Publications

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

Jolma A, Hernandez-Corchado A, Yang AWH, Fathi A, Laverty KU, Brechalov A, Razavi R, Albu M, Zheng H, Codebook Consortium, Kulakovskiy IV, Najafabadi HS, Hughes TR

Nature methods 23, 1775-1785 · 2026

DOIPubMed

An expanded codebook of human transcription factor DNA-binding specificity

Jolma A, Laverty KU, Fathi A, Yang AWH, Yellan I, Vorontsov IE, Gralak AJ, Kribelbauer-Swietek JF, Inukai S, Razavi R, Albu M, Brechalov A, Patel ZM, Nozdrin V, Meshcheryakov G, Buyan A, Kozin I, Abramov S, Boytsov A, Codebook Consortium, Morris Q, Weirauch MT, Fornes O, Makeev VJ, Grau J, Grosse I, Bucher P, Deplancke B, Kulakovskiy IV, Hughes TR

Nature 657, 275-283 · 2026

DOIPubMed

Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome

Dexheimer PJ, Hass MR, Edsall LE, Diouf AA, Jones SH, Donmez O, Yin C, Dunn KA, Forney C, Hesse HK, VonHandorf A, Chen X, Parameswaran S, Gittens OE, Viel KCMF, Razavi R, Gewurz BE, Zhao B, Lawson LP, Hughes TR, Kottyan LC, Weirauch MT

Cell genomics 6, 101303 · 2026

DOIPubMed

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

Gralak AJ, Faltejskova K, Yang AWH, Steiner C, Russeil J, Grenningloh N, Inukai S, Demir M, Dainese R, Owen C, Pankevich EV, Codebook/GRECO-BIT Consortium, Hughes TR, Kulakovskiy IV, Kribelbauer-Swietek JF, van Mierlo G, Deplancke B

Nature communications 17 · 2026

DOIPubMed

Extensive binding of poorly characterized human transcription factors to genomic dark matter

Razavi R, Fathi A, Yellan I, Brechalov A, Laverty KU, Jolma A, Hernandez-Corchado A, Zheng H, Yang AWH, Albu M, Barazandeh M, Hu C, Vorontsov IE, Patel ZM, Codebook Consortium, Kulakovskiy IV, Bucher P, Morris Q, Najafabadi HS, Hughes TR

Nature communications 17 · 2026

DOIPubMed

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function

Sasse A, Ray D, Laverty KU, Tam CL, Albu M, Zheng H, Levdansky Y, Lyudovyk O, Dalal T, Nie K, Magis C, Notredame C, Valkov E, Weirauch MT, Hughes TR, Morris Q

Nature biotechnology 44, 1226-1236 · 2026

DOIPubMed

CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs

Rosado-Tristani DA, Albu M, Chen X, Sasse A, Laverty KU, Ray D, Tam CL, Ernst K, Lawson LP, Morris QD, Hughes TR, Weirauch MT

Nucleic acids research 54, D98-D105 · 2026

DOIPubMed

Inferring binding specificities of human transcription factors with the wisdom of crowds

Gryzunov N, Penzar D, Kamenets V, Vyaltsev V, Kozin I, Eliseeva IA, Nozdrin V, Vorontsov IE, Bushuev S, Strekalovskikh V, Zinkevich A, Andrews G, Bedarew M, Blass I, Frolov D, Lariushina I, Moore J, Orenstein Y, Roev G, Salimov D, Shimshoviz N, Tziony I, Weng Z, IBIS Consortium, GRECO-BIT/Codebook Consortium, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Jolma A, Kolpakov FA, Makeev VJ, Hughes TR, Kulakovskiy IV

bioRxiv : the preprint server for biology · 2025

DOIPubMed

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

Vorontsov IE, Kozin I, Abramov S, Boytsov A, Jolma A, Albu M, Ambrosini G, Faltejskova K, Gralak AJ, Gryzunov N, Inukai S, Kolmykov S, Kravchenko P, Kribelbauer-Swietek JF, Laverty KU, Nozdrin V, Patel ZM, Penzar D, Plescher ML, Pour SE, Razavi R, Yang AWH, Yevshin I, Zinkevich A, Weirauch MT, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Kolpakov FA, Codebook/GRECO-BIT Consortium, Makeev VJ, Hughes TR, Kulakovskiy IV

Communications biology 8, 1545 · 2025

DOIPubMed

Differential usage of two, distinct DNA-binding domains regulates tissue-specific occupancy of the pioneer factor Zelda

