and Phizicky EM

Molecular cell 21(1):87, 2006 Jan 6 - Who cited this? | PubMed ID: 16387656 | Fulltext

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