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Research
Latest papers
MicroNucML enables machine learning-based micronuclei segmentation and micronuclei-nuclei association.
Cell reports methods · 2026 · senior author
An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.
Bioinformatics (Oxford, England) · 2026 · senior author
DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations.
Nucleic acids research · 2025 · senior author
Latest funding
- $120,000
An integrative framework to investigate the influence of age-associated CHIP mutations on solid tumours
CIHR · 2025 · Supervisor
- $120,000
Reaping Returns on Repair: Leveraging phased copy number and single nucleotide variants to improve DNA repair efficacy scoring for assessing genomic instability in tumours.
CIHR · 2024 · Supervisor
- $12,500
Integrative approaches to study the role of 3D-genome structure and dynamics in gene regulation
NSERC · 2023 · Principal investigator
9 publications.
MicroNucML enables machine learning-based micronuclei segmentation and micronuclei-nuclei association.
Wang Y, Boev NB, Garcia-Lepe UO, MacDonald KM, Harding SM, Kumar S
An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.
Bakhtiyari N, Masoudi-Sobhanzadeh Y, Farajnia S, Kumar S
DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations.
Boev NB, Gerstein MB, Kumar S
Plasma lipid levels predict chemotherapy response and survival in acute myeloid leukemia.
O'Brien C, Nursimulu N, Tyagi A, Culp-Hill R, Arruda A, Murphy T, Minden MD, Kent A, Stevens B, Pollyea DA, Hope K, Kumar S, Reisz JA, D'Alessandro A, Jones CL
Regulatory genome annotation.
Kumar S, Gerstein M
Guidelines for releasing a variant effect predictor.
Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA
Guidelines for releasing a variant effect predictor.
Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA
Unified views on variant impact across many diseases.
Kumar S, Gerstein M
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.
Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Z, Neale B, Sunyaev SR, Lin X
An integrative framework to investigate the influence of age-associated CHIP mutations on solid tumours
Principal investigators: Hanafi, Nour
Keywords: Aging; Bioinformatics; Cancer Genomics; Clonal Hematopoiesis; Driver Mutations
Reaping Returns on Repair: Leveraging phased copy number and single nucleotide variants to improve DNA repair efficacy scoring for assessing genomic instability in tumours.
Principal investigators: Boev, Nadejda B
Keywords: Clonal Evolution; Dna Repair; Drug Response; Tumour Mutational Burden; Whole Genome Sequencing
Integrative approaches to study the role of 3D-genome structure and dynamics in gene regulation
Principal investigators: Kumar, Sushant
Integrative approaches to study the role of 3D-genome structure and dynamics in gene regulation
Principal investigators: Kumar, Sushant
Keywords: 3D-genome structure; chromatin conformation capture; chromatin interactions; comparative genomics; gene expression; gene regulation; genome dynamics; genomic rearrangements; machine learning; Molecular modeling
Canada Research Chair - Tier 2
Principal investigators: Kumar, Sushant
Keywords: Crc
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
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