Torres-Zelada EF, Komori H, Liu HY, Larson ED, Yang AWH, Fitzpatrick ZA, Hughes TR, Rushlow CA, Lee CY, Harrison MM

bioRxiv : the preprint server for biology · 2025

DOIPubMed

A multimorphic variant in ThPOK causes an inborn error of immunity with T cell defects and fibrosis

Vaseghi-Shanjani M, Sharma M, Yousefi P, Samra S, Laverty KU, Jolma A, Razavi R, Yang AHW, Albu M, Golding L, Lee AF, Tan R, Richmond PA, Bosticardo M, Rayment JH, Yang CL, Hildebrand KJ, Brager R, Demos MK, Lau YL, Notarangelo LD, Hughes TR, Biggs CM, Turvey SE

The Journal of experimental medicine 222 · 2025

DOIPubMed

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Wang L, Taylor T, Rathnakumar K, Khyzha N, Liang M, Alizada A, Campitelli LF, Pour SE, Patel ZM, Antounians L, Tobias IC, Hou H, Hughes TR, Roy S, Mitchell JA, Fish JE, Wilson MD

Genome research 35, 1544-1559 · 2025

DOIPubMed

C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes

Nabeel-Shah S, Pu S, Burns JD, Braunschweig U, Ahmed N, Burke GL, Lee H, Radovani E, Zhong G, Tang H, Marcon E, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF

Molecular cell 84, 3810-3825.e10 · 2024

DOIPubMed

Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function

Vo NNT, Yang A, Leesutthiphonchai W, Liu Y, Hughes TR, Judelson HS

BMC genomics 25, 710 · 2024

DOIPubMed

The human genome contains over a million autonomous exons

Stepankiw N, Yang AWH, Hughes TR

Genome research 33, 1865-1878 · 2023

DOIPubMedWeb Supplement

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J

Developmental cell 58, 1898-1916.e9 · 2023

DOIPubMed

An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals

Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N

Current biology : CB 33, 3747-3758.e9 · 2023

DOIPubMed

Uncovering a mammalian neural-specific poly(A) binding protein with unique properties

Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR

Genes & development 37, 760-777 · 2023

DOIPubMed

A universal deep-learning model for zinc finger design enables transcription factor reprogramming

Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gionco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB

Nature biotechnology 41, 1117-1129 · 2023

DOIPubMed

Structural insights into DNA recognition by the BEN domain of the transcription factor BANP

Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J

The Journal of biological chemistry 299, 104734 · 2023

DOIPubMed

Known sequence features explain half of all human gene ends

Shkurin A, Pour SE, Hughes TR

NAR genomics and bioinformatics 5, lqad031 · 2023

DOIPubMedWeb Supplement

RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific

Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR

Scientific reports 13, 5238 · 2023

DOIPubMedWeb Supplement

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency

IRF4 International Consortium, Fornes O, Jia A, Kuehn HS, Min Q, Pannicke U, Schleussner N, Thouenon R, Yu Z, de Los Angeles Astbury M, Biggs CM, Galicchio M, Garcia-Campos JA, Gismondi S, Gonzalez Villarreal G, Hildebrand KJ, Hönig M, Hou J, Moshous D, Pittaluga S, Qian X, Rozmus J, Schulz AS, Staines-Boone AT, Sun B, Sun J, Uwe S, Venegas-Montoya E, Wang W, Wang X, Ying W, Zhai X, Zhou Q, Akalin A, André I, Barth TFE, Baumann B, Brüstle A, Burgio G, Bustamante JC, Casanova JL, Casarotto MG, Cavazzana M, Chentout L, Cockburn IA, Costanza M, Cui C, Daumke O, Del Bel KL, Eibel H, Feng X, Franke V, Gebhardt JCM, Götz A, Grunwald S, Hoareau B, Hughes TR, Jacobsen EM, Janz M, Jolma A, Lagresle-Peyrou C, Lai N, Li Y, Lin S, Lu HY, Lugo-Reyes SO, Meng X, Möller P, Moreno-Corona N, Niemela JE, Novakovsky G, Perez-Caraballo JJ, Picard C, Poggi L, Puig-Lombardi ME, Randall KL, Reisser A, Schmitt Y, Seneviratne S, Sharma M, Stoddard J, Sundararaj S, Sutton H, Tran LQ, Wang Y, Wasserman WW, Wen Z, Winkler W, Xiong E, Yang AWH, Yu M, Zhang L, Zhang H, Zhao Q, Zhen X, Enders A, Kracker S, Martinez-Barricarte R, Mathas S, Rosenzweig SD, Schwarz K, Turvey SE, Wang JY

