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Charles D. Johnson
Researcher at Texas A&M University
Publications - 28
Citations - 5852
Charles D. Johnson is an academic researcher from Texas A&M University. The author has contributed to research in topics: Deep sequencing & Transcriptome. The author has an hindex of 19, co-authored 26 publications receiving 5483 citations. Previous affiliations of Charles D. Johnson include Texas AgriLife Research & University of Louisville.
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Journal ArticleDOI
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Leming Shi,Laura H. Reid,Wendell D. Jones,Richard Shippy,Janet A. Warrington,Shawn C. Baker,Patrick J. Collins,Francoise de Longueville,Ernest S. Kawasaki,Kathleen Y. Lee,Yuling Luo,Yongming Andrew Sun,James C. Willey,Robert Setterquist,Gavin M. Fischer,Weida Tong,Yvonne P. Dragan,David J. Dix,Felix W. Frueh,Federico Goodsaid,Damir Herman,Roderick V. Jensen,Charles D. Johnson,Edward K. Lobenhofer,Raj K. Puri,Uwe Scherf,Jean Thierry-Mieg,Charles Wang,Michael A Wilson,Paul K. Wolber,Lu Zhang,William Slikker,Shashi Amur,Wenjun Bao,Catalin Barbacioru,Anne Bergstrom Lucas,Vincent Bertholet,Cecilie Boysen,Bud Bromley,Donna Brown,Alan Brunner,Roger D. Canales,Xiaoxi Megan Cao,Thomas A. Cebula,James J. Chen,Jing Cheng,Tzu Ming Chu,Eugene Chudin,John F. Corson,J. Christopher Corton,Lisa J. Croner,Christopher Davies,Timothy Davison,Glenda C. Delenstarr,Xutao Deng,David Dorris,Aron Charles Eklund,Xiaohui Fan,Hong Fang,Stephanie Fulmer-Smentek,James C. Fuscoe,Kathryn Gallagher,Weigong Ge,Lei Guo,Xu Guo,Janet Hager,Paul K. Haje,Jing Han,Tao Han,Heather Harbottle,Stephen C. Harris,Eli Hatchwell,Craig A. Hauser,Susan D. Hester,Huixiao Hong,Patrick Hurban,Scott A. Jackson,Hanlee P. Ji,Charles R. Knight,Winston Patrick Kuo,J. Eugene LeClerc,Shawn Levy,Quan Zhen Li,Chunmei Liu,Ying Liu,Michael Lombardi,Yunqing Ma,Scott R. Magnuson,Botoul Maqsodi,Timothy K. McDaniel,Nan Mei,Ola Myklebost,Baitang Ning,Natalia Novoradovskaya,Michael S. Orr,Terry Osborn,Adam Papallo,Tucker A. Patterson,Roger Perkins,Elizabeth Herness Peters,Ron L. Peterson,Kenneth L. Philips,P. Scott Pine,Lajos Pusztai,Feng Qian,Hongzu Ren,Mitch Rosen,Barry A. Rosenzweig,Raymond R. Samaha,Mark Schena,Gary P. Schroth,Svetlana Shchegrova,Dave D. Smith,Frank Staedtler,Zhenqiang Su,Hongmei Sun,Zoltan Szallasi,Zivana Tezak,Danielle Thierry-Mieg,Karol L. Thompson,Irina Tikhonova,Yaron Turpaz,Beena Vallanat,Christophe Van,Stephen J. Walker,Sue Jane Wang,Yonghong Wang,Russell D. Wolfinger,Alexander Wong,Jie Wu,Chunlin Xiao,Qian Xie,Jun Xu,Wen Yang,Liang Zhang,Sheng Zhong,Yaping Zong +136 more
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Journal ArticleDOI
The let-7 MicroRNA represses cell proliferation pathways in human cells
Charles D. Johnson,Aurora Esquela-Kerscher,Giovanni Stefani,Mike Byrom,Kevin Kelnar,Dmitriy Ovcharenko,Michael R. Wilson,Xiaowei Wang,Jeffrey Shelton,Jaclyn Shingara,Lena Chin,David F.M. Brown,Frank J. Slack +12 more
TL;DR: This work reveals the let-7 microRNA to be a master regulator of cell proliferation pathways and shows that multiple genes involved in cell cycle and cell division functions are also directly or indirectly repressed byLet-7.
