Zobrazeno 1 - 10
of 71
pro vyhledávání: '"Joshua F McMichael"'
Autor:
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
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 7, p e1004274 (2015)
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled
Externí odkaz:
https://doaj.org/article/8bd43ecac4d44f7cbb8d1a284c28cdab
Autor:
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
Publikováno v:
PLoS ONE, Vol 9, Iss 11, p e111153 (2014)
To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15
Externí odkaz:
https://doaj.org/article/1291a159fc7042a19c0e538ea5ad494d
Autor:
Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan Richters, Sharon L. Freshour, Zachary L. Skidmore, Huiming Xia, Joshua F. McMichael, Jason Kunisaki, Katie M. Campbell, Timothy Hung-Po Chen, Emily B. Rozycki, Douglas Adkins, Siddhartha Devarakonda, Sumithra Sankararaman, Yiing Lin, William C. Chapman, Christopher A. Maher, Vivek Arora, Gavin P. Dunn, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-18 (2023)
Analysing the regulatory consequences of mutations and splice variants at large scale in cancer requires efficient computational tools. Here, the authors develop RegTools, a software package that can identify splice-associated variants from large-sca
Externí odkaz:
https://doaj.org/article/a791b7f280e84d3d8c3cf984f3f564cd
Autor:
Kilannin Krysiak, Arpad M Danos, Jason Saliba, Joshua F McMichael, Adam C Coffman, Susanna Kiwala, Erica K Barnell, Lana Sheta, Cameron J Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Sarah Ridd, Nicholas C Spies, Veronica Andric, Andreea Chiorean, Damian T Rieke, Kaitlin A Clark, Caralyn Reisle, Ajay C Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horak, Deborah I Ritter, Xin Zhou, Benjamin J Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex R Marr, My H Hoang, Kartik Singhal, Mariam Khanfar, Brian V Li, Wan-Hsin Lin, Panieh Terraf, Laura B Corson, Yasser Salama, Katie M Campbell, Kirsten M Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C Cotto, Zachary L Skidmore, Jason R Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y Patel, Rachel H Giles, Raymond H Kim, Lynn M Schriml, Elaine R Mardis, Steven J M Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H Wagner, Malachi Griffith, Obi L Griffith
Publikováno v:
Nucleic Acids Research. 51:D1230-D1241
CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more pre
Autor:
Kilannin Krysiak, Arpad M. Danos, Susanna Kiwala, Joshua F. McMichael, Adam C. Coffman, Erica K. Barnell, Lana Sheta, Jason Saliba, Cameron J. Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Nicholas C. Spies, Andreea Chiorean, Damian T. Rieke, Kaitlin A. Clark, Payal Jani, Hideaki Takahashi, Peter Horak, Deborah I. Ritter, Xin Zhou, Benjamin J. Ainscough, Sean Delong, Mario Lamping, Alex R. Marr, Brian V. Li, Wan-Hsin Lin, Panieh Terraf, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Kelsy C. Cotto, Zachary L. Skidmore, Jason R. Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J. M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Obi L. Griffith, Malachi Griffith
