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Kelsy C. Cotto · SciRah

Researcher profile · Semantic Scholar

Kelsy C. Cotto

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Kelsy C. Cotto — researcher profile on SciRah

h-index: 12
Works: 46
Citations: 2,781

Most-cited papers

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts
Sharon L. Freshour, Susanna Kiwala, Kelsy C. Cotto, Adam C. Coffman +5 more
2020bioRxiv911 citations Open access
Semantic Scholar
DGIdb 3.0: a redesign and expansion of the drug–gene interaction database
Kelsy C. Cotto, A. Wagner, Yang-Yang Feng, Susanna Kiwala +6 more
2017bioRxiv802 citations Open access
Semantic Scholar
DGIdb 5.0: rebuilding the drug–gene interaction database for precision medicine and drug discovery platforms
M. Cannon, James Stevenson, Kathryn Stahl, Rohit Basu +10 more
2023Nucleic Acids Research471 citations Open access
Semantic Scholar
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
R. Lesurf, Kelsy C. Cotto, Grace Wang, M. Griffith +4 more
2015Nucleic Acids Res.179 citations Open access
Semantic Scholar
Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan M. Richters +20 more
2023Nature Communications112 citations Open access
Semantic Scholar
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Erica K. Barnell, Peter Ronning, Katie M. Campbell, K. Krysiak +20 more
2018Genetics in Medicine76 citations Open access
Semantic Scholar
RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Zachary L. Skidmore +11 more
202068 citations
Semantic Scholar
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase
K. Krysiak, Arpad M. Danos, J. Saliba, Joshua F. McMichael +61 more
2022Nucleic Acids Res.40 citations Open access
Semantic Scholar
Computational prediction of MHC anchor locations guides neoantigen identification and prioritization
Huiming Xia, Joshua F. McMichael, M. Becker-Hapak, Onyinyechi C Onyeador +21 more
2020bioRxiv35 citations Open access
Semantic Scholar
Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma
Erica K. Barnell, Zachary L. Skidmore, Kenneth F. Newcomer, Monique Chavez +22 more
2022Blood Advances19 citations Open access
Semantic Scholar
Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer
Erica K. Barnell, Bryan Fisk, Zachary L. Skidmore, Kelsy C. Cotto +11 more
2022Scientific Reports13 citations Open access
Semantic Scholar
A community approach to the cancer variant interpretation bottleneck
K. Krysiak, Arpad M. Danos, Susanna Kiwala, Joshua F. McMichael +48 more
2022Nature Cancer12 citations Open access
Semantic Scholar
CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase
A. Wagner, Susanna Kiwala, Adam C. Coffman, Joshua F. McMichael +8 more
2019bioRxiv12 citations Open access
Semantic Scholar
Exploring the genomic landscape of cancer patient cohorts with GenVisR
Zachary L. Skidmore, Katie M. Campbell, Kelsy C. Cotto, M. Griffith +1 more
2021Current Protocols11 citations Open access
Semantic Scholar
Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers
Zachary L. Skidmore, J. Kunisaki, Yiing Lin, Kelsy C. Cotto +14 more
2022Cancer Genetics7 citations Open access
Semantic Scholar
Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes
Erica K. Barnell, A. Waalkes, Matthew Mosior, K. Penewit +15 more
2019JCO Clinical Cancer Informatics6 citations Open access
Semantic Scholar
RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan M. Richters +20 more
2018bioRxiv6 citations Open access
Semantic Scholar
Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers
Zachary L. Skidmore, J. Kunisaki, Yiing Lin, Kelsy C. Cotto +14 more
2021bioRxiv5 citations Open access
Semantic Scholar
In silico epitope prediction analyses highlight the potential for distracting antigen immunodominance with allogeneic cancer vaccines
C. A. James, Peter Ronning, D. Cullinan, Kelsy C. Cotto +9 more
2021Cancer Research Communications5 citations Open access
Semantic Scholar
ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials
K. Singhal, Evelyn Schmidt, Susanna Kiwala, S. Goedegebuure +35 more
2025arXiv.org3 citations
Semantic Scholar
Abstract 2136: RegTools: Integrative analysis of genomic and transcriptomic data to identify splice altering mutations across 35 cancer types
Kelsy C. Cotto, Yang-Yang Feng, Zachary L. Skidmore, Avinash Ramu +8 more
2020Clinical research2 citations
Semantic Scholar
Abstract 2285: Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer
Yang-Yang Feng, Avinash Ramu, Zachary L. Skidmore, J. Kunisaki +3 more
2018Bioinformatics and Systems Biology2 citations
Semantic Scholar
pVACtools v6: A comprehensive suite for neoantigen prediction, visualization, and therapy design
M. Hoang, Susanna Kiwala, M. Richters, Luke Hendrickson +22 more
2026arXiv.org1 citations
Semantic Scholar
8. Integrating genomic and transcriptomic data to identify splice altering mutations across 35 cancer types
Kelsy C. Cotto, Yang-Yang Feng, Zachary L. Skidmore, Avinash Ramu +8 more
20201 citations
Semantic Scholar
