Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts
Freshour, Sharon L, Kiwala, Susanna, Cotto, Kelsy C, Coffman, Adam C, McMichael, Joshua F, Song, Jonathan J, Griffith, Malachi, Griffith, Obi L, Wagner, Alex H
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
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Journal Article
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
Lesurf, Robert, Cotto, Kelsy C, Wang, Grace, Griffith, Malachi, Kasaian, Katayoon, Jones, Steven J M, Montgomery, Stephen B, Griffith, Obi L
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
Cotto, Kelsy C, Feng, Yang-Yang, Ramu, Avinash, Richters, Megan, Freshour, Sharon L, Skidmore, Zachary L, Xia, Huiming, McMichael, Joshua F, Kunisaki, Jason, Campbell, Katie M, Chen, Timothy Hung-Po, Rozycki, Emily B, Adkins, Douglas, Devarakonda, Siddhartha, Sankararaman, Sumithra, Lin, Yiing, Chapman, William C, Maher, Christopher A, Arora, Vivek, Dunn, Gavin P, Uppaluri, Ravindra, Govindan, Ramaswamy, Griffith, Obi L, Griffith, Malachi
Published in Nature communications (22.03.2023)
Published in Nature communications (22.03.2023)
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Journal Article
DGIdb 3.0: a redesign and expansion of the drug–gene interaction database
Cotto, Kelsy C, Wagner, Alex H, Feng, Yang-Yang, Kiwala, Susanna, Coffman, Adam C, Spies, Gregory, Wollam, Alex, Spies, Nicholas C, Griffith, Obi L, Griffith, Malachi
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer
Barnell, Erica K, Fisk, Bryan, Skidmore, Zachary L, Cotto, Kelsy C, Basu, Anamika, Anand, Aparna, Richters, Megan M, Luo, Jingqin, Fronick, Catrina, Anurag, Meenakshi, Fulton, Robert, Ellis, Matthew J, Griffith, Obi L, Griffith, Malachi, Ademuyiwa, Foluso O
Published in Scientific reports (22.10.2022)
Published in Scientific reports (22.10.2022)
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Journal Article
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Barnell, Erica K, Ronning, Peter, Campbell, Katie M, Krysiak, Kilannin, Ainscough, Benjamin J, Sheta, Lana M, Pema, Shahil P, Schmidt, Alina D, Richters, Megan, Cotto, Kelsy C, Danos, Arpad M, Ramirez, Cody, Skidmore, Zachary L, Spies, Nicholas C, Hundal, Jasreet, Sediqzad, Malik S, Kunisaki, Jason, Gomez, Felicia, Trani, Lee, Matlock, Matthew, Wagner, Alex H, Swamidass, S Joshua, Griffith, Malachi, Griffith, Obi L
Published in Genetics in medicine (01.04.2019)
Published in Genetics in medicine (01.04.2019)
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Journal Article
Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR
Skidmore, Zachary L., Campbell, Katie M., Cotto, Kelsy C., Griffith, Malachi, Griffith, Obi L.
Published in Current protocols (01.09.2021)
Published in Current protocols (01.09.2021)
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Journal Article
Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers
Skidmore, Zachary L, Kunisaki, Jason, Lin, Yiing, Cotto, Kelsy C, Barnell, Erica K, Hundal, Jasreet, Krysiak, Kilannin, Magrini, Vincent, Trani, Lee, Walker, Jason R, Fulton, Robert, Brunt, Elizabeth M, Miller, Christopher A, Wilson, Richard K, Mardis, Elaine R, Griffith, Malachi, Chapman, William, Griffith, Obi L
Published in Cancer genetics (01.06.2022)
Published in Cancer genetics (01.06.2022)
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Journal Article
Computational prediction of MHC anchor locations guides neoantigen identification and prioritization
Xia, Huiming, McMichael, Joshua, Becker-Hapak, Michelle, Onyeador, Onyinyechi C, Buchli, Rico, McClain, Ethan, Pence, Patrick, Supabphol, Suangson, Richters, Megan M, Basu, Anamika, Ramirez, Cody A, Puig-Saus, Cristina, Cotto, Kelsy C, Freshour, Sharon L, Hundal, Jasreet, Kiwala, Susanna, Goedegebuure, S Peter, Johanns, Tanner M, Dunn, Gavin P, Ribas, Antoni, Miller, Christopher A, Gillanders, William E, Fehniger, Todd A, Griffith, Obi L, Griffith, Malachi
Published in Science immunology (14.04.2023)
Published in Science immunology (14.04.2023)
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Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma
Barnell, Erica K., Skidmore, Zachary L., Newcomer, Kenneth F., Chavez, Monique, Campbell, Katie M., Cotto, Kelsy C., Spies, Nicholas C., Ruzinova, Marianna B., Wang, Tianjiao, Abro, Brooj, Kreisel, Friederike, Parikh, Bijal A., Duncavage, Eric J., Frater, John L., Lee, Yi-Shan, Hassan, Anjum, King, Justin A., Kohnen, Daniel R., Fiala, Mark A., Welch, John S., Uy, Geoffrey L., Vij, Kiran, Vij, Ravi, Griffith, Malachi, Griffith, Obi L., Wartman, Lukas D.