Science immunology 8, eade7953 · 2023

DOIPubMed

PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins

Laverty KU, Jolma A, Pour SE, Zheng H, Ray D, Morris Q, Hughes TR

Nucleic acids research 50, e111 · 2022

DOIPubMedGitHub Code

Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1

Song J, Nabeel-Shah S, Pu S, Lee H, Braunschweig U, Ni Z, Ahmed N, Marcon E, Zhong G, Ray D, Ha KCH, Guo X, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF

Molecular cell 82, 3135-3150.e9 · 2022

DOIPubMed

Reconstruction of full-length LINE-1 progenitors from ancestral genomes

Campitelli LF, Yellan I, Albu M, Barazandeh M, Patel ZM, Blanchette M, Hughes TR

Genetics 221 · 2022

DOIPubMedWeb Supplement

The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians

Spruce T, Plass M, Gohr A, Ray D, Martínez de Lagrán M, Rot G, Nóvoa A, Burguera D, Permanyer J, Miret M, Zheng H, Swanson MS, Morris Q, Mallo M, Dierssen M, Hughes TR, Pernaute B, Irimia M

PLoS biology 20, e3001615 · 2022

DOIPubMed

Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins

Zheng L, Liu J, Niu L, Kamran M, Yang AWH, Jolma A, Dai Q, Hughes TR, Patel DJ, Zhang L, Prasanth SG, Yu Y, Ren A, Lai EC

Genes & development 36, 225-240 · 2022

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Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms

Patel ZM, Hughes TR

Genome biology 22, 285 · 2021

DOIPubMed

Known sequence features can explain half of all human gene ends

Shkurin A, Hughes TR

NAR genomics and bioinformatics 3, lqab042 · 2021

DOIPubMedRetraction notice

Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons

Yellan I, Yang AWH, Hughes TR

Molecular biology and evolution 38, 2070-2075 · 2021

DOIPubMedWeb Supplement

Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains

Zhang M, Lei M, Qin S, Dong A, Yang A, Li Y, Loppnau P, Hughes TR, Min J, Liu Y

Biochimica et biophysica acta. Gene regulatory mechanisms 1864, 194688 · 2021

DOIPubMed

The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation

Kosti A, de Araujo PR, Li WQ, Guardia GDA, Chiou J, Yi C, Ray D, Meliso F, Li YM, Delambre T, Qiao M, Burns SS, Lorbeer FK, Georgi F, Flosbach M, Klinnert S, Jenseit A, Lei X, Sandoval CR, Ha K, Zheng H, Pandey R, Gruslova A, Gupta YK, Brenner A, Kokovay E, Hughes TR, Morris QD, Galante PAF, Tiziani S, Penalva LOF

Genome biology 21, 195 · 2020

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Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

Jolma A, Zhang J, Mondragón E, Morgunova E, Kivioja T, Laverty KU, Yin Y, Zhu F, Bourenkov G, Morris Q, Hughes TR, Maher LJ, Taipale J

Genome research 30, 962-973 · 2020

DOIPubMed

A bacteriophage mimic of the bacterial nucleoid-associated protein Fis

Chakraborti S, Balakrishnan D, Trotter AJ, Gittens WH, Yang AWH, Jolma A, Paterson JR, Świątek S, Plewka J, Curtis FA, Bowers LY, Pålsson LO, Hughes TR, Taube M, Kozak M, Heddle JG, Sharples GJ

The Biochemical journal 477, 1345-1362 · 2020

DOIPubMed

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

Nature genetics 51, 981-989 · 2019

DOIPubMedCisBP Webserver

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 research 47, 2856-2870 · 2019

DOIPubMedProteomeXchange

Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Buckley MA, Woods NT, Tyrer JP, Mendoza-Fandiño G, Lawrenson K, Hazelett DJ, Najafabadi HS, Gjyshi A, Carvalho RS, Lyra PC, Coetzee SG, Shen HC, Yang AW, Earp MA, Yoder SJ, Risch H, Chenevix-Trench G, Ramus SJ, Phelan CM, Coetzee GA, Noushmehr H, Hughes TR, Sellers TA, Goode EL, Pharoah PD, Gayther SA, Monteiro ANA, Ovarian Cancer Association Consortium

