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Author: Johnson, Charles D.

Noushin Ghaffari, Osama A. Arshad, Hyundoo Jeong, John Thiltges, Michael F. Criscitiello, Byung-Jun Yoon, Aniruddha Datta, Charles D. Johnson, "Examining de novo transcriptome assemblies via a quality assessment pipeline", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 2, pp. 494-505, 2018.  (Journal Publication)  [More Details]  [Online]

J. Abante, N. Ghaffari, C. Johnson and A. Datta, "HiMMe: Using Genetic Patterns as a Proxy for Genome Assembly Reliability Assessment", BMC Genomics, 18:694, 2017.   (Book Chapter)  [More Details]  [Online]

N. Ghaffari, O. A. Arshad, H. Jeong, J. Thiltges, M. F. Criscitiello, B.-J. Yoon, A. Datta and C. D. Johnson, "Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline",   (Journal Publication)  [More Details]  [Online]

Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul M. Seabury, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury, "A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene", PLOS ONE, March 2014, Volume 9, Issue 3  (Journal Publication)  [More Details]  [Online]

SEQC/MAQC-III Consortium, "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium", Nature Biotechnology (2014) doi:10.1038/nbt.2957  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan, Karina D. Garcia-Orozco, Patricia L. Chen, Adrian Ochoa-Leyva, Alonso A. Lopez-Zavala, J. Salvador Carrasco, Chris Hong, Luis G. Brieba, Enrique Rudiño-Piñera, Philip D. Blood, Jason E. Sawyer, Charles D. Johnson, Scott V. Dindot, Rogerio R. Sotelo-Mundo, Michael F. Criscitiello, "Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture", Nature Scientific Reports 4, Article number: 7081  (Journal Publication)  [More Details]  [Online]

Fangjun Li, Cheng Cheng, Fuhao Cui, Marcos VV de Oliveira, Xiao Yu, Xiangzong Meng, Aline C Intorne, Kevin Babilonia, Maoying Li, Bo Li, Sixue Chen, Xianfeng Ma, Shunyuan Xiao, Yi Zheng, Zhangjun Fei, Richard P Metz, Charles D Johnson, Hisashi Koiwa, Wenxian Sun, Zhaohu Li, Gonçalo A de Souza Filho, Libo Shan, Ping He, "Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity", Cell Host & Microbe doi:10.1016/j.chom.2014.10.018  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Mohammadmahdi R Yousefi, Charles D Johnson, Ivan Ivanov and Edward R Dougherty, "Modeling the next generation sequencing sample processing pipeline for the purposes of classification", BMC Bioinformatics 2013, 14:307  (Journal Publication)  [More Details]  [Online]

Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charles D Johnson, Scott V Dindot, "Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare", BMC Genomics, 2012; 13 (1): 78  (Journal Publication)  [More Details]  [Online]

Alfonso Clavijo, Amir Nikooienejad, Mohammad Shahrokh , Richard P. Metz, Scott Schwartz, Esmaeil Atashpaz Gargari, Thomas J. Deliberto, Mark W. Lutman, Kerri Pedersen , Luis R. Bazan, Leo G. Koster, Melinda Jenkins-Moore, Sabrina L. Swenson, Mike Zang, Tammy Beckham, Charles D. Johnson , Mangkey Bounpheng, "Identification and Analysis of the First 2009 Pandemic H1N1 Influenza Virus from U.S. Feral Swine", Zoonoses and Public Health. DOI: 10.1111/zph.12006  (Journal Publication)  [More Details]  [Online]

Y. Wang, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, and H. Zhou, "Evaluation of Coverage and Depth of Transcriptome by RNA-Seq in Chickens", BMC Bioinformatics, 12 (Suppl 10):S5, 2011  (Journal Publication)  [More Details]  [Online]

Leming et. al., "The MicroArray Quality Control (MAQC) Consortium. “MAQC-II Project: a comprehensive survey of common practices for the development and validation of microarray-based predictive models", Nat Biotechnology, 24(9), 2010, pp 827-838X.  (Journal Publication)  [More Details]  [Online]

Dmitriy Ovcharenko, Kevin Kelnar, Charles Johnson, Nan Leng, David Brown, "Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway", Cancer Res 2007;67(22):10782–8  (Journal Publication)  [More Details]  [Online]

Charles D Johnson, Yoganand Balagurunathan, Edward R Dougherty, Cynthia A Afshari, Qiang He, Kenneth S Ramos, "Insight into redox-regulated gene networks in vascular cells", Bioinformation, 2007; 1(10); 379-383  (Journal Publication)  [More Details]  [Online]

Charles D Johnson, Aurora Esquela-Kerscher, Giovanni Stefani, Mike Byrom, Kevin Kelnar, Dmitriy Ovcharenko, Mike Wilson, Xiaowei Wang, Jeffrey Shelton, Jaclyn Shingara, Lena Chin, David Brown, Frank J Slack, "The let-7 MicroRNA Represses Cell Proliferation Pathways in Human Cells", Cancer Res 2007; 67: (16). August 15, 2007  (Journal Publication)  [More Details]  [Online]

Timothy S. Davison, Charles D. Johnson, Bernard F. Andruss, "[2] Analyzing Micro‐RNA Expression Using Microarrays", Methods in Enzymology Volume 411, 2006, Pages 14–34  (Journal Publication)  [More Details]  [Online]

MAQC Consortium, "The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements", Nat Biotechnol. 2006 September; 24(9): 1151–1161.  (Journal Publication)  [More Details]  [Online]