Clinical implications of neoepitope landscapes for adult and pediatric cancers

by Yang-Yang Feng, Obi L. Griffith, Malachi Griffith
Published 2017-08-01

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud.

by Malachi Griffith, Jason R Walker, Nicholas C Spies, Benjamin J Ainscough, Obi L Griffith
Published 2015-08-01

Best practices for bioinformatic characterization of neoantigens for clinical utility

by Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Obi L. Griffith, Malachi Griffith
Published 2019-08-01

Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches.

by Shirley Chu, Zachary L Skidmore, Jason Kunisaki, Jason R Walker, Malachi Griffith, Obi L Griffith, Jeffrey N Bryan
Published 2021-01-01

Text-mining clinically relevant cancer biomarkers for curation into the CIViC database

by Jake Lever, Martin R. Jones, Arpad M. Danos, Kilannin Krysiak, Melika Bonakdar, Jasleen K. Grewal, Luka Culibrk, Obi L. Griffith, Malachi Griffith, Steven J. M. Jones
Published 2019-12-01

RNA Sequencing of Tumor-Associated Microglia Reveals Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth

by Anne C. Solga, Winnie W. Pong, Keun-Young Kim, Patrick J. Cimino, Joseph A. Toonen, Jason Walker, Todd Wylie, Vincent Magrini, Malachi Griffith, Obi L. Griffith, Amy Ly, Mark H. Ellisman, Elaine R. Mardis, David H. Gutmann
Published 2015-10-01

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF.

by Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary Skidmore, Takaharu Ueno, Jun-Ichi Fujisawa, Daniel A Rauch, Grant A Challen, Michael P Martinez, Patrick Green, Malachi Griffith, Jacqueline E Payton, John R Edwards, Lee Ratner
Published 2021-05-01

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

by Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G F Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A Marra, Martin Hirst, Torsten O Nielsen, S Cenk Sahinalp, David Huntsman, Sohrab P Shah
Published 2011-05-01

Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation

by Olivia Alder, Rebecca Cullum, Sam Lee, Arohumam C. Kan, Wei Wei, Yuyin Yi, Victoria C. Garside, Misha Bilenky, Malachi Griffith, A. Sorana Morrissy, Gordon A. Robertson, Nina Thiessen, Yongjun Zhao, Qian Chen, Duojia Pan, Steven J.M. Jones, Marco A. Marra, Pamela A. Hoodless
Published 2014-10-01

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

by Christopher A Miller, Brian S White, Nathan D Dees, Malachi Griffith, John S Welch, Obi L Griffith, Ravi Vij, Michael H Tomasson, Timothy A Graubert, Matthew J Walter, Matthew J Ellis, William Schierding, John F DiPersio, Timothy J Ley, Elaine R Mardis, Richard K Wilson, Li Ding
Published 2014-08-01

F11R is a novel monocyte prognostic biomarker for malignant glioma.

by Winnie W Pong, Jason Walker, Todd Wylie, Vincent Magrini, Jingqin Luo, Ryan J Emnett, Jaebok Choi, Matthew L Cooper, Malachi Griffith, Obi L Griffith, Joshua B Rubin, Gregory N Fuller, David Piwnica-Worms, Xi Feng, Dolores Hambardzumyan, John F DiPersio, Elaine R Mardis, David H Gutmann
Published 2013-01-01

Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers

by Christopher A. Miller, Yevgeniy Gindin, Charles Lu, Obi L Griffith, Malachi Griffith, Dong Shen, Jeremy Hoog, Tiandao Li, David E. Larson, Mark Watson, Sherri R Davies, Kelly Hunt, Vera J. Suman, Jacqueline Snider, Thomas Walsh, Graham A. Colditz, Katherine DeSchryver, Richard K. Wilson, Elaine R. Mardis, Matthew J. Ellis
Published 2016-08-01

Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas

by Obi L. Griffith, Szeman Ruby Chan, Malachi Griffith, Kilannin Krysiak, Zachary L. Skidmore, Jasreet Hundal, Julie A. Allen, Cora D. Arthur, Daniele Runci, Mattia Bugatti, Alexander P. Miceli, Heather Schmidt, Lee Trani, Krishna-Latha Kanchi, Christopher A. Miller, David E. Larson, Robert S. Fulton, William Vermi, Richard K. Wilson, Robert D. Schreiber, Elaine R. Mardis
Published 2016-09-01

Clonal architectures and driver mutations in metastatic melanomas.

by Li Ding, Minjung Kim, Krishna L Kanchi, Nathan D Dees, Charles Lu, Malachi Griffith, David Fenstermacher, Hyeran Sung, Christopher A Miller, Brian Goetz, Michael C Wendl, Obi Griffith, Lynn A Cornelius, Gerald P Linette, Joshua F McMichael, Vernon K Sondak, Ryan C Fields, Timothy J Ley, James J Mulé, Richard K Wilson, Jeffrey S Weber
Published 2014-01-01