Cancer research 79, 467-481 · 2019

DOIPubMed

A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci

Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H

Genome research 29, 146-156 · 2019

DOIPubMed

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 7 · 2018

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Motif models for RNA-binding proteins

Sasse A, Laverty KU, Hughes TR, Morris QD

Current opinion in structural biology 53, 115-123 · 2018

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How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome

Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B

Nucleic acids research 46, 10514-10529 · 2018

DOIPubMed

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 chemical biology 13, 3000-3010 · 2018

DOIPubMed

The Human Transcription Factors

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT

Cell 175, 598-599 · 2018

DOIPubMedOriginal article

Neurospora crassa developmental control mediated by the FLB-3 transcription factor

Boni AC, Ambrósio DL, Cupertino FB, Montenegro-Montero A, Virgilio S, Freitas FZ, Corrocher FA, Gonçalves RD, Yang A, Weirauch MT, Hughes TR, Larrondo LF, Bertolini MC

Fungal biology 122, 570-582 · 2018

DOIPubMed

Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA

Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J

The Journal of biological chemistry 293, 7344-7354 · 2018

DOIPubMed

The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor

Townsend PD, Dixon CH, Slootweg EJ, Sukarta OCA, Yang AWH, Hughes TR, Sharples GJ, Pålsson LO, Takken FLW, Goverse A, Cann MJ

The Journal of biological chemistry 293, 3218-3233 · 2018

DOIPubMed

The Human Transcription Factors

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT

Cell 172, 650-665 · 2018

DOIPubMedCorrectionHumantTFs Webserver

Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins

Barazandeh M, Lambert SA, Albu M, Hughes TR

G3 (Bethesda, Md.) 8, 219-229 · 2018

DOIPubMedWeb Supplement

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants

Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J

Structure (London, England : 1993) 26, 85-95.e3 · 2018

DOIPubMed

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR

Genome biology 18, 167 · 2017

DOIPubMed

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 (San Diego, Calif.) 126, 18-28 · 2017

DOIPubMedWeb Supplement

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 32, 101-114.e8 · 2017

DOIPubMed

Transcription factors read epigenetics

Hughes TR, Lambert SA

Science (New York, N.Y.) 356, 489-490 · 2017

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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 (San Diego, Calif.) 118-119, 3-15 · 2017

DOIPubMed

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ

Molecular cell 65, 539-553.e7 · 2017

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Multiparameter functional diversity of human C2H2 zinc finger proteins

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

Genome research 26, 1742-1752 · 2016

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Motif comparison based on similarity of binding affinity profiles

Lambert SA, Albu M, Hughes TR, Najafabadi HS

Bioinformatics (Oxford, England) 32, 3504-3506 · 2016

DOIPubMedMosbat Webserver

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

van der Does HC, Fokkens L, Yang A, Schmidt SM, Langereis L, Lukasiewicz JM, Hughes TR, Rep M

PLoS genetics 12, e1006401 · 2016

DOIPubMedCorrection

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N

eLife 5 · 2016

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Affinity regression predicts the recognition code of nucleic acid-binding proteins

Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS

Nature biotechnology 33, 1242-1249 · 2015

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The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G

Cell reports 13, 1206-1220 · 2015

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A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM

Nucleic acids research 43, 9147-57 · 2015

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Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE

Najafabadi HS, Albu M, Hughes TR

Bioinformatics (Oxford, England) 31, 2879-81 · 2015

DOIPubMedRCADE Webserver

A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT

Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B

PLoS pathogens 11, e1004967 · 2015

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Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA

Genome biology 16, 94 · 2015

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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

Nature biotechnology 33, 555-62 · 2015

DOIPubMedWeb Supplement

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR

eLife 4 · 2015

DOIPubMedCisBP WebserverWeb Supplement

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 (New York, N.Y.) 347, 1254806 · 2015

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High-throughput characterization of protein-RNA interactions

Cook KB, Hughes TR, Morris QD

Briefings in functional genomics 14, 74-89 · 2015

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Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA

Cell reports 8, 2015-2030 · 2014

DOIPubMed

Determination and inference of eukaryotic transcription factor sequence specificity

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 AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR

Cell 158, 1431-1443 · 2014

DOIPubMedCisBP WebserverWeb Supplement

A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types

Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA

Molecular cell 54, 946-959 · 2014

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Identifying mRNA sequence elements for target recognition by human Argonaute proteins

Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z

Genome research 24, 775-85 · 2014

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A novel C2H2 transcription factor that regulates gliA expression interdependently with GliZ in Aspergillus fumigatus