Publikováno v:
Nat Cancer
As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ed50e6a9356f3f2f4e3e63d326c2871
https://eprints.gla.ac.uk/279775/1/279775.pdf
https://eprints.gla.ac.uk/279775/1/279775.pdf
Autor:
Obi L. Griffith, Sharon Freshour, Joshua F. McMichael, Susanna Kiwala, Adam C. Coffman, Kelsy C. Cotto, Jonathan J Song, Malachi Griffith, Alex H. Wagner
Publikováno v:
Nucleic Acids Research
The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normal
Autor:
Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E. Rood, Orr Ashenberg, Ethan Cerami, Robert J. Coffey, Emek Demir, Li Ding, Edward D. Esplin, James M. Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W. Gray, Justin Guinney, Sean E. Hanlon, Shannon K. Hughes, E. Shelley Hwang, Christine A. Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E. Johnson, Ken S. Lau, Tracy Lively, Sarah A. Mazzilli, Dana Pe’er, Sandro Santagata, Alex K. Shalek, Denis Schapiro, Michael P. Snyder, Peter K. Sorger, Avrum E. Spira, Sudhir Srivastava, Kai Tan, Robert B. West, Elizabeth H. Williams, Denise Aberle, Samuel I. Achilefu, Foluso O. Ademuyiwa, Andrew C. Adey, Rebecca L. Aft, Rachana Agarwal, Ruben A. Aguilar, Fatemeh Alikarami, Viola Allaj, Christopher Amos, Robert A. Anders, Michael R. Angelo, Kristen Anton, Jon C. Aster, Ozgun Babur, Amir Bahmani, Akshay Balsubramani, David Barrett, Jennifer Beane, Diane E. Bender, Kathrin Bernt, Lynne Berry, Courtney B. Betts, Julie Bletz, Katie Blise, Adrienne Boire, Genevieve Boland, Alexander Borowsky, Kristopher Bosse, Matthew Bott, Ed Boyden, James Brooks, Raphael Bueno, Erik A. Burlingame, Qiuyin Cai, Joshua Campbell, Wagma Caravan, Hassan Chaib, Joseph M. Chan, Young Hwan Chang, Deyali Chatterjee, Ojasvi Chaudhary, Alyce A. Chen, Bob Chen, Changya Chen, Chia-hui Chen, Feng Chen, Yu-An Chen, Milan G. Chheda, Koei Chin, Roxanne Chiu, Shih-Kai Chu, Rodrigo Chuaqui, Jaeyoung Chun, Luis Cisneros, Graham A. Colditz, Kristina Cole, Natalie Collins, Kevin Contrepois, Lisa M. Coussens, Allison L. Creason, Daniel Crichton, Christina Curtis, Tanja Davidsen, Sherri R. Davies, Ino de Bruijn, Laura Dellostritto, Angelo De Marzo, David G. DeNardo, Dinh Diep, Sharon Diskin, Xengie Doan, Julia Drewes, Stephen Dubinett, Michael Dyer, Jacklynn Egger, Jennifer Eng, Barbara Engelhardt, Graham Erwin, Laura Esserman, Alex Felmeister, Heidi S. Feiler, Ryan C. Fields, Stephen Fisher, Keith Flaherty, Jennifer Flournoy, Angelo Fortunato, Allison Frangieh, Jennifer L. Frye, Robert S. Fulton, Danielle Galipeau, Siting Gan, Jianjiong Gao, Long Gao, Peng Gao, Vianne R. Gao, Tim Geiger, Ajit George, Gad Getz, Marios Giannakis, David L. Gibbs, William E. Gillanders, Simon P. Goedegebuure, Alanna Gould, Kate Gowers, William Greenleaf, Jeremy Gresham, Jennifer L. Guerriero, Tuhin K. Guha, Alexander R. Guimaraes, David Gutman, Nir Hacohen, Sean Hanlon, Casey