Standard operating procedure for curation and clinical interpretation of variants in cancer

by Arpad M. Danos, Kilannin Krysiak, Erica K. Barnell, Adam C. Coffman, Joshua F. McMichael, Susanna Kiwala, Nicholas C. Spies, Lana M. Sheta, Shahil P. Pema, Lynzey Kujan, Kaitlin A. Clark, Amber Z. Wollam, Shruti Rao, Deborah I. Ritter, Dmitriy Sonkin, Gordana Raca, Wan-Hsin Lin, Cameron J. Grisdale, Raymond H. Kim, Alex H. Wagner, Subha Madhavan, Malachi Griffith, Obi L. Griffith
Published 2019-11-01

Wikidata as a knowledge graph for the life sciences

by Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, Obi L Griffith, Kristina Hanspers, Henning Hermjakob, Toby S Hudson, Kevin Hybiske, Sarah M Keating, Magnus Manske, Michael Mayers, Daniel Mietchen, Elvira Mitraka, Alexander R Pico, Timothy Putman, Anders Riutta, Nuria Queralt-Rosinach, Lynn M Schriml, Thomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew I Su
Published 2020-03-01

Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer

by Alex H. Wagner, Siddhartha Devarakonda, Zachary L. Skidmore, Kilannin Krysiak, Avinash Ramu, Lee Trani, Jason Kunisaki, Ashiq Masood, Saiama N. Waqar, Nicholas C. Spies, Daniel Morgensztern, Jason Waligorski, Jennifer Ponce, Robert S. Fulton, Leonard B. Maggi, Jason D. Weber, Mark A. Watson, Christopher J. O’Conor, Jon H. Ritter, Rachelle R. Olsen, Haixia Cheng, Anandaroop Mukhopadhyay, Ismail Can, Melissa H. Cessna, Trudy G. Oliver, Elaine R. Mardis, Richard K. Wilson, Malachi Griffith, Obi L. Griffith, Ramaswamy Govindan
Published 2018-09-01

Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer

by Obi L. Griffith, Nicholas C. Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Luo, Dongsheng Tu, Belinda Yeo, Jason Kunisaki, Christopher A Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J Ainscough, Zachary L. Skidmore, Katie Campbell, Runjun Kumar, Catrina Fronick, Lisa Cook, Jacqueline E. Snider, Sherri Davies, Shyam M. Kavuri, Eric C. Chang, Vincent Magrini, David E. Larson, Robert S Fulton, Shuzhen Liu, Samuel Leung, David Voduc, Ron Bose, Mitch Dowsett, Richard K. Wilson, Torsten O. Nielsen, Elaine R Mardis, Matthew J. Ellis
Published 2018-11-01

The prognostic effects of somatic mutations in ER-positive breast cancer

by Obi L. Griffith, Nicholas C. Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Luo, Dongsheng Tu, Belinda Yeo, Jason Kunisaki, Christopher A Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J Ainscough, Zachary L. Skidmore, Katie Campbell, Runjun Kumar, Catrina Fronick, Lisa Cook, Jacqueline E. Snider, Sherri Davies, Shyam M. Kavuri, Eric C. Chang, Vincent Magrini, David E. Larson, Robert S Fulton, Shuzhen Liu, Samuel Leung, David Voduc, Ron Bose, Mitch Dowsett, Richard K. Wilson, Torsten O. Nielsen, Elaine R Mardis, Matthew J. Ellis
Published 2018-09-01

Genome Modeling System: A Knowledge Management Platform for Genomics.

by Malachi Griffith, Obi L Griffith, Scott M Smith, Avinash Ramu, Matthew B Callaway, Anthony M Brummett, Michael J Kiwala, Adam C Coffman, Allison A Regier, Ben J Oberkfell, Gabriel E Sanderson, Thomas P Mooney, Nathaniel G Nutter, Edward A Belter, Feiyu Du, Robert L Long, Travis E Abbott, Ian T Ferguson, David L Morton, Mark M Burnett, James V Weible, Joshua B Peck, Adam Dukes, Joshua F McMichael, Justin T Lolofie, Brian R Derickson, Jasreet Hundal, Zachary L Skidmore, Benjamin J Ainscough, Nathan D Dees, William S Schierding, Cyriac Kandoth, Kyung H Kim, Charles Lu, Christopher C Harris, Nicole Maher, Christopher A Maher, Vincent J Magrini, Benjamin S Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy E Hawkins, Todd G Hepler, Todd N Wylie, Shawn M Leonard, William E Schroeder, Xiaoqi Shi, Lynn K Carmichael, Matthew R Weil, Richard W Wohlstadter, Gary Stiehr, Michael D McLellan, Craig S Pohl, Christopher A Miller, Daniel C Koboldt, Jason R Walker, James M Eldred, David E Larson, David J Dooling, Li Ding, Elaine R Mardis, Richard K Wilson
Published 2015-07-01