Journal ArticleDOI
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
Zhenqiang Su,Paweł P. Łabaj,Sheng Li,Jean Thierry-Mieg,Danielle Thierry-Mieg,Wei Shi,Charles Wang,Gary P. Schroth,Robert Setterquist,John F. Thompson,Wendell D. Jones,Wenzhong Xiao,Wenzhong Xiao,Weihong Xu,Roderick V. Jensen,Reagan Kelly,Joshua Xu,Ana Conesa,Cesare Furlanello,Hanlin Gao,Huixiao Hong,Nadereh Jafari,Stan Letovsky,Yang Liao,Fei Lu,Edward J. Oakeley,Zhiyu Peng,Craig A. Praul,Javier Santoyo-Lopez,Andreas Scherer,Tieliu Shi,Gordon K. Smyth,Frank Staedtler,Peter Sykacek,Xin Xing Tan,E. Aubrey Thompson,Jo Vandesompele,May D. Wang,Jian Wang,Russell D. Wolfinger,Jiri Zavadil,Jiri Zavadil,Scott S. Auerbach,Wenjun Bao,Hans Binder,Thomas M. Blomquist,Murray H. Brilliant,Pierre R. Bushel,Weimin Cai,Jennifer G. Catalano,Ching-Wei Chang,Tao Chen,Geng Chen,Rong Chen,Marco Chierici,Tzu Ming Chu,Djork-Arné Clevert,Youping Deng,Adnan Derti,Viswanath Devanarayan,Zirui Dong,Joaquín Dopazo,Tingting Du,Hong Fang,Yongxiang Fang,Mario Fasold,Anita Fernandez,Matthias Fischer,Pedro Furió-Tarí,James C. Fuscoe,Florian Caimet,Stan Gaj,Jorge Gandara,Huan Gao,Weigong Ge,Yoichi Gondo,Binsheng Gong,Meihua Gong,Zhuolin Gong,Bridgett Green,Chao Guo,Lei Guo,Li Wu Guo,James Hadfield,Jan Hellemans,Sepp Hochreiter,Meiwen Jia,Min Jian,Charles D. Johnson,Suzanne Kay,Jos C. S. Kleinjans,Samir Lababidi,Shawn Levy,Quan Zhen Li,Li Li,Peng Li,Yan Li,Haiqing Li,Jianying Li,Shiyong Li,Simon Lin,Francisco Javier López,Xin Lu,Heng Luo,Xiwen Ma,Joseph Meehan,Dalila B. Megherbi,Nan Mei,Bing Mu,Baitang Ning,Akhilesh Pandey,Javier Pérez-Florido,Roger Perkins,Ryan Peters,John H. Phan,Mehdi Pirooznia,Feng Qian,Tao Qing,Lucille Rainbow,Philippe Rocca-Serra,Laure Sambourg,Susanna-Assunta Sansone,Scott Schwartz,Ruchir R. Shah,Jie Shen,Todd M. Smith,Oliver Stegle,Nancy Stralis-Pavese,Elia Stupka,Yutaka Suzuki,Lee Thomas Szkotnicki,Matthew Tinning,Bimeng Tu,Joost H.M. van Delft,Alicia Vela-Boza,Elisa Venturini,Stephen J. Walker,Liqing Wan,Wei Wang,Jinhui Wang,Jun Wang,Jun Wang,Eric D. Wieben,James C. Willey,Po Yen Wu,Jiekun Xuan,Yong Yang,Zhan Ye,Ye Yin,Ying Yu,Yate Ching Yuan,John Zhang,Ke Zhang,Wenqian Zhang,Wenwei Zhang,Yanyan Zhang,Chen Zhao,Yuanting Zheng,Yiming Zhou,Paul Zumbo,Weida Tong,David P. Kreil,David P. Kreil,Christopher E. Mason,Leming Shi +164 more
TL;DR: The complete SEQC data sets, comprising >100 billion reads, provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings, and measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling.