Published in Blood advances (24.01.2023)
Published in Blood advances (24.01.2023)
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Journal Article
In silico epitope prediction analyses highlight the potential for distracting antigen immunodominance with allogeneic cancer vaccines
James, C Alston, Ronning, Peter, Cullinan, Darren, Cotto, Kelsy C, Barnell, Erica K, Campbell, Katie M, Skidmore, Zachary L, Sanford, Dominic E, Goedegebuure, S Peter, Gillanders, William E, Griffith, Obi L, Hawkins, William G, Griffith, Malachi
Published in Cancer research communications (01.11.2021)
Published in Cancer research communications (01.11.2021)
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Journal Article
CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase
Wagner, Alex H, Kiwala, Susanna, Coffman, Adam C, McMichael, Joshua F, Cotto, Kelsy C, Mooney, Thomas B, Barnell, Erica K, Krysiak, Kilannin, Danos, Arpad M, Walker, Jason, Griffith, Obi L, Griffith, Malachi
Published in JCO clinical cancer informatics (19.03.2020)
Published in JCO clinical cancer informatics (19.03.2020)
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Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes
Barnell, Erica K, Waalkes, Adam, Mosior, Matt C, Penewit, Kelsi, Cotto, Kelsy C, Danos, Arpad M, Sheta, Lana M, Campbell, Katie M, Krysiak, Kilannin, Rieke, Damian, Spies, Nicholas C, Skidmore, Zachary L, Pritchard, Colin C, Fehniger, Todd A, Uppaluri, Ravindra, Govindan, Ramaswamy, Griffith, Malachi, Salipante, Stephen J, Griffith, Obi L
Published in JCO clinical cancer informatics (16.10.2019)
Published in JCO clinical cancer informatics (16.10.2019)
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Journal Article
DGIdb 5.0: rebuilding the drug–gene interaction database for precision medicine and drug discovery platforms
Cannon, Matthew, Stevenson, James, Stahl, Kathryn, Basu, Rohit, Coffman, Adam, Kiwala, Susanna, McMichael, Joshua F, Kuzma, Kori, Morrissey, Dorian, Cotto, Kelsy, Mardis, Elaine R, Griffith, Obi L, Griffith, Malachi, Wagner, Alex H
Published in Nucleic acids research (05.01.2024)
Published in Nucleic acids research (05.01.2024)
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Journal Article
Abstract 1418: Identification of recurrent regulatory mutations in breast cancer
Cotto, Kelsy C., Danos, Arpad, Lesurf, Robert, Park, Morag, Griffith, Malachi, Griffith, Obi L.
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Journal Article
26. Improving interoperability of therapeutics and their targets for clinical and precision medicine applications
Cannon, Matthew, Stevenson, James, Stahl, Kathryn, Coffman, Adam, Kiwala, Susanna, McMichael, Joshua, Cotto, Kelsy, Griffith, Obi, Griffith, Malachi, Wagner, Alex
Published in Cancer genetics (01.11.2023)
Published in Cancer genetics (01.11.2023)
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Journal Article
93. Surveying the genomic landscape of Mantle Cell Lymphoma
Li, Brian, Gomez, Felicia, Mosior, Matthew, Thornton, Vera, Skidmore, Zach, Cotto, Kelsy, Kahl, Brad, Griffith, Malachi, Griffith, Obi L.
Published in Cancer genetics (01.11.2022)
Published in Cancer genetics (01.11.2022)
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Journal Article
111. pVACsplice: Predicting neoantigens from tumor-specific alternative splicing events derived from regulatory mutations
Richters, Megan, Cotto, Kelsy, Kiwala, Susanna, Xia, Huiming, Carreno, Beatriz, Dunn, Gavin, Ribas, Antoni, Griffith, Obi L., Griffith, Malachi
Published in Cancer genetics (01.11.2022)
Published in Cancer genetics (01.11.2022)
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Journal Article
Abstract 2285: Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer
Feng, Yang-Yang, Ramu, Avinash, Skidmore, Zachary L., Kunisaki, Jason, Cotto, Kelsy C., Griffith, Obi L., Griffith, Malachi
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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