Anne Condon, University of British Columbia

Research

Read how they describe their research on their University of British Columbia profile.

Algorithms Bioinformatics & Computational Biology

Latest papers

CellUntangler: Separating distinct biological signals in single-cell data with deep generative models.
Cell genomics · 2026
Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks.
Bioinformatics advances · 2025
A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.
Briefings in bioinformatics · 2025

All 27 publications

Latest funding

Models and Algorithms for Molecular Programming
NSERC · 2022 · Principal investigator
$144,000
Engendering success in STEM: a research consortium for gender equality in science and technology
SSHRC · 2017 · Co-investigator
$2,217,628
Advancing theory and tools for molecular programming
NSERC · 2016 · Principal investigator
$276,000

All 11 grants and awards

27 publications.

01

CellUntangler: Separating distinct biological signals in single-cell data with deep generative models.

Chen S, Regev A, Condon A, Ding J

Cell genomics2026

DOI: 10.1016/j.xgen.2025.101073 PMID: 41330382

02

Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks.

Zhang C, Condon A, Dao Duc K

Bioinformatics advances2025

DOI: 10.1093/bioadv/vbaf179 PMID: 40831760

03

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.

Zhang C, Condon A, Dao Duc K

Briefings in bioinformatics2025

DOI: 10.1093/bib/bbaf322 PMID: 40645653

04

Factorization and pseudofactorization of weighted graphs.

Sheridan K, Berleant J, Bathe M, Condon A, Williams VV

Discrete applied mathematics (Amsterdam, Netherlands : 1988)2023

DOI: 10.1016/j.dam.2023.04.019 PMID: 37213330

05

Isometric Hamming embeddings of weighted graphs.

Berleant J, Sheridan K, Condon A, Williams VV, Bathe M

Discrete applied mathematics (Amsterdam, Netherlands : 1988)2023

DOI: 10.1016/j.dam.2023.02.005 PMID: 37982050

06

Predicting DNA kinetics with a truncated continuous-time Markov chain method.

Zolaktaf S, Dannenberg F, Schmidt M, Condon A, Winfree E

Computational biology and chemistry2023

DOI: 10.1016/j.compbiolchem.2023.107837 PMID: 36858009

07

Will biologists become computer scientists? A truly interdisciplinary effort by computer scientists and biologists to understand how cells process information may yield new insights for both fields.

Condon A, Kirchner H, Larivière D, Marshall W, Noireaux V, Tlusty T, Fourmentin E

EMBO reports2018First author

DOI: 10.15252/embr.201846628 PMID: 30061101

08

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

Ding J, Condon A, Shah SP

Nature communications2018

DOI: 10.1038/s41467-018-04368-5 PMID: 29784946

09

Design of nucleic acid strands with long low-barrier folding pathways.

Condon A, Kirkpatrick B, Maňuch J

Natural computing2017First author

DOI: 10.1007/s11047-016-9587-9 PMID: 28690474

10

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Ding J, Shah S, Condon A

Bioinformatics (Oxford, England)2016Senior author

DOI: 10.1093/bioinformatics/btw227 PMID: 27153661

Models and Algorithms for Molecular Programming

Principal investigatorNSERC2022Discovery Grants Program - Individual

Principal investigators: Condon, Anne

Keywords: chemical reaction networks; strand displacement systems; algorithms; distributed computing; population protocols; dna kinetics; continuous time markov chain models

$144,000

Engendering success in STEM: a research consortium for gender equality in science and technology

Co-investigatorSSHRC2017Partnership Grants

Keywords: social psychology; implicit gender bias; women in science; intergroup contact; science outreach; organizational culture

$2,217,628

Advancing theory and tools for molecular programming

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Condon, Anne

$276,000

Engendering success in STEM: a research consortium for gender equality in science and technology

Co-investigatorSSHRC2016Partnership Grants

Keywords: social psychology; implicit gender bias; women in science; intergroup contact; science outreach; organizational culture

$282,328

PNW-CWIC: Pacific Northwest Celebration of Women in Computing ""Regional Hopper"" Conference

Principal investigatorNSERC2013Regional Office Discretionary Funds

Principal investigators: Condon, Anne

$3,000

Prediction and design of nucleic acid secondary structure and folding pathways: from theory to tools

Principal investigatorNSERC2011Discovery Grants Program - Individual

Principal investigators: Condon, Anne

$245,000

Improving computational inference of single nucleotide variants from next generation sequencing of cancer genomes.

