Profile - Charles Johnson, MS, Ph.D

Charles Johnson is the president of BioMath Solutions. He brings his extensive background in the development, commercialization and analysis of high throughput molecular technologies to every project.

Before founding BioMath Solutions he established the Statistics and Bioinformatics Services Group at Ambion, Inc., now Asuragen, Inc. He brings years of experience in research consulting, experimental design, statistical modeling, and signal processing. He headed the analysis portion of FDA Microarray Quality Control (MAQC) project at Ambion that resulted in the development of a novel microarray platform assessment tool that was used in several publications in Nature Biotechnology. He directed the informatics team that designed and created the first Affymetrix miRNA array (DiscovArray®) and associated data analysis workflows. DiscovArray®, launched in the summer of 2007, was not only the first Affymetrix miRNA array, but was and is the largest miRNA array ever commercially offered. He led the team that was responsible for creation of the transformational, industry leading miRInform® data processing and delivery system for the DiscovArray®.

Prior to his work at Ambion, he conducted research in gene network prediction, focusing on a number of key toxicological gene networks. Dr. Johnson has published numerous scientific articles and book chapters on data clustering and miRNA array signal processing. Dr. Johnson is a recognized leader in the field of microarray data analysis.

Selected publications [See All]

• Johnson CD, Balagurunathan Y, Lu KP, Tadesse M, Falahatpisheh MH, Carroll RJ, Dougherty ER, Afshari CA, Ramos KS. Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol Genomics. 2003 May 13;13(3):263-75. PMID: 12657712
• Johnson CD, Balagurunathan Y, Tadesse MG, Falahatpisheh MH, Brun M, Walker MK, Dougherty ER, Ramos KS. Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environ Health Perspect. 2004 Mar;112(4):403-12. PMID: 15033587
• Richard Shippy, Paul Wolber, Wendell D. Jones, Roderick V. Jensen, Stephanie Fulmer-Smentek, Charles D. Johnson, P. Scott Pine, Cecilie Boysen, Xu Guo, Eugene Chudin, Yongming Andrew Sun, James C. Willey, Jean Thierry-Mieg, Danielle Thierry-Mieg, Robert A. Setterquist, Mike Wilson, Anne Bergstrom Lucas, Natalia Novoradovskaya, Adam Papallo, Yaron Turpaz, Shawn C. Baker, Janet A Warrington, Leming Shi, and Damir Herman. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol. 2006 Sep;24(9):1123-31.
• Leming Shi, Laura H. Reid, Richard Shippy, Shawn C. Baker, Patrick J. Collins, Francoise de Longueville, Ernest S. Kawasaki, Kathleen Y. Lee, Yuling Luo, Yongming Andrew Sun, Janet A. Warrington, James C. Willey, Robert A. Setterquist, Gavin M. Fischer, David J. Dix, Yvonne P. Dragan, Federico M. Goodsaid, Damir Herman, Roderick V. Jensen, Charles D. Johnson, Wendell D. Jones, Edward K. Lobenhofer, Raj K. Puri, Uwe Scherf, Jean Thierry-Mieg, Weida Tong, Charles Wang, Mike Wilson,, Lu Zhang,, William Slikker, Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep 8;24(9):1151-1161
• Charles Johnson, Aurora Esquela-Kerscher, Giovanni Stefani, Mike Byrom, Kevin Kelnar, Dmitriy Ovcharenko, Mike Wilson, Xiaowei Wang, Jeffrey Shelton, Jaclyn Shingara, Lena Chin, David Brown and Frank J. Slack. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res. 2007 Aug 15;67 (16):7713-22 17699775

Book Chapters

• Brun M., Johnson C.D., and Ramos K.S.. Clustering: revealing intrinsic dependencies in microarray data, Genomic Signal Processing: Perspectives, Genomic Signal Processing and Statistics, eds. E. R. Dougherty, I. Shmulevich, J. Chen, and Z. J. Wang, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, 2005.
• Davison, T. S., Johnson, C. D., and Andruss, B. F. (2006). Analyzing Micro-RNA Expression Using Microarrays. Methods Enzymol. 411, 14-34.

Patents

Listed as an inventor on 18 plus patent applications.