Timothy Hughes, University of Toronto

Research

Read how they describe their research on their University of Toronto profile.

Genomics Genetics Systems biology Molecular genetics Cellular interactions (including adhesion, matrix and cell wall)

Latest papers

At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.
The New phytologist · 2025
A TATA-box-binding protein binds single-stranded DNA in two modes: To poly(G) tracts and to flexible DNA regions.
The Journal of biological chemistry · 2025
At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.
bioRxiv : the preprint server for biology · 2024

All 6 publications

Latest funding

Codebook: comprehensive and accurate motifs for human transcription factors
CIHR · 2023 · Nominated PI
$1,411,425
Systematic analysis of human C2H2 zinc finger proteins
CIHR · 2023 · Nominated PI
$1,201,050
Sequence Determinants of Human Gene Identity
CIHR · 2022 · Nominated PI
$906,525

All 23 grants and awards

6 publications.

01

At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.

Köster T, Venhuizen P, Lewinski M, Petrillo E, Marquez Y, Fuchs A, Ray D, Nimeth BA, Riegler S, Franzmeier S, Rodríguez FS, Aballay FE, Tognacca RS, Zheng H, Hughes T, Morris Q, Barta A, Staiger D, Kalyna M

The New phytologist2025

DOI: 10.1111/nph.70221 PMID: 40415535

02

A TATA-box-binding protein binds single-stranded DNA in two modes: To poly(G) tracts and to flexible DNA regions.

Freitag K, Marlow M, Joseph J, Ta R, Krekhno J, Schuett E, Yang A, Ray D, Hughes T, Rafferty S, Yee J

The Journal of biological chemistry2025

DOI: 10.1016/j.jbc.2025.108552 PMID: 40300727

03

At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.

Köster T, Venhuizen P, Lewinski M, Petrillo E, Marquez Y, Fuchs A, Ray D, Nimeth BA, Riegler S, Franzmeier S, Zheng H, Hughes T, Morris Q, Barta A, Staiger D, Kalyna M

bioRxiv : the preprint server for biology2024

DOI: 10.1101/2024.12.04.626797 PMID: 39677721

04

An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.

Collins KM, Kainov YA, Christodolou E, Ray D, Morris Q, Hughes T, Taylor IA, Makeyev EV, Ramos A

Nucleic acids research2017

DOI: 10.1093/nar/gkx225 PMID: 28379442

05

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

Blencowe B, Brenner S, Hughes T, Morris Q

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2009

PMID: 19209730

06

The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.

Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sánchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM

The Journal of biological chemistry2005

DOI: 10.1074/jbc.m414421200 PMID: 15701634

Codebook: comprehensive and accurate motifs for human transcription factors

Nominated PICIHR2023Project Grant

Principal investigators: Hughes, Timothy R

Keywords: Biochemistry; Computational Biology; Dna; Gene Regulation; Genomics; Molecular Biology; Molecular Genetics; Transcription Factors

$1,411,425

Systematic analysis of human C2H2 zinc finger proteins

Nominated PICIHR2023Project Grant

Principal investigators: Hughes, Timothy R; Shateri Najafabadi, Hamed

Keywords: Gene Regulation; Human Genetics; Modeling; Transcription Factors; Zinc Fingers

$1,201,050

Sequence Determinants of Human Gene Identity

Nominated PICIHR2022Project Grant

Principal investigators: Hughes, Timothy R

Keywords: Gene Regulation; Machine Learning; Mrna; Polyadenylation; Rna Processing; Splicing; Transcription

$906,525

Systematic functional characterization of transcriptional repressors

Co-investigatorCIHR2020Project Grant

Principal investigators: Taipale, Mikko

Keywords: Functional Genomics; Transcriptional Repression

$1,021,275

Canada Research Chairs - Tier 1

Nominated PICIHR2019Canada Research Chairs - CIHR Funded - Tier 1

Principal investigators: Hughes, Timothy R

Keywords: Crc

$1,400,000

Comprehensive analysis of RNA-binding proteins and their cellular function

Co-investigatorCIHR2018Project Grant

Principal investigators: Morris, Quaid D

Keywords: Clip; Deep Learning; High-Throughput Sequencing; Machine Learning; Motifs; Post-Transcriptional Regulation; Rna Secondary Structure; Rna-Binding Domains; Rna-Binding Proteins; Rna-Binding Sequences

$1,139,850

Function and evolution of zinc finger transcription factors

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Hughes, Timothy

$366,000

Systematic analysis of cooperativity between RNA-binding proteins

Co-investigatorCIHR2016Project Grant

Principal investigators: Morris, Quaid D

Keywords: Bioinformatics; Gene Expression; Genomics; In Vitro Binding Assays; Post-Transcriptional Regulation; Regulatory Networks; Rna-Binding Proteins

$100,000

Endogenous Retroelements and the Evolution of Vertebrate Transcription Factors

Principal investigatorNSERC2015Discovery Grants Program - Individual

Principal investigators: Hughes, Timothy

$38,000

Decoding gene regulation

Nominated PICIHR2015Foundation Grant

Principal investigators: Hughes, Timothy R

Keywords: C Elegans; C2h2 Zinc Fingers; Chromatin; Dna Binding Motifs; Enhancers; Functional Genomics; Regulatory Genomics; Sequence Analysis; Transcription Factors; Yeast

$5,860,205

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

Frequent collaborators

Donnelly Centre
Terrence Donnelly Centre for Cellular and Biomolecular Research
Chemical Engineering and Applied Chemistry

Co-authors at University of Toronto, colored by department. Thicker lines mean more shared papers; select anyone to open their profile and their own map.

Quaid Morris

Donnelly Centre

2 shared papers, latest 2017

Benjamin Blencowe

Donnelly Centre

1 shared papers, latest 2009

Alexei Savchenko

Chemical Engineering and Applied Chemistry

1 shared papers, latest 2005

Jack Greenblatt

Donnelly Centre

1 shared papers, latest 2005

Write to this professor

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Applying for

Paper to mentionMention their CIHR grant from 2023

Subject: Prospective PhD student: Genomics Dear Professor Hughes, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways." (2025), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your CIHR-funded project "Codebook: comprehensive and accurate motifs for human transcription factors" (2023), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]