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
GenVisR: Genomic Visualizations in R
Skidmore, Zachary L, Wagner, Alex H, Lesurf, Robert, Campbell, Katie M, Kunisaki, Jason, Griffith, Obi L, Griffith, Malachi
Published in Bioinformatics (Oxford, England) (01.10.2016)
Published in Bioinformatics (Oxford, England) (01.10.2016)
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Journal Article
SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
Miller, Christopher A, White, Brian S, Dees, Nathan D, Griffith, Malachi, Welch, John S, Griffith, Obi L, Vij, Ravi, Tomasson, Michael H, Graubert, Timothy A, Walter, Matthew J, Ellis, Matthew J, Schierding, William, DiPersio, John F, Ley, Timothy J, Mardis, Elaine R, Wilson, Richard K, Ding, Li
Published in PLoS computational biology (01.08.2014)
Published in PLoS computational biology (01.08.2014)
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Journal Article
Best practices for bioinformatic characterization of neoantigens for clinical utility
Richters, Megan M, Xia, Huiming, Campbell, Katie M, Gillanders, William E, Griffith, Obi L, Griffith, Malachi
Published in Genome medicine (28.08.2019)
Published in Genome medicine (28.08.2019)
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Journal Article
Single-agent ibrutinib in relapsed or refractory follicular lymphoma: a phase 2 consortium trial
Bartlett, Nancy L., Costello, Brian A., LaPlant, Betsy R., Ansell, Stephen M., Kuruvilla, John G., Reeder, Craig B., Thye, Lim S., Anderson, Daniel M., Krysiak, Kilannin, Ramirez, Cody, Qi, Jing, Siegel, Barry A., Griffith, Malachi, Griffith, Obi L., Gomez, Felicia, Fehniger, Todd A.
Published in Blood (11.01.2018)
Published in Blood (11.01.2018)
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Journal Article
Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma
Krysiak, Kilannin, Gomez, Felicia, White, Brian S., Matlock, Matthew, Miller, Christopher A., Trani, Lee, Fronick, Catrina C., Fulton, Robert S., Kreisel, Friederike, Cashen, Amanda F., Carson, Kenneth R., Berrien-Elliott, Melissa M., Bartlett, Nancy L., Griffith, Malachi, Griffith, Obi L., Fehniger, Todd A.
Published in Blood (26.01.2017)
Published in Blood (26.01.2017)
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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
High-performance web services for querying gene and variant annotation
Xin, Jiwen, Mark, Adam, Afrasiabi, Cyrus, Tsueng, Ginger, Juchler, Moritz, Gopal, Nikhil, Stupp, Gregory S, Putman, Timothy E, Ainscough, Benjamin J, Griffith, Obi L, Torkamani, Ali, Whetzel, Patricia L, Mungall, Christopher J, Mooney, Sean D, Su, Andrew I, Wu, Chunlei
Published in Genome Biology (06.05.2016)
Published in Genome Biology (06.05.2016)
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Journal Article
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Griffith, Malachi, Walker, Jason R, Spies, Nicholas C, Ainscough, Benjamin J, Griffith, Obi L
Published in PLoS computational biology (01.08.2015)
Published in PLoS computational biology (01.08.2015)
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Journal Article
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
Jones, Steven, Robertson, Gordon, Hirst, Martin, Bainbridge, Matthew, Bilenky, Misha, Zhao, Yongjun, Zeng, Thomas, Euskirchen, Ghia, Bernier, Bridget, Varhol, Richard, Delaney, Allen, Thiessen, Nina, Griffith, Obi L, He, Ann, Marra, Marco, Snyder, Michael
Published in Nature methods (01.08.2007)
Published in Nature methods (01.08.2007)
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Journal Article
The prognostic effects of somatic mutations in ER-positive breast cancer
Griffith, Obi L, Spies, Nicholas C, Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L, Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E, Davies, Sherri, Kavuri, Shyam M, Chang, Eric C, Magrini, Vincent, Larson, David E, Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K, Nielsen, Torsten O, Mardis, Elaine R, Ellis, Matthew J
Published in Nature communications (04.09.2018)
Published in Nature communications (04.09.2018)
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Journal Article
FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer
Fu, Xiaoyong, Jeselsohn, Rinath, Pereira, Resel, Hollingsworth, Emporia F., Creighton, Chad J., Li, Fugen, Shea, Martin, Nardone, Agostina, De Angelis, Carmine, Heiser, Laura M., Anur, Pavana, Wang, Nicholas, Grasso, Catherine S., Spellman, Paul T., Griffith, Obi L., Tsimelzon, Anna, Gutierrez, Carolina, Huang, Shixia, Edwards, Dean P., Trivedi, Meghana V., Rimawi, Mothaffar F., Lopez-Terrada, Dolores, Hilsenbeck, Susan G., Gray, Joe W., Brown, Myles, Osborne, C. Kent, Schiff, Rachel
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
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Journal Article
Wikidata as a knowledge graph for the life sciences
Waagmeester, Andra, Stupp, Gregory, Burgstaller-Muehlbacher, Sebastian, Good, Benjamin M, Griffith, Malachi, Griffith, Obi L, Hanspers, Kristina, Hermjakob, Henning, Hudson, Toby S, Hybiske, Kevin, Keating, Sarah M, Manske, Magnus, Mayers, Michael, Mietchen, Daniel, Mitraka, Elvira, Pico, Alexander R, Putman, Timothy, Riutta, Anders, Queralt-Rosinach, Nuria, Schriml, Lynn M, Shafee, Thomas, Slenter, Denise, Stephan, Ralf, Thornton, Katherine, Tsueng, Ginger, Tu, Roger, Ul-Hasan, Sabah, Willighagen, Egon, Wu, Chunlei, Su, Andrew I
Published in eLife (17.03.2020)
Published in eLife (17.03.2020)
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Journal Article
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens
Hundal, Jasreet, Kiwala, Susanna, McMichael, Joshua, Miller, Christopher A, Xia, Huiming, Wollam, Alexander T, Liu, Connor J, Zhao, Sidi, Feng, Yang-Yang, Graubert, Aaron P, Wollam, Amber Z, Neichin, Jonas, Neveau, Megan, Walker, Jason, Gillanders, William E, Mardis, Elaine R, Griffith, Obi L, Griffith, Malachi
Published in Cancer immunology research (01.03.2020)
Published in Cancer immunology research (01.03.2020)
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Journal Article
DoCM: a database of curated mutations in cancer
Ainscough, Benjamin J, Griffith, Malachi, Coffman, Adam C, Wagner, Alex H, Kunisaki, Jason, Choudhary, Mayank Nk, McMichael, Joshua F, Fulton, Robert S, Wilson, Richard K, Griffith, Obi L, Mardis, Elaine R
Published in Nature methods (01.10.2016)
Published in Nature methods (01.10.2016)
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Journal Article
Accounting for proximal variants improves neoantigen prediction
Hundal, Jasreet, Kiwala, Susanna, Feng, Yang-Yang, Liu, Connor J, Govindan, Ramaswamy, Chapman, William C, Uppaluri, Ravindra, Swamidass, S Joshua, Griffith, Obi L, Mardis, Elaine R, Griffith, Malachi
Published in Nature genetics (01.01.2019)
Published in Nature genetics (01.01.2019)
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Journal Article
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
Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches
Chu, Shirley, Skidmore, Zachary L, Kunisaki, Jason, Walker, Jason R, Griffith, Malachi, Griffith, Obi L, Bryan, Jeffrey N
Published in PloS one (08.02.2021)
Published in PloS one (08.02.2021)
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