Schoberle TJ, Nguyen-Coleman CK, Herold J, Yang A, Weirauch M, Hughes TR, McMurray JS, May GS

PLoS genetics 10, e1004336 · 2014

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Poly-dA:dT tracts form an in vivo nucleosomal turnstile

de Boer CG, Hughes TR

PloS one 9, e110479 · 2014

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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 research 24, 154-66 · 2014

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Early evolution of the T-box transcription factor family

Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I

Proceedings of the National Academy of Sciences of the United States of America 110, 16050-5 · 2013

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Mapping yeast transcriptional networks

Hughes TR, de Boer CG

Genetics 195, 9-36 · 2013

DOIPubMed

Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network

Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJ

Molecular cell 51, 116-27 · 2013

DOIPubMed

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 499, 172-7 · 2013

DOIPubMedCisBP-RNA Webserver

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR

eLife 2, e00675 · 2013

DOIPubMed

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo

Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C

Genome research 23, 988-97 · 2013

DOIPubMed

A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription

van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C

PLoS genetics 9, e1003479 · 2013

DOIPubMedWeb Supplement

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

Nature biotechnology 31, 126-34 · 2013

DOIPubMedWeb Supplement

DNA-binding specificities of human transcription factors

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J

Cell 152, 327-39 · 2013

DOIPubMed

Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints

Smith SA, Ray D, Cook KB, Mallory MJ, Hughes TR, Lynch KW

PloS one 8, e80701 · 2013

DOIPubMed

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

de Boer CG, Hughes TR

Nucleic acids research 40, D169-79 · 2012

DOIPubMedYetfasco Server

The draft genome and transcriptome of Cannabis sativa

van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE

Genome biology 12, R102 · 2011

DOIPubMedCanabis Genome Browser

BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium

Huang E, Talukder S, Hughes TR, Curk T, Zupan B, Shaulsky G, Katoh-Kurasawa M

Developmental biology 358, 137-46 · 2011

DOIPubMed

An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming

Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, Nagy A, Wrana JL, Blencowe BJ

Cell 147, 132-46 · 2011

DOIPubMed

Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J

Proceedings of the National Academy of Sciences of the United States of America 108, 10690-5 · 2011

DOIPubMed

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR

Nucleic acids research 39, 4680-90 · 2011

DOIPubMedWeb Supplement

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays

Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L, Ray D, van Bakel H, Hughes TR, Kushner SR

Nucleic acids research 39, 3188-203 · 2011

DOIPubMed

RBPDB: a database of RNA-binding specificities

Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR

Nucleic acids research 39, D301-8 · 2011

DOIPubMedRBPDB Server

Introduction to "a handbook of transcription factors"

Hughes TR

Sub-cellular biochemistry 52, 1-6 · 2011

DOIPubMed

A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution

Weirauch MT, Hughes TR

Sub-cellular biochemistry 52, 25-73 · 2011

DOIPubMed

Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences

Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ

Nucleic acids research 38, 7927-42 · 2010

DOIPubMed

Information propagation within the Genetic Network of Saccharomyces cerevisiae

Chowdhury S, Lloyd-Price J, Smolander OP, Baici WC, Hughes TR, Yli-Harja O, Chua G, Ribeiro AS

