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Publications

The Hughes lab has published over 50 papers since its start in 2001, encompassing independent research, collaborative work, and review papers. The following publications highlight projects orchestrated by students and postdocs in the lab, and represent the general nature of our research. Bold indicates current or former Hughes lab members. * indicates co-first authorship.

See all our publications in PubMed.


Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR. (2016) Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Research. 26(12):1742-1752.

Hamed S. Najafabadi, Mihai Albu, Timothy R. Hughes. (2015) Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinformatics. doi:10.1093/bioinformatics/btv284

Narasimhan K, Lambert S, Yang A, Ridell J, Mnaimneh S, Hong Z, Albu M, Najafabadi H, Reece-Hoyes J, Fuxman B, Walhout A, Weirauch M, Hughes T, Friedman N. (2015) Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife. 10.7554/eLife.06967

Najafabadi H, Mnaimneh S, Schmitges F, Garton M, Lam K, Yang A, Albu M, Weirauch M, Radovani E, Kim P, Greenblatt, Frey B, Hughes T. (2015) C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotech. 10.1038/nbt.3128

Weirauch MT*, Yang A*, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 158(6):1431-43.

de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. (2014) A unified model for yeast transcript definition. Genome Res. 24(1): 154-66.

Hughes TR, de Boer CG. (2014) Mapping yeast transcriptional networks. Genetics. 195(1): 9-36.

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 LOF, Lei EP, Fraser AG, Blencowe BJ, Morris QD & Hughes TR (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499(7457):172–177.

van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. (2013) A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet. 9(5): e1003479.

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. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 31(2):126-34.

de Boer CG, Hughes TR (2012) YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.
Nucleic Acids Res. 2012 Jan;40(Database issue):D169-79. Epub 2011 Nov 18.

van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR and Page JE.
(2011) The draft genome and transcriptome of Cannabis sativa. Genome Biol 12:R102

Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR.
(2011) Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res. 39(11):4680-90

Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR.
(2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 39(Database issue):D301-8. Epub 2010 Oct 29

Weirauch MT, Hughes TR. (2010) Dramatic changes in transcription factor binding over evolutionary time. 11(6):122. Epub 2010 Jun 1.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR.
(2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol. 8(5):e1000371.

Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR.
(2010) High nucleosome occupancy is encoded at human regulatory sequences. PLoS One. 5(2):e9129.

Weirauch MT and Hughes TR.
(2010) Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 26(2):66-74.

Tillo D and Hughes TR. (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics. Dec 22;10(1):442.

Debashish Ray, Hilal Kazan, Esther T. Chan, Lourdes Peņa-Castillo, Sidharth Chaudhry, Shaheynoor Talukder, Benjamin J. Blencowe, Quaid D. Morris, and Timothy R. Hughes
RNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotech. Jul;27(7):667-70

Badis G*, Berger MF*, Philippakis AA*, Talukder S*, Gehrke AR*, Jaeger SA*, Chan ET*, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang C-F, Coburn D, Newburger D, Morris QD, Hughes TR and Bulyk ML
(2009) Diversity and complexity in DNA recognition by transcription factors. Science, in press

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
(2009) Conservation of core gene expression in vertebrate tissues. J Biol Apr 16;8(3):33

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, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C and Hughes TR
(2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell Dec 26;32(6):878-87

Alleyne TM, Peņa-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD and Hughes TR
(2008) Predicting the Binding Preference of Transcription Factors to Individual DNA k-mers. Bioinformatics Dec 16. [Epub ahead of print]

Peņa-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, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.
(2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 9 Suppl 1:S2.

Berger MF*, Badis G*, Gehrke AR*, Talukder S*, Philippakis AA*, Peņa-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML and Hughes TR
(2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell Jun 27;133(7):1266-76

Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD
(2007) Using expression profiling data to identify human microRNA targets. Nat Methods Dec;4(12):1045-9

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C
(2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet Oct;39(10):1235-44

Chen X, Hughes TR, Morris Q
(2007) RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics Jul 1;23(13):i72-9

Pena-Castillo L and Hughes TR
(2007) Why are there still over 1000 uncharacterized yeast genes? Genetics 176:7-14.

Babak T, Blencowe BJ, and Hughes TR
(2007) Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics 8:33

Zhang W, Walker E, Tamplin OJ, Rossant J, Stanford WL and Hughes TR
(2006) Zfp206 regulates ES cell gene expression and differentiation. NAR 34:4780-90.

Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, and Hughes TR
(2006) Identifying transcription factor functions and targets by phenotypic activation. PNAS 103:12045-12050.

Davierwala AP, Haynes J, Li Z, Brost RL, Robinson MD, Yu L, Mnaimneh S, Ding H, Zhu H, Chen Y, Cheng X, Brown GW, Boone C, Andrews BJ and Hughes TR
(2005) The synthetic genetic interaction spectrum of essential genes. Nature Genetics 37:1147-52.

Frey BJ*, Mohammad N*, Morris QD*, Zhang W*, Robinson MD, Mnaimneh S, Shai O, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, and Hughes TR
(2005) Genome-wide analysis of mouse transcription using exon-resolution microarrays and factor graphs. Nature Genetics 37:991-996.

Babak T, Blencowe BJ, and Hughes TR
(2005) A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005 6:104.

Hiley SL, Jackman J, Babak T, Trochesset M, Morris Q, Phizicky E, and Hughes TR
(2005) Detection and discovery of RNA modifications using microarrays. Nucleic Acids Research 33(1):e2.

Zhang W*, Morris Q*, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson M, Zirnglibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng W-T, Krogan, NJ, Greenblatt, JF, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, and Hughes TR
(2004) The functional landscape of mouse gene expression. Journal of Biology 3:21.

Babak T, Zhang W, Morris Q, Blencowe BJ, and Hughes, TR
(2004) Profiling microRNAs with microarrays: tissue specificity and functional inference. RNA 10:1813-9.

Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng W-T, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ and Hughes TR
(2004) Exploration of essential gene functions via titratable promoter alleles. Cell 118:31-44.

Peng W-T, Robinson MD, Mnaimneh S, Krogan N, Cagney G, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Morris Q, Frey BJ, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Boone C, Emili A, Greenblatt J and Hughes TR
(2003) A panoramic view of yeast non-coding RNA processing. Cell 113:919-33.

r17 - 01 Feb 2017 - 02:12:25 - Main.mihai
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