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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. .png)
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SaveComputational prediction of MHC anchor locations guides neoantigen identification and prioritizationXia, 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 Share Save Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancerCotto, 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 Share Save Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myelomaBarnell, 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.; Wartma, Lukas D. Share Save CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebaseKrysiak, Kilannin; Danos, Arpad M.; Saliba, Jason; McMichael, Joshua F.; Coffman, Adam C.; Kiwala, Susanna; Barnell, Erica K.; Sheta, Lana; Grisdale, Cameron J.; Kujan, Lynzey; Pema, Shahil; Lever, Jake; Ridd, Sarah; Spies, Nicholas C.; Andric, Veronica; Chiorean, Andreea; Rieke, Damian T.; Clark, Kaitlin A.; Reisle, Caralyn; Venigalla, Ajay C.; Evans, Mark; Jani, Payal; Takahashi, Hideaki; Suda, Avila; Horak, Peter; Ritter, Deborah, I; Zhou, Xin; Ainscough, Benjamin J.; Delong, Sean; Kesserwan, Chimene; Lamping, Mario; Shen, Haolin; Marr, Alex R.; Hoang, My H.; Singhal, Kartik; Khanfar, Mariam; Li, Brian, V; Lin, Wan-Hsin; Terraf, Panieh; Corson, Laura B.; Salama, Yasser; Campbell, Katie M.; Farncombe, Kirsten M.; Ji, Jianling; Zhao, Xiaonan; Xu, Xinjie; Kanagal-Shamanna, Rashmi; King, Ian; Cotto, Kelsy C.; Skidmore, Zachary L.; Walker, Jason R.; Zhang, Jinghui; Milosavljevic, Aleksandar; Patel, Ronak Y.; Giles, Rachel H.; Kim, Raymond H.; Schriml, Lynn M.; Mardis, Elaine R.; Jones, Steven J. M.; Raca, Gordana; Rao, Shruti; Madhavan, Subha; Wagner, Alex H.; Griffith, Malachi; Griffith, Obi L. Share Save Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancerBarnell, 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. Share Save A community approach to the cancer-variant-interpretation bottleneckKrysiak, Kilannin; Danos, Arpad M.; Kiwala, Susanna; McMichael, Joshua F.; Coffman, Adam C.; Barnell, Erica K.; Sheta, Lana; Saliba, Jason; Grisdale, Cameron J.; Kujan, Lynzey; Pema, Shahil; Lever, Jake; Spies, Nicholas C.; Chiorean, Andreea; Rieke, Damian T.; Clark, Kaitlin A.; Jani, Payal; Takahashi, Hideaki; Horak, Peter; Ritter, Deborah, I; Zhou, Xin; Ainscough, Benjamin J.; Delong, Sean; Lamping, Mario; Marr, Alex R.; Li, Brian, V; Lin, Wan-Hsin; Terraf, Panieh; Salama, Yasser; Campbell, Katie M.; Farncombe, Kirsten M.; Ji, Jianling; Zhao, Xiaonan; Xu, Xinjie; Kanagal-Shamanna, Rashmi; Cotto, Kelsy C.; Skidmore, Zachary L.; Walker, Jason R.; Zhang, Jinghui; Milosavljevic, Aleksandar; Patel, Ronak Y.; Giles, Rachel H.; Kim, Raymond H.; Schriml, Lynn M.; Mardis, Elaine R.; Jones, Steven J. M.; Raca, Gordana; Rao, Shruti; Madhavan, Subha; Wagner, Alex H.; Griffith, Obi L.; Griffith, Malachi Share Save Share Save CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC KnowledgebaseWagner, 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 Share Save Accurate neoantigen prediction depends on mutation position relative to patient-specific MHC anchor locationXia, Huiming; Richters, Megan M.; Ramirez, Cody A.; Puig-Saus, Cristina; Cotto, Kelsy C.; Dunn, Gavin P.; Fehniger, Todd; Ribas, Antoni; Gillanders, William E.; Griffith, Obi L.; Griffith, Malachi Share Save Adding CIViC knowledge to variant annotation pipelines with CIViCpyKiwala, Susanna; Wagner, Alex H.; Coffman, Adam C.; McMichael, Joshua F.; Cotto, Kelsy C.; Mooney, Thomas B.; Barnell, Erica K.; Krysiak, Kilannin; Danos, Arpad M.; Walker, Jason M.; Griffith, Obi L.; Griffith, Malachi Share Save RegTools: Integrative analysis of genomic and transcriptomic data to identify splice altering mutations across 35 cancer typesCotto, Kelsy C.; Feng, Yang-Yang; Skidmore, Zachary L.; Ramu, Avinash; Kunisaki, Jason; Conrad, Donald F.; Lin, Yiing; Chapman, William; Uppaluri, Ravindra; Govindan, Ramaswamy; Griffith, Obi L.; Griffith, Malachi Share Save Share Save Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samplesBarnell, 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. Share Save Share Save Share Save Share Save 
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