BMC systems biology 4, 143 · 2010

DOIPubMed

FuncBase: a resource for quantitative gene function annotation

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP

Bioinformatics (Oxford, England) 26, 1806-7 · 2010

DOIPubMed

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J

The EMBO journal 29, 2147-60 · 2010

DOIPubMed

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins

Kazan H, Ray D, Chan ET, Hughes TR, Morris Q

PLoS computational biology 6, e1000832 · 2010

DOIPubMed

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J

Genome research 20, 861-73 · 2010

DOIPubMed

Most "dark matter" transcripts are associated with known genes

van Bakel H, Nislow C, Blencowe BJ, Hughes TR

PLoS biology 8, e1000371 · 2010

DOIPubMedWeb Supplement

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

Jaeger SA, Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML

Genomics 95, 185-95 · 2010

DOIPubMed

High nucleosome occupancy is encoded at human regulatory sequences

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

PloS one 5, e9129 · 2010

DOIPubMed

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

Weirauch MT, Hughes TR

Trends in genetics : TIG 26, 66-74 · 2010

DOIPubMed

Dramatic changes in transcription factor binding over evolutionary time

Weirauch MT, Hughes TR

Genome biology 11, 122 · 2010

DOIPubMed

G+C content dominates intrinsic nucleosome occupancy

Tillo D, Hughes TR

BMC bioinformatics 10, 442 · 2009

DOIPubMed

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300

Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ

RNA (New York, N.Y.) 15, 2174-85 · 2009

DOIPubMed

Establishing legitimacy and function in the new transcriptome

van Bakel H, Hughes TR

Briefings in functional genomics & proteomics 8, 424-36 · 2009

DOIPubMed

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

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

Molecular cell 35, 340-51 · 2009

DOIPubMed

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

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

Nature biotechnology 27, 667-70 · 2009

DOIPubMedWeb Supplement

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

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

Methods (San Diego, Calif.) 48, 258-64 · 2009

DOIPubMed

Diversity and complexity in DNA recognition by transcription factors

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, Bulyk ML

Science (New York, N.Y.) 324, 1720-3 · 2009

DOIPubMed

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 (Oxford, England) 25, 1012-8 · 2009

DOIPubMedWeb Supplement

The DNA-encoded nucleosome organization of a eukaryotic genome

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

Nature 458, 362-6 · 2009

DOIPubMed

TFCat: the curated catalog of mouse and human transcription factors

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

Genome biology 10, R29 · 2009

DOIPubMed

Prediction and verification of mouse tRNA gene families

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

RNA biology 6, 195-202 · 2009

DOIPubMed

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

Journal of biology 8, 33 · 2009

DOIPubMedWeb Supplement

'Validation' in genome-scale research

Hughes TR

Journal of biology 8, 3 · 2009

DOIPubMed

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

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, Hughes TR

Molecular cell 32, 878-87 · 2008

DOIPubMedWeb Supplement

Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome

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

PLoS biology 6, e277 · 2008

DOIPubMed

Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes

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

PLoS genetics 4, e1000112 · 2008

DOIPubMed

A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae

Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J

Molecular biology of the cell 19, 3028-39 · 2008

DOIPubMed

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 133, 1266-76 · 2008

DOIPubMedWeb Supplement

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

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

PLoS pathogens 4, e1000068 · 2008

DOIPubMed

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

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

Journal of proteome research 7, 1529-41 · 2008

DOIPubMed

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

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

The Journal of cell biology 180, 563-78 · 2008

DOIPubMed

miRNA and piRNA localization in the male mammalian meiotic nucleus

Marcon E, Babak T, Chua G, Hughes T, Moens PB

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 16, 243-60 · 2008

DOIPubMed

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

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, 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

Genome biology 9 Suppl 1, S2 · 2008

DOIPubMed

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

Nature methods 4, 1045-9 · 2007

DOIPubMed

Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford JL

Genes & development 21, 2580-92 · 2007

DOIPubMed

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

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

Cell 131, 174-87 · 2007

DOIPubMed

A high-resolution atlas of nucleosome occupancy in yeast

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

Nature genetics 39, 1235-44 · 2007

DOIPubMedWeb Supplement

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

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, Coulombe B

Molecular cell 27, 262-274 · 2007

DOIPubMedWeb Supplement

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

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

Molecular cell 27, 275-288 · 2007

DOIPubMed

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

Chen X, Hughes TR, Morris Q

Bioinformatics (Oxford, England) 23, i72-9 · 2007

DOIPubMed

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

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

Cell stem cell 1, 71-86 · 2007

DOIPubMed

Why are there still over 1000 uncharacterized yeast genes?

Peña-Castillo L, Hughes TR

Genetics 176, 7-14 · 2007

DOIPubMed

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

Babak T, Blencowe BJ, Hughes TR

BMC bioinformatics 8, 33 · 2007

DOIPubMed

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

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

Developmental cell 12, 143-55 · 2007

DOIPubMed

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 biology 8, R108 · 2007

DOIPubMed

Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria

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

BMC genomics 7, 295 · 2006

DOIPubMedWeb Supplement

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

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

Molecular biology of the cell 17, 4736-47 · 2006

DOIPubMed

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 126, 611-25 · 2006

DOIPubMed

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

Proceedings of the National Academy of Sciences of the United States of America 103, 12045-50 · 2006

