Johnson, Charles individual record
Executive Director, Genomics and Bioinformatics
Positions:
overview

Agrigenomics and bioinformatics research and technology development. Research focusing on high throughput next generation sequencing technologies and its application in agriculture. Building an ever growing collaborative network of spanning 62 departments across Texas A&M system, and a rapidly growing list of international collaborators ( 45 countries) and industrial partners. Founding Executive Director of the Center for Bioinformatics and Genomic Systems Engineering (CBGSE).

selected publications
Academic Articles51
  • Liang, Y., Wang, S., Harper, C. L., Subramanian, N. K., Tabien, R. E., Johnson, C. D., Bailey-Serres, J., & Septiningsih, E. M. (2021). Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1. Plants. 10(12), 2740-2740.
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  • Neuman, B. W., Brashear, W. A., Brun, M., Chaki, S. P., Fischer, R., Guidry, S. J., ... Zuelke, K. (2021). Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. The American Journal of Tropical Medicine and Hygiene. 105(5), 1227-1229.
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  • Dhakal, S., Liu, X., Chu, C., Yang, Y., Rudd, J. C., Ibrahim, A., ... Liu, S. (2021). Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments. PeerJ. 9, e12350-e12350.
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  • Song, Q., Joshi, M., Wang, S., Johnson, C. D., & Joshi, V. (2021). Comparative Analysis of Root Transcriptome Profiles of Sesame (Sesamum indicum L.) in Response to Osmotic Stress. Journal of Plant Growth Regulation. 40(4), 1787-1801.
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  • Dhakal, S., Liu, X., Girard, A., Chu, C., Yang, Y., Wang, S., ... Liu, S. (2021). Genetic dissection of end‐use quality traits in two widely adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’. Crop Science. 61(3), 1944-1959.
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Chapters1
  • Davison, T. S., Johnson, C. D., & Andruss, B. F. (2006). Analyzing micro-RNA expression using microarrays.. MACROMOLECULAR CRYSTALLOGRAPHY, PT D. Methods in Enzymology. 14-34. Elsevier.
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Conference Papers14
  • Balasubramanian, S., Curtis-Robles, R., Chirra, B., Auckland, L., Johnson, C., Metz, R., ... Hamer, S. (2018). CHARACTERIZING WILDLIFE, DOMESTIC ANIMALS, AND HUMANS AS SOURCES OF TRIATOMINE BLOODMEALS: COMPARISON OF SANGER SEQUENCING AND AMPLICON DEEP SEQUENCING. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE. 99(4), 483-483.
  • Tian, B., Wang, S., Johnson, C. D., Tang, G., & Trick, H. N. (2017). Global Scale Investigation of Soybean MicroRNAs Responsive to Soybean Cyst Nematodes Infection. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL. 53, S32-S32.
  • Ghaffari, N., Abante, J., Singh, R., Blood, P. D., & Johnson, C. D. (2016). Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data. Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, XSEDE16: Diversity, Big Data, and Science at Scale. 17-21-July-2016, 1-4.
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  • Ghaffari, N., Arshad, O. A., Jeong, H., Thiltges, J., Criscitiello, M. F., Yoon, B., Datta, A., & Johnson, C. D. (2014). De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp. 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP), 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP). 1342-1343.
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  • Nikooienejad, A., Metz, R., Yoon, B., & Johnson, C. D. (2012). Fast DNA barcode generating algorithm using Radix Coding method. Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). 26-30.
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Repository Documents / Preprints4
  • Wells, K., He, K., Pandey, A., Cabello, A., Zhang, D., Yang, J., ... de Figueiredo, P. (2021). Diverse pathogens activate the host RIDD pathway to subvert BLOS1-directed immune defense.
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  • Ghaffari, N., Sanchez-Flores, A., Doan, R., Garcia-Orozco, K. D., Chen, P. L., Ochoa-Leyva, A., ... Criscitiello, M. F. (2014). Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Scientific Reports.
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awards and honors
Email
Charlie@ag.tamu.edu
First Name
Charles
Last Name
Johnson
mailing address
Texas A&M Agrilife Research; Genomics & Bioinformatics Services; 2125 TAMU
College Station, TX 77843-2125
USA