Journal ArticleDOI
The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Leming Shi,Gregory Campbell,Wendell D. Jones,Fabien Campagne,Zhining Wen,Stephen J. Walker,Zhenqiang Su,Tzu Ming Chu,Federico Goodsaid,Lajos Pusztai,John D. Shaughnessy,André Oberthuer,Russell S. Thomas,Richard S. Paules,Mark R. Fielden,Bart Barlogie,Weijie Chen,Pan Du,Matthias Fischer,Cesare Furlanello,Brandon D. Gallas,Xijin Ge,Dalila B. Megherbi,W. Fraser Symmans,May D. Wang,John Zhang,Hans Bitter,Benedikt Brors,Pierre R. Bushel,Max Bylesjö,Minjun Chen,Jie Cheng,Jing Cheng,Jeff W. Chou,Timothy Davison,Mauro Delorenzi,Youping Deng,Viswanath Devanarayan,David J. Dix,Joaquín Dopazo,Kevin C. Dorff,Fathi Elloumi,Jianqing Fan,Shicai Fan,Xiaohui Fan,Hong Fang,Nina Gonzaludo,Kenneth R. Hess,Huixiao Hong,Jun Huan,Rafael A. Irizarry,Richard S. Judson,Dilafruz Juraeva,Samir Lababidi,Christophe G. Lambert,Li Li,Yanen Li,Zhen Li,Simon Lin,Guozhen Liu,Edward K. Lobenhofer,J. Luo,Wen Luo,Matthew N. McCall,Yuri Nikolsky,Gene Pennello,Roger Perkins,Reena Philip,Vlad Popovici,Nathan D. Price,Feng Qian,Andreas Scherer,Tieliu Shi,Weiwei Shi,Jaeyun Sung,Danielle Thierry-Mieg,Jean Thierry-Mieg,Venkata Thodima,Johan Trygg,Lakshmi Vishnuvajjala,Sue Jane Wang,Jianping Wu,Yichao Wu,Qian Xie,Waleed A. Yousef,Liang Zhang,Xuegong Zhang,Sheng Zhong,Yiming Zhou,Sheng Zhu,Dhivya Arasappan,Wenjun Bao,Anne Bergstrom Lucas,Frank Berthold,Richard J. Brennan,Andreas Buness,Jennifer G. Catalano,Chang Chang,Rong Chen,Yiyu Cheng,Jian Cui,Wendy Czika,Francesca Demichelis,Xutao Deng,Damir Dosymbekov,Roland Eils,Yang Feng,Jennifer Fostel,Stephanie Fulmer-Smentek,James C. Fuscoe,Laurent Gatto,Weigong Ge,Darlene R. Goldstein,Li Guo,Donald N. Halbert,Jing Han,Stephen C. Harris,Christos Hatzis,Damir Herman,Jianping Huang,Roderick V. Jensen,Rui Jiang,Charles D. Johnson,Giuseppe Jurman,Yvonne Kahlert,Sadik A. Khuder,Matthias Kohl,Jianying Li,Li Lee,Menglong Li,Quan Zhen Li,Shao Li,Zhiguang Li,Jie Liu,Ying Liu,Zhichao Liu,Lu Meng,Manuel Madera,Francisco Martinez-Murillo,Ignacio Medina,Joseph Meehan,K. Miclaus,Richard A. Moffitt,David Montaner,Piali Mukherjee,George Mulligan,Padraic Neville,Tatiana Nikolskaya,Baitang Ning,Grier P. Page,Joel S. Parker,R. Mitchell Parry,Xuejun Peng,Ron L. Peterson,John H. Phan,Brian Quanz,Yi Ren,Samantha Riccadonna,Alan H. Roter,Frank W. Samuelson,Martin Schumacher,Joseph D. Shambaugh,Qiang Shi,Richard Shippy,Shengzhu Si,Aaron Smalter,Christos Sotiriou,Mat Soukup,Frank Staedtler,Guido Steiner,Todd H. Stokes,Qinglan Sun,Pei Yi Tan,Rong Tang,Zivana Tezak,Brett T. Thorn,Marina Tsyganova,Yaron Turpaz,S. Vega,Roberto Visintainer,Juergen Von Frese,Charles Wang,Eric Wang,Junwei Wang,Wei Wang,Frank Westermann,James C. Willey,Matthew Woods,Shujian Wu,Nianqing Xiao,Joshua Xu,Lei Xu,Lun Yang,Xiao Zeng,Jialu Zhang,Li Zheng,Min Zhang,Chen Zhao,Raj K. Puri,Uwe Scherf,Weida Tong,Russell D. Wolfinger +201 more
TL;DR: P predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans are generated.
Journal ArticleDOI
Genome-Scale MicroRNA and Small Interfering RNA Screens Identify Small RNA Modulators of TRAIL-Induced Apoptosis Pathway
TL;DR: Libraries of synthetic small interfering RNA (siRNA) and microRNAs (miRNA) were used to probe the TRAIL pathway and revealed novel genes, including CDK4, the only member of the cyclin-dependent kinase gene family that bore a unique function in apoptotic signal transduction.