Matthew Scott, University of Waterloo

Research

bacterial physiology growth laws gene expression constraints quantitative proteomics bacteriophage infection

Latest papers

A revised ribosome-antibiotic model with proportional feedback synthesis explains recovery from translation inhibition.
Journal of theoretical biology · 2026 · senior author
Membrane and proteome allocation constraints in Escherichia coli models during overflow metabolism.
Biophysical journal · 2026
Proteome partitioning constraints in long-term laboratory evolution.
Nature communications · 2024 · senior author

All 13 publications

Latest funding

Physiological constraints on bacterial gene expression
NSERC · 2024 · Principal investigator
$41,000
Physiological constraints on DNA replication and fidelity
NSERC · 2016 · Principal investigator
$186,000
Cell sorter for university facility
NSERC · 2014 · Co-investigator
$150,000

All 4 grants and awards

13 publications.

01

A revised ribosome-antibiotic model with proportional feedback synthesis explains recovery from translation inhibition.

Howell B, Scott M

Journal of theoretical biology2026Senior author

DOI: 10.1016/j.jtbi.2026.112576 PMID: 42617968

02

Membrane and proteome allocation constraints in Escherichia coli models during overflow metabolism.

Garcia-Benitez M, Scott M, Carlson R, Mahadevan R

Biophysical journal2026

DOI: 10.1016/j.bpj.2026.01.028 PMID: 41580894

03

Proteome partitioning constraints in long-term laboratory evolution.

Mori M, Patsalo V, Euler C, Williamson JR, Scott M

Nature communications2024Senior author

DOI: 10.1038/s41467-024-48447-2 PMID: 38744842

04

Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats.

Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD

The ISME journal2024

DOI: 10.1093/ismejo/wrae041 PMID: 38470309

05

Shaping bacterial gene expression by physiological and proteome allocation constraints.

Scott M, Hwa T

Nature reviews. Microbiology2023First author

DOI: 10.1038/s41579-022-00818-6 PMID: 36376406

06

Growth-dependent heterogeneity in the DNA damage response in Escherichia coli.

Jaramillo-Riveri S, Broughton J, McVey A, Pilizota T, Scott M, El Karoui M

Molecular systems biology2022

DOI: 10.15252/msb.202110441 PMID: 35620827

07

Metabolic models predict evolutionary dynamics.

Scott M

Nature ecology & evolution2021First author

DOI: 10.1038/s41559-021-01405-3 PMID: 33664487

08

Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review.

Jun S, Si F, Pugatch R, Scott M

Reports on progress in physics. Physical Society (Great Britain)2018Senior author

DOI: 10.1088/1361-6633/aaa628 PMID: 29313526

09

Obtaining Arbitrary Prescribed Mean Field Dynamics for Recurrently Coupled Networks of Type-I Spiking Neurons with Analytically Determined Weights.

Nicola W, Tripp B, Scott M

Frontiers in computational neuroscience2016Senior author

DOI: 10.3389/fncom.2016.00015 PMID: 26973503

10

Emergence of robust growth laws from optimal regulation of ribosome synthesis.

Scott M, Klumpp S, Mateescu EM, Hwa T

Molecular systems biology2014First author

DOI: 10.15252/msb.20145379 PMID: 25149558

Physiological constraints on bacterial gene expression

Principal investigatorNSERC2024Discovery Grants Program - Individual

Principal investigators: Scott, Matthew

Keywords: bacterial physiology; growth laws; gene expression constraints; quantitative proteomics; bacteriophage infection

$41,000

Physiological constraints on DNA replication and fidelity

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Scott, Matthew

$186,000

Cell sorter for university facility

Co-investigatorNSERC2014Research Tools and Instruments - Category 1 (<$150,000)

Principal investigators: Dixon, Brian

$150,000

Exploiting bacterial growth laws to characterize indirect mechanisms for generating phenotypic heterogeneity from isogenic populations

Principal investigatorNSERC2011Discovery Grants Program - Individual

Principal investigators: Scott, Matthew

$170,810

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

Applied Mathematics
Systems Design Engineering
Philosophy
Natural Sciences and Engineering
Department of Chemical Engineering and Applied Chemistry

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

Radhakrishnan Mahadevan

Department of Chemical Engineering and Applied Chemistry

1 shared papers, latest 2026

Bryan Tripp

Systems Design Engineering

1 shared papers, latest 2016

Christian Euler

Natural Sciences and Engineering

1 shared papers, latest 2024

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their NSERC grant from 2024

Subject: Prospective PhD student: bacterial physiology Dear Professor Scott, 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 "A revised ribosome-antibiotic model with proportional feedback synthesis explains recovery from translation inhibition." (2026), 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 NSERC-funded project "Physiological constraints on bacterial gene expression" (2024), 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]

Matthew Scott

Research

Latest papers

Latest funding

A revised ribosome-antibiotic model with proportional feedback synthesis explains recovery from translation inhibition.

Membrane and proteome allocation constraints in Escherichia coli models during overflow metabolism.

Proteome partitioning constraints in long-term laboratory evolution.

Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats.

Shaping bacterial gene expression by physiological and proteome allocation constraints.

Growth-dependent heterogeneity in the DNA damage response in Escherichia coli.

Metabolic models predict evolutionary dynamics.

Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review.

Obtaining Arbitrary Prescribed Mean Field Dynamics for Recurrently Coupled Networks of Type-I Spiking Neurons with Analytically Determined Weights.

Emergence of robust growth laws from optimal regulation of ribosome synthesis.

Physiological constraints on bacterial gene expression

Physiological constraints on DNA replication and fidelity

Cell sorter for university facility

Exploiting bacterial growth laws to characterize indirect mechanisms for generating phenotypic heterogeneity from isogenic populations

Frequent collaborators

Radhakrishnan Mahadevan

Bryan Tripp

Chris Eliasmith

Christian Euler