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T

Timothy R. Hughes

university of toronto

96H-index
288Paper Count
5.0WCitation Count
Published Papers 137
Publication Date
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Extensive binding of poorly characterized human transcription factors to genomic dark matter
errNature Communications
IF15.7
err2026-08-05
err0
errOAAI
errRozita Razavi; Ali Fathi; Isaac Yellan; Alexander Brechalov; Kaitlin U. Laverty; Arttu Jolma; Aldo Hernandez-Corchado; Hong Zheng; Ally W. H. Yang; Mihai Albu; Marjan Barazandeh; Chun Hu; Ilya E. Vorontsov; Zain M. Patel; Ivan V. Kulakovskiy; Philipp Bucher; Quaid Morris; Hamed S. Najafabadi; Timothy R. Hughes
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errSave
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors
errNature Methods
IF32.1
err2026-08-05
err0
errOAAI
errArttu Jolma; Aldo Hernandez-Corchado; Ally W. H. Yang; Ali Fathi; Kaitlin U. Laverty; Alexander Brechalov; Rozita Razavi; Mihai Albu; Hong Zheng; Ivan V. Kulakovskiy; Hamed S. Najafabadi; Timothy R. Hughes
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errSave
An expanded codebook of human transcription factor DNA-binding specificity
errNature
IF48.5
err2026-08-05
err0
errOAAI
errArttu Jolma; Kaitlin U. Laverty; Ali Fathi; Ally W. H. Yang; Isaac Yellan; Ilya E. Vorontsov; Antoni J. Gralak; Judith F. Kribelbauer-Swietek; Sachi Inukai; Rozita Razavi; Mihai Albu; Alexander Brechalov; Zain M. Patel; Vladimir Nozdrin; Georgy Meshcheryakov; Andrey Buyan; Ivan Kozin; Sergey Abramov; Alexandr Boytsov; Quaid Morris; Matthew T. Weirauch; Oriol Fornes; Vsevolod J. Makeev; Jan Grau; Ivo Grosse; Philipp Bucher; Bart Deplancke; Ivan V. Kulakovskiy; Timothy R. Hughes
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errSave
Identification of methylation-sensitive human transcription factors using meSMiLE-seq
errNature Communications
IF15.7
err2026-08-05
err0
errOAAI
errAntoni J. Gralak; Katerina Faltejskova; Ally W. H. Yang; Clemence Steiner; Julie Russeil; Nadia Grenningloh; Sachi Inukai; Mustafa Demir; Riccardo Dainese; Cooper Owen; Eugenia V. Pankevich; Timothy R. Hughes; Ivan V. Kulakovskiy; Judith F. Kribelbauer-Swietek; Guido van Mierlo; Bart Deplancke
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errSave
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
errCommunications Biology
IF5.1
err2025-11-07
err0
errOAAI
errIlya E. Vorontsov; Ivan Kozin; Sergey Abramov; Alexandr Boytsov; Arttu Jolma; Mihai Albu; Giovanna Ambrosini; Katerina Faltejskova; Antoni J. Gralak; Nikita Gryzunov; Sachi Inukai; Semyon Kolmykov; Pavel Kravchenko; Judith F. Kribelbauer-Swietek; Kaitlin U. Laverty; Vladimir Nozdrin; Zain M. Patel; Dmitry Penzar; Marie-Luise Plescher; Sara E. Pour; Rozita Razavi; Ally W. H. Yang; Ivan Yevshin; Arsenii Zinkevich; Matthew T. Weirauch; Philipp Bucher; Bart Deplancke; Oriol Fornes; Jan Grau; Ivo Grosse; Fedor A. Kolpakov; Vsevolod J. Makeev; Timothy R. Hughes; Ivan V. Kulakovskiy
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errSave
CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-10-01
err1
errOAAI
errRosado-Tristani, Diego A.; Albu, Mihai; Chen, Xiaoting; Sasse, Alexander; Laverty, Kaitlin U.; Ray, Debashish; Tam, Cyrus L.; Ernst, Kevin; Lawson, Lucinda P.; Morris, Quaid D.; Hughes, Timothy R.; Weirauch, Matthew T.
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errSave
At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways
errNEW PHYTOLOGIST
IF8.1
err2025-05-26
err0
errOAAI
errKoester, Tino; Venhuizen, Peter; Lewinski, Martin; Petrillo, Ezequiel; Marquez, Yamile; Fuchs, Armin; Ray, Debashish; Nimeth, Barbara A.; Riegler, Stefan; Franzmeier, Sophie; Rodriguez, Florencia S.; Aballay, Federico E.; Tognacca, Rocio S.; Zheng, Hong; Hughes, Timothy; Morris, Quaid; Barta, Andrea; Staiger, Dorothee; Kalyna, Maria
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errSave
A multimorphic variant in ThPOK causes an inborn error of immunity with T cell defects and fibrosis
errJOURNAL OF EXPERIMENTAL MEDICINE
IF10.6
err2025-05-20
err0
PREAI