DOIPubMedWeb Supplement

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

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, Emili A

Cell 125, 173-86 · 2006

DOIPubMed

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF

Nature 440, 637-43 · 2006

DOIPubMed

Mapping pathways and phenotypes by systematic gene overexpression

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

Molecular cell 21, 319-30 · 2006

DOIPubMed

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

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

Cell 124, 133-45 · 2006

DOIPubMed

Rapid tRNA decay can result from lack of nonessential modifications

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

Molecular cell 21, 87-96 · 2006

DOIPubMed

Zfp206 regulates ES cell gene expression and differentiation

Zhang W, Walker E, Tamplin OJ, Rossant J, Stanford WL, Hughes TR

Nucleic acids research 34, 4780-90 · 2006

DOIPubMedWeb Supplement

The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis

Leeds NB, Small EC, Hiley SL, Hughes TR, Staley JP

Molecular and cellular biology 26, 513-22 · 2006

DOIPubMedWeb Supplement

Microarray analysis of RNA processing and modification

Hughes TR, Hiley SL, Saltzman AL, Babak T, Blencowe BJ

Methods in enzymology 410, 300-16 · 2006

DOIPubMed

Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex

Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ

Cell 123, 593-605 · 2005

DOIPubMed

The synthetic genetic interaction spectrum of essential genes

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, Hughes TR

Nature genetics 37, 1147-52 · 2005

DOIPubMedWeb Supplement

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

Nature genetics 37, 991-6 · 2005

DOIPubMedWeb Supplement

BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex

Laribee RN, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD

Current biology : CB 15, 1487-93 · 2005

DOIPubMed

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

Babak T, Blencowe BJ, Hughes TR

BMC genomics 6, 104 · 2005

DOIPubMedWeb Supplement

Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III

Henras AK, Sam M, Hiley SL, Wu H, Hughes TR, Feigon J, Chanfreau GF

RNA (New York, N.Y.) 11, 1225-37 · 2005

DOIPubMed

Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction

Hoang T, Peng WT, Vanrobays E, Krogan N, Hiley S, Beyer AL, Osheim YN, Greenblatt J, Hughes TR, Lafontaine DL

Molecular and cellular biology 25, 5523-34 · 2005

DOIPubMedWeb Supplement

H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex

Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL

Molecular and cellular biology 25, 1162-72 · 2005

DOIPubMed

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

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

Trends in genetics : TIG 21, 73-7 · 2005

DOIPubMed

Detection and discovery of RNA modifications using microarrays

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

Nucleic acids research 33, e2 · 2005

DOIPubMedWeb Supplement

Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing

Hiley SL, Babak T, Hughes TR

Nucleic acids research 33, 3048-56 · 2005

DOIPubMedWeb Supplement

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

Molecular cell 16, 929-41 · 2004

DOIPubMed

Probing microRNAs with microarrays: tissue specificity and functional inference

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

RNA (New York, N.Y.) 10, 1813-9 · 2004

DOIPubMedWeb Supplement

The promise of functional genomics: completing the encyclopedia of a cell

Hughes TR, Robinson MD, Mitsakakis N, Johnston M

Current opinion in microbiology 7, 546-54 · 2004

DOIPubMed

Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4

Krogan NJ, Baetz K, Keogh MC, Datta N, Sawa C, Kwok TC, Thompson NJ, Davey MG, Pootoolal J, Hughes TR, Emili A, Buratowski S, Hieter P, Greenblatt JF

Proceedings of the National Academy of Sciences of the United States of America 101, 13513-8 · 2004

DOIPubMed

RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits

Jeronimo C, Langelier MF, Zeghouf M, Cojocaru M, Bergeron D, Baali D, Forget D, Mnaimneh S, Davierwala AP, Pootoolal J, Chandy M, Canadien V, Beattie BK, Richards DP, Workman JL, Hughes TR, Greenblatt J, Coulombe B

Molecular and cellular biology 24, 7043-58 · 2004

DOIPubMed

Exploration of essential gene functions via titratable promoter alleles

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, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR

Cell 118, 31-44 · 2004

DOIPubMedWeb Supplement

Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors

Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR

Molecular and cellular biology 24, 5534-47 · 2004

DOIPubMedWeb Supplement

The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs

Xing F, Hiley SL, Hughes TR, Phizicky EM

The Journal of biological chemistry 279, 17850-60 · 2004

DOIPubMedWeb Supplement

High-definition macromolecular composition of yeast RNA-processing complexes

Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP, Beattie BK, Lalev A, Zhang W, Davierwala AP, Mnaimneh S, Starostine A, Tikuisis AP, Grigull J, Datta N, Bray JE, Hughes TR, Emili A, Greenblatt JF

Molecular cell 13, 225-39 · 2004

DOIPubMedWeb Supplement

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

Journal of biology 3, 21 · 2004

DOIPubMedWeb Supplement

MyMed: A database system for biomedical research on MEDLINE data

Lewis, K., Robinson, M., Hughes, T.R., and Hogue, C.