R. Hansen, Olivier Harismendy, Kathleen A. Harris, Aaron Hata, Akimasa Hayashi, Cody Heiser, Karla Helvie, John M. Herndon, Gilliam Hirst, Frank Hodi, Travis Hollmann, Aaron Horning, James J. Hsieh, Shannon Hughes, Won Jae Huh, Stephen Hunger, Shelley E. Hwang, Heba Ijaz, Benjamin Izar, Connor A. Jacobson, Samuel Janes, Reyka G. Jayasinghe, Lihua Jiang, Brett E. Johnson, Bruce Johnson, Tao Ju, Humam Kadara, Klaus Kaestner, Jacob Kagan, Lukas Kalinke, Robert Keith, Aziz Khan, Warren Kibbe, Albert H. Kim, Erika Kim, Junhyong Kim, Annette Kolodzie, Mateusz Kopytra, Eran Kotler, Robert Krueger, Kostyantyn Krysan, Anshul Kundaje, Uri Ladabaum, Blue B. Lake, Huy Lam, Rozelle Laquindanum, Ashley M. Laughney, Hayan Lee, Marc Lenburg, Carina Leonard, Ignaty Leshchiner, Rochelle Levy, Jerry Li, Christine G. Lian, Kian-Huat Lim, Jia-Ren Lin, Yiyun Lin, Qi Liu, Ruiyang Liu, William J.R. Longabaugh, Teri Longacre, Cynthia X. Ma, Mary Catherine Macedonia, Tyler Madison, Christopher A. Maher, Anirban Maitra, Netta Makinen, Danika Makowski, Carlo Maley, Zoltan Maliga, Diego Mallo, John Maris, Nick Markham, Jeffrey Marks, Daniel Martinez, Robert J. Mashl, Ignas Masilionais, Jennifer Mason, Joan Massagué, Pierre Massion, Marissa Mattar, Richard Mazurchuk, Linas Mazutis, Eliot T. McKinley, Joshua F. McMichael, Daniel Merrick, Matthew Meyerson, Julia R. Miessner, Gordon B. Mills, Meredith Mills, Suman B. Mondal, Motomi Mori, Yuriko Mori, Elizabeth Moses, Yael Mosse, Jeremy L. Muhlich, George F. Murphy, Nicholas E. Navin, Michel Nederlof, Reid Ness, Stephanie Nevins, Milen Nikolov, Ajit Johnson Nirmal, Garry Nolan, Edward Novikov, Brendan O’Connell, Michael Offin, Stephen T. Oh, Anastasiya Olson, Alex Ooms, Miguel Ossandon, Kouros Owzar, Swapnil Parmar, Tasleema Patel, Gary J. Patti, Itsik Pe'er, Tao Peng, Daniel Persson, Marvin Petty, Hanspeter Pfister, Kornelia Polyak, Kamyar Pourfarhangi, Sidharth V. Puram, Qi Qiu, Álvaro Quintanal-Villalonga, Arjun Raj, Marisol Ramirez-Solano, Rumana Rashid, Ashley N. Reeb, Mary Reid, Adam Resnick, Sheila M. Reynolds, Jessica L. Riesterer, Scott Rodig, Joseph T. Roland, Sonia Rosenfield, Asaf Rotem, Sudipta Roy, Charles M. Rudin, Marc D. Ryser, Maria Santi-Vicini, Kazuhito Sato, Deborah Schrag, Nikolaus Schultz, Cynthia L. Sears, Rosalie C. Sears, Subrata Sen, Triparna Sen, Alex Shalek, Jeff Sheng, Quanhu Sheng, Kooresh I. Shoghi, Martha J. Shrubsole, Yu Shyr, Alexander B. Sibley, Kiara Siex, Alan J. Simmons, Dinah S. Singer, Shamilene Sivagnanam, Michal Slyper, Artem Sokolov, Sheng-Kwei Song, Austin Southard-Smith, Avrum Spira, Janet Stein, Phillip Storm, Elizabeth Stover, Siri H. Strand, Timothy Su, Damir Sudar, Ryan Sullivan, Lea Surrey, Mario Suvà, Nadezhda V. Terekhanova, Luke Ternes, Lisa Thammavong, Guillaume Thibault, George V. Thomas, Vésteinn Thorsson, Ellen Todres, Linh Tran, Madison Tyler, Yasin Uzun, Anil Vachani, Eliezer Van Allen, Simon Vandekar, Deborah J. Veis, Sébastien Vigneau, Arastoo Vossough, Angela Waanders, Nikhil Wagle, Liang-Bo Wang, Michael C. Wendl, Robert West, Chi-yun Wu, Hao Wu, Hung-Yi Wu, Matthew A. Wyczalkowski, Yubin Xie, Xiaolu Yang, Clarence Yapp, Wenbao Yu, Yinyin Yuan, Dadong Zhang, Kun Zhang, Mianlei Zhang, Nancy Zhang, Yantian Zhang, Yanyan Zhao, Daniel Cui Zhou, Zilu Zhou, Houxiang Zhu, Qin Zhu, Xiangzhu Zhu, Yuankun Zhu, Xiaowei Zhuang
