Lila Kari, University of Waterloo

Research

Biodiversity informatics Bio-inspired computing Biomolecular (DNA) computing Comparative genomics DNA computing & combinatorics on words Genomic signatures Machine learning Natural computation

Latest papers

Genome-wide pervasiveness and localized variation of [Formula: see text]-mer-based genomic signatures in eukaryotes.
Scientific reports · 2026 · senior author
BarcodeBERT: transformers for biodiversity analyses.
Bioinformatics advances · 2026
Life at the extremes: maximally divergent microbes with similar genomic signatures linked to extreme environments.
NAR genomics and bioinformatics · 2025 · senior author

All 17 publications

Latest funding

Foundations and Applications of Biocomputing and Biodiversity Informatics
NSERC · 2023 · Principal investigator
$92,000
Advanced imaging system for accelerating and automating arthropod bio-surveillance
NSERC · 2020 · Co-investigator
$143,583
BIOSCAN: Tracing the Patterns of Life on a Changing Planet
SSHRC · 2020 · Co-investigator
$8,000,000

All 5 grants and awards

17 publications.

01

Genome-wide pervasiveness and localized variation of [Formula: see text]-mer-based genomic signatures in eukaryotes.

Sadjadi N, de Souza CPE, Randhawa GS, Hill KA, Kari L

Scientific reports2026Senior author

DOI: 10.1038/s41598-026-40591-7 PMID: 42285985

02

BarcodeBERT: transformers for biodiversity analyses.

Millan Arias P, Sadjadi N, Safari M, Gong Z, Wang AT, Haurum JB, Zarubiieva I, Steinke D, Kari L, Chang AX, Lowe SC, Taylor GW

Bioinformatics advances2026

DOI: 10.1093/bioadv/vbag054 PMID: 41878470

03

Life at the extremes: maximally divergent microbes with similar genomic signatures linked to extreme environments.

Safari M, Butler J, Randhawa GS, Hill KA, Kari L

NAR genomics and bioinformatics2025Senior author

DOI: 10.1093/nargab/lqaf189 PMID: 41446505

04

CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences.

Alipour F, Hill KA, Kari L

BMC genomics2024Senior author

DOI: 10.1186/s12864-024-11135-y PMID: 39695938

05

Leveraging machine learning for taxonomic classification of emerging astroviruses.

Alipour F, Holmes C, Lu YY, Hill KA, Kari L

Frontiers in molecular biosciences2023Senior author

DOI: 10.3389/fmolb.2023.1305506 PMID: 38274100

06

Environment and taxonomy shape the genomic signature of prokaryotic extremophiles.

Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L

Scientific reports2023Senior author

DOI: 10.1038/s41598-023-42518-y PMID: 37752120

07

iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences.

Millan Arias P, Hill KA, Kari L

Bioinformatics (Oxford, England)2023Senior author

DOI: 10.1093/bioinformatics/btad508 PMID: 37589603

08

MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes.

Li W, Kari L, Yu Y, Hug LA

PloS one2023

DOI: 10.1371/journal.pone.0283536 PMID: 37594964

09

Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.

Chen D, Randhawa GS, Soltysiak MP, de Souza CP, Kari L, Singh SM, Hill KA

JMIR bioinformatics and biotechnology2022

DOI: 10.2196/42243 PMID: 38935965

10

SomaticSiMu: a mutational signature simulator.

Chen D, Randhawa GS, Soltysiak MPM, de Souza CPE, Kari L, Singh SM, Hill KA

Bioinformatics (Oxford, England)2022

DOI: 10.1093/bioinformatics/btac128 PMID: 35258549

Foundations and Applications of Biocomputing and Biodiversity Informatics

Principal investigatorNSERC2023Discovery Grants Program - Individual

Principal investigators: Kari, Lila

Keywords: biodiversity informatics; comparative genomics; genomic signatures; machine learning; natural computation; bio-inspired computing; biomolecular (dna) computing; watson-crick complementarity in formal languages; dna computing & combinatorics on words

$92,000

Advanced imaging system for accelerating and automating arthropod bio-surveillance

Co-investigatorNSERC2020Research Tools and Instruments

Principal investigators: Hebert, Paul

$143,583

BIOSCAN: Tracing the Patterns of Life on a Changing Planet

Co-investigatorSSHRC2020New Frontiers in Research Fund - Transformation

Principal investigators: Hebert, Paul

$8,000,000

BIOSCAN: Tracing the Patterns of Life on a Changing Planet

Co-investigatorSSHRC2020New Frontiers in Research Fund - Transformation

Principal investigators: Hebert, Paul

Keywords: Global change biology Ecological & environmental policy Machine learning Metagenomics Systematics & taxonomy Biodiversity genomics Data Science Environmental management Environmental law Conservation Evolution Statistical ecology Environmental economics Ecosystem Sustainability

$8,000,000

Foundational aspects of bioinformation and biocomputation

Principal investigatorNSERC2017Discovery Grants Program - Individual

Principal investigators: Kari, Lila

$251,999

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, David R. Cheriton School of
Pathology and Laboratory Medicine
Mathematics and Computing Science
David R. Cheriton School of Computer Science

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.

Yaoliang Yu

David R. Cheriton School of Computer Science

1 shared papers, latest 2023

Stavros Konstantinidis

Mathematics and Computing Science

1 shared papers, latest 2016

Art Poon

Pathology and Laboratory Medicine

1 shared papers, latest 2018

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 2023

Subject: Prospective PhD student: Biodiversity informatics Dear Professor Kari, 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 "Genome-wide pervasiveness and localized variation of [Formula: see text]-mer-based genomic signatures in eukaryotes." (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 "Foundations and Applications of Biocomputing and Biodiversity Informatics" (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]