IBM Systems Journal 43:4. · 2004

Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways

Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C

Nature biotechnology 22, 62-9 · 2004

DOIPubMed

ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae

Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR

Nucleic acids research 32, 1993-9 · 2004

DOIPubMed

A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1

Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF

Molecular cell 12, 1565-76 · 2003

DOIPubMed

RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesis

Nelson B, Kurischko C, Horecka J, Mody M, Nair P, Pratt L, Zougman A, McBroom LD, Hughes TR, Boone C, Luca FC

Molecular biology of the cell 14, 3782-803 · 2003

DOIPubMed

Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends

Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J

The Journal of biological chemistry 278, 33000-10 · 2003

DOIPubMedWeb Supplement

A panoramic view of yeast noncoding RNA processing

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, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR

Cell 113, 919-33 · 2003

DOIPubMed

FunSpec: a web-based cluster interpreter for yeast

Robinson MD, Grigull J, Mohammad N, Hughes TR

BMC bioinformatics 3, 35 · 2002

DOIPubMedFunspec Server (Internal server)

Yeast and drug discovery

Hughes TR

Functional & integrative genomics 2, 199-211 · 2002

DOIPubMed

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters

Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ

Nature genetics 31, 255-65 · 2002

DOIPubMedWeb Supplement

Conserved structure for single-stranded telomeric DNA recognition

Mitton-Fry RM, Anderson EM, Hughes TR, Lundblad V, Wuttke DS

Science (New York, N.Y.) 296, 145-7 · 2002

DOIPubMed

Role of scaffolds in MAP kinase pathway specificity revealed by custom design of pathway-dedicated signaling proteins

Harris K, Lamson RE, Nelson B, Hughes TR, Marton MJ, Roberts CJ, Boone C, Pryciak PM

Current biology : CB 11, 1815-24 · 2001

PubMed

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS

Nature biotechnology 19, 342-7 · 2001

DOIPubMed

Cdc13 both positively and negatively regulates telomere replication

Chandra A, Hughes TR, Nugent CI, Lundblad V

Genes & development 15, 404-14 · 2001

DOIPubMed

A novel gene conserved from yeast to humans is involved in sterol biosynthesis

Gachotte D, Eckstein J, Barbuch R, Hughes T, Roberts C, Bard M

Journal of lipid research 42, 150-4 · 2001

PubMed

Functional discovery via a compendium of expression profiles

Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH

Cell 102, 109-26 · 2000

DOIPubMedWeb Supplement

Widespread aneuploidy revealed by DNA microarray expression profiling

Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ

Nature genetics 25, 333-7 · 2000

DOIPubMedWeb Supplement

The Est3 protein is a subunit of yeast telomerase

Hughes TR, Evans SK, Weilbaecher RG, Lundblad V

Current biology : CB 10, 809-12 · 2000

DOIPubMed

Identification of the single-strand telomeric DNA binding domain of the Saccharomyces cerevisiae Cdc13 protein

Hughes TR, Weilbaecher RG, Walterscheid M, Lundblad V

Proceedings of the National Academy of Sciences of the United States of America 97, 6457-62 · 2000

DOIPubMed

Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles

Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH

Science (New York, N.Y.) 287, 873-80 · 2000

DOIPubMedWeb Supplement

Genetic selection of peptide inhibitors of biological pathways

Norman TC, Smith DL, Sorger PK, Drees BL, O'Rourke SM, Hughes TR, Roberts CJ, Friend SH, Fields S, Murray AW

Science (New York, N.Y.) 285, 591-5 · 1999

DOIPubMed

Three Ever Shorter Telomere (EST) genes are dispensable for in vitro yeast telomerase activity

Lingner J, Cech TR, Hughes TR, Lundblad V

Proceedings of the National Academy of Sciences of the United States of America 94, 11190-5 · 1997

DOIPubMed

Reverse transcriptase motifs in the catalytic subunit of telomerase

Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V, Cech TR

Science (New York, N.Y.) 276, 561-7 · 1997

DOIPubMed

Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance

Nugent CI, Hughes TR, Lue NF, Lundblad V

Science (New York, N.Y.) 274, 249-52 · 1996

DOIPubMed

Analysis of the distal 5' region of the human CYP17 gene

Maghsoudlou SS, Hughes TR, Hornsby PJ

Genome 38, 845-9 · 1995

DOIPubMed