Publikováno v:
Cell
Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spat
Autor:
Daniel Cui Zhou, Reyka G. Jayasinghe, Siqi Chen, John M. Herndon, Michael D. Iglesia, Pooja Navale, Michael C. Wendl, Wagma Caravan, Kazuhito Sato, Erik Storrs, Chia-Kuei Mo, Jingxian Liu, Austin N. Southard-Smith, Yige Wu, Nataly Naser Al Deen, John M. Baer, Robert S. Fulton, Matthew A. Wyczalkowski, Ruiyang Liu, Catrina C. Fronick, Lucinda A. Fulton, Andrew Shinkle, Lisa Thammavong, Houxiang Zhu, Hua Sun, Liang-Bo Wang, Yize Li, Chong Zuo, Joshua F. McMichael, Sherri R. Davies, Elizabeth L. Appelbaum, Keenan J. Robbins, Sara E. Chasnoff, Xiaolu Yang, Ashley N. Reeb, Clara Oh, Mamatha Serasanambati, Preet Lal, Rajees Varghese, Jay R. Mashl, Jennifer Ponce, Nadezhda V. Terekhanova, Lijun Yao, Fang Wang, Lijun Chen, Michael Schnaubelt, Rita Jui-Hsien Lu, Julie K. Schwarz, Sidharth V. Puram, Albert H. Kim, Sheng-Kwei Song, Kooresh I. Shoghi, Ken S. Lau, Tao Ju, Ken Chen, Deyali Chatterjee, William G. Hawkins, Hui Zhang, Samuel Achilefu, Milan G. Chheda, Stephen T. Oh, William E. Gillanders, Feng Chen, David G. DeNardo, Ryan C. Fields, Li Ding
Publikováno v:
Nature genetics. 54(9)
Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics,
Autor:
Robert S. Fulton, Matthew A. Wyczalkowski, Christopher J. Yoon, Justin King, Steven M. Foltz, Timothy J. Ley, Julie O'Neal, Ravi Vij, Erik Storrs, Ruiyang Liu, Amila Weerasinghe, Julia Tianjiao Wang, Scott R. Goldsmith, Hua Sun, Michael C. Wendl, Michael P. Rettig, Stephen T. Oh, Song Cao, Mark A. Fiala, Catrina Fronick, Daniel R. Kohnen, Sunantha Sethuraman, Lijun Yao, John F. DiPersio, Reyka G Jayasinghe, Jared S. Fowles, Joshua F. McMichael, Li Ding, Qingsong Gao
Publikováno v:
Nature Communications
Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021)
Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021)
Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply
Autor:
Li Ding, Michael C. Wendl, Tina Primeau, Christopher R. Kinsinger, R. Reid Townsend, Adam D. Scott, Kuan-lin Huang, Shunqiang Li, Sherri R. Davies, Kimberly J. Johnson, David Fenyö, Joshua F. McMichael, Yuqian Gao, Yi-Ting Wang, Samuel H. Payne, Yige Wu, Jason M. Held, Arvin C. Dar, Mehdi Mesri, Kelly V. Ruggles, Steven A. Carr, Song Cao, Tao Liu, Henry Rodriguez, Feng Chen, Matthew J. Ellis
Publikováno v:
Mol Cell Proteomics
Aberrant phospho-signaling is a hallmark of cancer. We investigated kinase-substrate regulation of 33,239 phosphorylation sites (phosphosites) in 77 breast tumors and 24 breast cancer xenografts. Our search discovered 2134 quantitatively correlated k