65. Accurate neoantigen prediction depends on mutation position relative to patient-specific MHC anchor locations
Huiming Xia, Megan M. Richters, Cody A. Ramirez, Cristina Puig Saus +7 more
20201 citations
Semantic Scholar
Abstract 2487: Application of RegTools to TCGA samples for the identification of tumor-specific splice variants
Kelsy C. Cotto, Yang-Yang Feng, Zachary L. Skidmore, O. Griffith +1 more
2019Bioinformatics, Convergence Science, and Systems Biology1 citations
Semantic Scholar
Automating neoantigen selection for personalized cancer vaccine design
Jennie X Yao, K. Singhal, Susanna Kiwala, Evelyn Schmidt +25 more
2026medRxiv0 citations Open access
Semantic Scholar
Surveying the Genomic Landscape of Mantle Cell Lymphoma Indicates the Importance of Multimodal Genomic and Transcriptomic Exploration
Charlz Nithin Jerold, Brian V. Li, Matthew Mosior, D. Russler-Germain +8 more
2026medRxiv0 citations Open access
Semantic Scholar
335 Discovery and characterization of MAGE-A1-specific TCR candidates for TCR-based cancer therapy
Kaitao Li, Michael J Malone, Yih-Yang Chen, Sonali Kanaya +9 more
2025Regular and Young Investigator Award Abstracts0 citations Open access
Semantic Scholar
11. Developing a robust bioinformatics workflow to support personalized neoantigen vaccine clinical trials
K. Singhal, Susanna Kiwala, Peter S. Goedegebuure, C. Miller +24 more
2024Cancer Genetics0 citations
Semantic Scholar
76. Automating immunogenomic tumor board decision-making for neoantigen cancer vaccine design
Jennie X Yao, K. Singhal, Susanna Kiwala, Peter S. Goedegebuure +16 more
2024Cancer Genetics0 citations
Semantic Scholar
26. Improving interoperability of therapeutics and their targets for clinical and precision medicine applications
M. Cannon, James Stevenson, Kathryn Stahl, Adam C. Coffman +6 more
2023Cancer Genetics0 citations
Semantic Scholar
48. Refining the drug-gene interaction database for precision medicine
M. Cannon, James Stevenson, K. Kuzma, C. O'Sullivan +10 more
2022Cancer Genetics0 citations
Semantic Scholar
111. pVACsplice: Predicting neoantigens from tumor-specific alternative splicing events derived from regulatory mutations
Megan M. Richters, Kelsy C. Cotto, Susanna Kiwala, Huiming Xia +5 more
2022Cancer Genetics0 citations
Semantic Scholar
68. Integrative analysis of genomic and transcriptomic data using RegTools to identify splice-altering mutations within bulk
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan M. Richters +13 more
2022Cancer Genetics0 citations
Semantic Scholar
Abstract 1197: Refining the drug-gene interaction database for precision medicine pipelines
M. Cannon, James Stevenson, K. Kuzma, C. O'Sullivan +10 more
2022Cancer Research0 citations
Semantic Scholar
Abstract 5639: Computational prediction of MHC anchor locations guide neoantigen prediction and prioritization
Huiming Xia, Joshua F. McMichael, M. Becker-Hapak, Onyinyechi C Onyeador +20 more
2022Cancer Research0 citations
Semantic Scholar
Abstract 1215: pVACsplice: Predicting neoantigens from tumor-specific alternative splicing events derived from cis-acting regulatory mutations using whole exome and RNA sequencing data
Megan M. Richters, Kelsy C. Cotto, Susanna Kiwala, Huiming Xia +5 more
2022Cancer Research0 citations
Semantic Scholar
Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community
K. Krysiak, Arpad M. Danos, Susanna Kiwala, Joshua F. McMichael +48 more
2021bioRxiv0 citations Open access
Semantic Scholar
Abstract 206: CIViC knowledgebase adapts to field experts and community input
Lana M. Sheta, Arpad M. Danos, J. Saliba, K. Krysiak +15 more
2021Bioinformatics and Systems Biology0 citations
Semantic Scholar
Abstract 4413: Accurate neoantigen prediction depends on mutation position relative to patient-specific MHC anchor location
Huiming Xia, Megan M. Richters, Cody A. Ramirez, Cristina Puig-Saus +7 more
2020Clinical research0 citations
Semantic Scholar
Abstract 5462: Adding CIViC knowledge to variant annotation pipelines with CIViCpy
Susanna Kiwala, A. Wagner, Adam C. Coffman, Joshua F. McMichael +8 more
2020Clinical research0 citations
Semantic Scholar
24. Identification of recurrent, non-coding mutations across breast cancer molecular subtypes
Kelsy C. Cotto, Arpad M. Danos, R. Lesurf, Morag Park +2 more
2019Cancer Genetics0 citations
Semantic Scholar
Surveying the genomic landscape of tumours and tumour models – the next frontier
O. Griffith, K. Krysiak, Katie M. Campbell, N. Spies +7 more
2019Pathology (Sydney)0 citations
Semantic Scholar
Abstract 1418: Identification of recurrent regulatory mutations in breast cancer
Kelsy C. Cotto, Arpad M. Danos, R. Lesurf, Morag Park +2 more
2018Molecular and Cellular Biology / Genetics0 citations
Semantic Scholar
Genomic and transcriptomic somatic alterations of hepatocellular Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers carcinoma in non-cirrhotic livers
Zachary L. Skidmore, J. Kunisaki, Yiing Lin, Kelsy C. Cotto +15 more
0 citations
Semantic Scholar

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