Ulrike Stege, University of Victoria

Research

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

Computational biology parameterized complexity design of heuristics graph theory cognitive psychology

Latest papers

Are the tools fit for purpose? Network inference algorithms evaluated on a simulated lipidomics network.
Bioinformatics advances · 2025
CParty: hierarchically constrained partition function of RNA pseudoknots.
Bioinformatics (Oxford, England) · 2024
Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.
PLoS computational biology · 2024

All 5 publications

Latest funding

Quantum computing for optimal mobility
NSERC · 2023 · Co-investigator
$150,000
NSERC CREATE in Quantum Computing
NSERC · 2020 · Co-investigator
$1,348,225
e-Ink font design for quilla eWriter
NSERC · 2018 · Principal investigator
$24,068

All 12 grants and awards

5 publications.

01

Are the tools fit for purpose? Network inference algorithms evaluated on a simulated lipidomics network.

Archinuk F, Greenyer H, Stege U, Bennett SAL, Cuperlovic-Culf M, Jabbari H

Bioinformatics advances2025

DOI: 10.1093/bioadv/vbaf286 PMID: 41278007

02

CParty: hierarchically constrained partition function of RNA pseudoknots.

Gray M, Trinity L, Stege U, Ponty Y, Will S, Jabbari H

Bioinformatics (Oxford, England)2024

DOI: 10.1093/bioinformatics/btae748 PMID: 39700413

03

Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.

Trinity L, Stege U, Jabbari H

PLoS computational biology2024

DOI: 10.1371/journal.pcbi.1011787 PMID: 38713726

04

Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.

Trinity L, Wark I, Lansing L, Jabbari H, Stege U

PLoS computational biology2023Senior author

DOI: 10.1371/journal.pcbi.1010922 PMID: 36854032

05

Supervised promoter recognition: a benchmark framework.

Perez Martell RI, Ziesel A, Jabbari H, Stege U

BMC bioinformatics2022Senior author

DOI: 10.1186/s12859-022-04647-5 PMID: 35366794

Quantum computing for optimal mobility

Co-investigatorNSERC2023Alliance Grants

Principal investigators: Taghipour, Sharareh S

Keywords: drone delivery planning; on-demand public transit; optimal mobility; prescriptive maintenance; prognostics; quantum machine learning; quantum optimization

$150,000

NSERC CREATE in Quantum Computing

Co-investigatorNSERC2020Collaborative Research and Training Experience

Principal investigators: Chrostowski, Lukas L

Keywords: quantum algorithms; quantum architecture; quantum computing; quantum machine learning; quantum photonics; quantum simulations; quantum software; spin-based qubits; superconducting circuits

$1,348,225

e-Ink font design for quilla eWriter

Principal investigatorNSERC2018Engage Grants Program

Principal investigators: Stege, Ulrike

$24,068

Intelligent automatic music curator and recommender system

Principal investigatorNSERC2017Engage Plus Grants Program

Principal investigators: Stege, Ulrike

$12,498

Computational Problems & Cognitive Functions: Modeling, Characterizations, and Solutions

Principal investigatorNSERC2016Discovery Grants Program - Individual

Principal investigators: Stege, Ulrike

$132,000

Content-aware music recommender system using emotion recognition

Principal investigatorNSERC2016Engage Grants Program

Principal investigators: Stege, Ulrike

$24,999

Self-Adaptive Smarter Systems Optimization Laboratory

Co-investigatorNSERC2012Research Tools and Instruments - Category 1 (<$150,000)

Principal investigators: Muller, Hausi

$66,115

Computational problems & tractable algorithms: Bridging the gap between problem definitions and solutions

Principal investigatorNSERC2011Discovery Grants Program - Individual

Principal investigators: Stege, Ulrike

$120,000

The C-SIDE project: computer science initiatives for diversity in education

Principal investigatorNSERC2007PromoScience

Principal investigators: Stege, Ulrike

$10,000

Parameterized complexity in computational biology and cognitive psychology

Principal investigatorNSERC2006Discovery Grants Program - Individual

Principal investigators: Stege, Ulrike

$95,000

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

Computer Science
Biomedical Engineering
Biochemistry, Microbiology & Immunology

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

Hosna Jabbari

Biomedical Engineering

5 shared papers, latest 2025

Miroslava Cuperlovic-Culf

Biochemistry, Microbiology & Immunology

1 shared papers, latest 2025

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Paper to mention

Subject: Prospective PhD student: Computational biology Dear Professor Stege, 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 "Are the tools fit for purpose? Network inference algorithms evaluated on a simulated lipidomics network." (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.] 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]