Co-investigatorCIHR2009Catalyst Grant: Bioinformatics Approaches to Cancer Research

Principal investigators: Aparicio, Samuel J

Keywords: Bayesian Statistics; Next Generation Sequencing Data; Probabilistic Inference; Sequence Alignment; Single Nucleotide Variants; Statistical Modeling

$99,078

CIHR Training Grant in Bioinformatics for Health Research

Co-investigatorCIHR2008Training Grant

Principal investigators: Jones, Steven; Brinkman, Fiona S

Keywords: Bioinformatics; Computer Science; Epidemiology; Genomics; Proteomics; Statistics

$1,950,000

Topics in complexity theory and DNA computation

Principal investigatorNSERC2003Discovery Grants Program - Individual

Principal investigators: Condon, Anne

$329,000

The Jade Project: Expanding and Strengthening the Pipeline of Canadian Women in Computer Science and Related Fields - The University of British Columbia

Principal investigatorNSERC2002Chairs for Women in Science and Engineering - Project

Principal investigators: Condon, Anne

$350,000

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

Molecular Oncology
Computer Science at UBC
Pathology and Laboratory Medicine
Mathematics
Department of Microbiology and Immunology
Other

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

Samuel Aparicio

Molecular Oncology

2 shared papers, latest 2015

Ali Bashashati

Pathology and Laboratory Medicine

2 shared papers, latest 2015

Martin Hirst

Department of Microbiology and Immunology

1 shared papers, latest 2012

David Huntsman

Molecular Oncology

1 shared papers, latest 2015

Sohrab Shah

Faculty

1 shared papers, latest 2016

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 2022

Subject: Prospective PhD student: Algorithms Bioinformatics & Computational Biology Dear Professor Condon, 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 "CellUntangler: Separating distinct biological signals in single-cell data with deep generative models." (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 "Models and Algorithms for Molecular Programming" (2022), 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]

Anne Condon

Research

Latest papers

Latest funding

CellUntangler: Separating distinct biological signals in single-cell data with deep generative models.

Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks.

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.

Factorization and pseudofactorization of weighted graphs.

Isometric Hamming embeddings of weighted graphs.

Predicting DNA kinetics with a truncated continuous-time Markov chain method.

Will biologists become computer scientists? A truly interdisciplinary effort by computer scientists and biologists to understand how cells process information may yield new insights for both fields.

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

Design of nucleic acid strands with long low-barrier folding pathways.

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Models and Algorithms for Molecular Programming

Engendering success in STEM: a research consortium for gender equality in science and technology

Advancing theory and tools for molecular programming

Engendering success in STEM: a research consortium for gender equality in science and technology

PNW-CWIC: Pacific Northwest Celebration of Women in Computing ""Regional Hopper"" Conference

Prediction and design of nucleic acid secondary structure and folding pathways: from theory to tools

Improving computational inference of single nucleotide variants from next generation sequencing of cancer genomes.

CIHR Training Grant in Bioinformatics for Health Research

Topics in complexity theory and DNA computation

The Jade Project: Expanding and Strengthening the Pipeline of Canadian Women in Computer Science and Related Fields - The University of British Columbia

Frequent collaborators

Jiarui Ding

Khanh Dao Duc

Samuel Aparicio

Ali Bashashati

Andrew Roth

Martin Hirst

Mark Schmidt

David Huntsman

Sohrab Shah