errVaseghi-Shanjani, Maryam; Sharma, Mehul; Yousefi, Pariya; Samra, Simran; Laverty, Kaitlin U.; Jolma, Arttu; Razavi, Rozita; Yang, Ally H. W.; Albu, Mihai; Golding, Liam; Lee, Anna F.; Tan, Ryan; Richmond, Phillip A.; Bosticardo, Marita; Rayment, Jonathan H.; Yang, Connie L.; Hildebrand, Kyla J.; Brager, Rae; Demos, Michelle K.; Lau, Yu-Lung; Notarangelo, Luigi D.; Hughes, Timothy R.; Biggs, Catherine M.
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errSave
Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function
errBMC GENOMICS
IF3.7
err2024-07-23
err0
errOAAI
errVo, Nguyen N. T.; Yang, Ally; Leesutthiphonchai, Wiphawee; Liu, Yulong; Hughes, Timothy R.; Judelson, Howard S.
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errSave
The human genome contains over a million autonomous exons
errGENOME RESEARCH
IF5.5
err2023-11-09
err3
errOAAI
errStepankiw, Nicholas; Yang, Ally W. H.; Hughes, Timothy R.
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errSave
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
errDEVELOPMENTAL CELL
IF8.7
err2023-10-01
err16
errOAAI
errBrennan, Kaelan J.; Weilert, Melanie; Krueger, Sabrina; Pampari, Anusri; Liu, Hsiao-yun; Yang, Ally W. H.; Morrison, Jason A.; Hughes, Timothy R.; Rushlow, Christine A.; Kundaje, Anshul; Zeitlinger, Julia
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errSave
An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals
errCURRENT BIOLOGY
IF7.5
err2023-09-01
err4
errOAAI
errCoyle, Maxwell C.; Tajima, Adia M.; Leon, Fredrick; Choksi, Semil P.; Yang, Ally; Espinoza, Sarah; Hughes, Timothy R.; Reiter, Jeremy F.; Booth, David S.; King, Nicole
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errSave
Structural insights into DNA recognition by the BEN domain of the transcription factor BANP
errJOURNAL OF BIOLOGICAL CHEMISTRY
IF3.9
err2023-06-01
err4
errOAAI
errLiu, Ke; Zhang, Jin; Xiao, Yuqing; Yang, Ally; Song, Xiaosheng; Li, Yanjun; Chen, Yunxia; Hughes, Timothy R.; Min, Jinrong
errShare
errSave
Known sequence features explain half of all human gene ends
errgenomics proteomics bioinformatics
IF2.8
err2023-04-05
err0
errOAAI
errShkurin, Aleksei; Pour, Sara E.; Hughes, Timothy R.
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errSave
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
errSCIENTIFIC REPORTS
IF3.9
err2023-03-31
err26
errOAAI
errRay, Debashish; Laverty, Kaitlin U.; Jolma, Arttu; Nie, Kate; Samson, Reuben; Pour, Sara E.; Tam, Cyrus L.; von Krosigk, Niklas; Nabeel-Shah, Syed; Albu, Mihai; Zheng, Hong; Perron, Gabrielle; Lee, Hyunmin; Najafabadi, Hamed; Blencowe, Benjamin; Greenblatt, Jack; Morris, Quaid; Hughes, Timothy R.
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errSave
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-27
err147
errOAAI
errIngvarsdottir, K; Krogan, NJ; Emre, NCT; Wyce, A; Thompson, NJ; Emili, A; Hughes, TR; Greenblatt, JF; Berger, SL
errShare
errSave
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-27
err335
errOAAI
errGrigull, J; Mnaimneh, S; Pootoolal, J; Robinson, MD; Hughes, TR
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errSave
Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-27
err38
errOAAI
errHoang, T; Peng, WT; Vanrobays, E; Krogan, N; Hiley, S; Beyer, AL; Osheim, YN; Greenblatt, J; Hughes, TR; Lafontaine, DLJ
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errSave
RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-27
err71
errOAAI
errJeronimo, 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
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errSave
The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-27
err118
errOAAI
errLeeds, NB; Small, EC; Hiley, SL; Hughes, TR; Staley, JP
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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M Snyder
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Jean‐Laurent Casanova
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Joseph R. Ecker
H-index: 168 · Papers: 535
P
Paul D.P. Pharoah
H-index: 150 · Papers: 1.8K
J
Janet Rossant
H-index: 149 · Papers: 1.1K
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