HR job title
- Director Institute
- Contact Info
- 1 979 862 3262
- Websites
- ORCiD
- 0000-0003-3892-7082
Johnson, Charles Director, Institute Genomics and Bioinformatics Service
Positions
- Director Institute, Texas A&M AgriLife Research, Texas A&M University
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).
Research Areas
- Overview
- Publications
- Research
- Teaching
- Background
- Contact
- Other
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Overview
Publications
selected publications
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academic article
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Adak, A., Murray, S. C., Varela, J. I., Infante, V., Wilker, J., Caldern, C. I., ... Zhang, H.
(2024).
Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize. Field Crops Research.
311, 109380-109380.
-
Adak, A., Murray, S. C., Caldern, C. I., Infante, V., Wilker, J., Varela, J. I., ... Johnson, C. D.
(2023).
Genetic mapping and prediction for novel lesion mimic in maize demonstrates quantitative effects from genetic background, environment and epistasis. 136(7), 155.
-
Bendele, K. G., Guerrero, F. D., Lohmeyer, K. H., Foil, L. D., Metz, R. P., & Johnson, C. D.
(2023).
Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance. Data in Brief.
48, 109272-109272.
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Thapa, R., Tabien, R. E., Johnson, C. D., & Septiningsih, E. M.
(2023).
Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC GENOMICS.
24(1), 185.
-
Cerit, M., Wang, Z., Dogan, M., Yu, S., Valenzuela-Antelo, J. L., Chu, C., ... Liu, S.
(2023).
Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 x Gallagher. Agronomy.
13(9), 2402-2402.
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Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of race 1 anthracnose resistance in a watermelon (Citrullus lanatus var. lanatus) biparental mapping population. Euphytica.
218(11), 157.
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Chu, C., Wang, S., Rudd, J. C., Ibrahim, A., Xue, Q., Devkota, R. N., ... Liu, S.
(2022).
A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding. Molecular Breeding.
42(4), 18.
-
Balasubramanian, S., Curtis-Robles, R., Chirra, B., Auckland, L. D., Mai, A., Bocanegra-Garcia, V., ... Hamer, S. A.
(2022).
Characterization of triatomine bloodmeal sources using direct Sanger sequencing and amplicon deep sequencing methods. Scientific Reports.
12(1), 10234.
-
Fang, Z., Kapoor, R., Datta, A., Liu, S., Stull, M. A., Seitz, P. G., Johnson, C. D., & Okumoto, S.
(2022).
Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks. International Journal of Molecular Sciences.
23(20), 12660-12660.
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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. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE.
105(5), 1227-1229.
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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 indicumL.) in Response to Osmotic Stress. 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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Guerrero, F. D., Ghaffari, N., Bendele, K. G., Metz, R. P., Dickens, C. M., Blood, P. D., ... Johnson, C. D.
(2021).
Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus. Data in Brief.
35, 106852-106852.
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Chu, C., Wang, S., Paetzold, L. i., Wang, Z., Hui, K., Rudd, J. C., ... Liu, S.
(2021).
RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'. 11(1), 4301.
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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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Ing, N. H., Konganti, K., Ghaffari, N., Johnson, C. D., Forrest, D. W., Love, C. C., & Varner, D. D.
(2020).
Identification and quantification of coding and long non-coding RNAs in stallion spermatozoa separated by density. ANDROLOGY.
8(5), 1409-1418.
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Yang, Y., Dhakal, S., Chu, C., Wang, S., Xue, Q., Rudd, J. C., ... Liu, S.
(2020).
Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112. 2020.07.27.222703.
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Qiu, C., Jin, H., Vvedenskaya, I., Llenas, J. A., Zhao, T., Malik, I., ... Kaplan, C. D.
(2020).
Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. 21(1), 132.
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Hunt, C. L., Yu, L., Cochran, M., Liu, J., Mccarl, B., Johnson, C. D., Brun, M., & Berquist, M.
(2020).
A case study approach to high-containment laboratory workflows promoting sustainability, networking and innovation. OIE Revue Scientifique et Technique.
39(3), 663-673.
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Seabury, C. M., Oldeschulte, D. L., Bhattarai, E. K., Legare, D., Ferro, P. J., Metz, R. P., ... Nichols, T. A.
(2020).
Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer. G3: Genes, Genomes, Genetics.
10(4), 1433-1441.
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Yang, Y., Dhakal, S., Chu, C., Wang, S., Xue, Q., Rudd, J. C., ... Liu, S.
(2020).
Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112. 15(12), e0237293-e0237293.
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Qiu, C., Jin, H., Vvedenskaya, I., Llenas, J. A., Zhao, T., Malik, I., ... Kaplan, C. D.
(2020).
Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the shooting gallery. 810127-810127.
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Guerrero, F. D., Bendele, K. G., Ghaffari, N., Guhlin, J., Gedye, K. R., Lawrence, K. E., ... Tompkins, D. M.
(2019).
The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901. Data in Brief.
27, 104602-104602.
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Yang, Y., Basnet, B. R., Ibrahim, A., Rudd, J. C., Chen, X., Bowden, R. L., ... Liu, S.
(2019).
Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping-by-Sequencing SNPs. Crop Science.
59(1), 165-175.
-
Ing, N. H., Konganti, K., Ghaffari, N., Johnson, C. D., Forrest, D. W., Love, C. C., & Varner, D. D.
(2018).
Functional RNAs in Stallion Sperm: Potential Indicators of Sperm Quality and Contributors to Fertility. Journal of Equine Veterinary Science.
66, 31-31.
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Ghaffari, N., Arshad, O. A., Jeong, H., Thiltges, J., Criscitiello, M. F., Yoon, B., Datta, A., & Johnson, C. D.
(2018).
Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. 15(2), 494-505.
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Janeka, J. E., Davis, B. W., Ghosh, S., Paria, N., Das, P. J., Orlando, L., ... Raudsepp, T.
(2018).
Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communications.
9(1), 2945.
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Ghaffari, N., Abante, J., Singh, R., Blood, P. D., Pipes, L., Mason, C., & Johnson, C. D.
(2017).
What are the most influencing factors in reconstructing a reliable transcriptome assembly?. 220269.
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Abante, J., Ghaffari, N., Johnson, C. D., & Datta, A.
(2017).
HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment. BMC GENOMICS.
18(1), 694.
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Oldeschulte, D. L., Halley, Y. A., Wilson, M. L., Bhattarai, E. K., Brashear, W., Hill, J., ... Seabury, C. M.
(2017).
Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3: Genes, Genomes, Genetics.
7(9), 3047-3058.
-
Tian, B., Wang, S., Todd, T. C., Johnson, C. D., Tang, G., & Trick, H. N.
(2017).
Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC GENOMICS.
18(1), 572.
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Blank, H. M., Perez, R., He, C., Maitra, N., Metz, R., Hill, J., ... Polymenis, M.
(2017).
Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO Journal.
36(4), 487-502.
-
Ing, N. H., Konganti, K., Ghaffari, N., Johnson, C. D., Forrest, D. W., Love, C. C., & Varner, D. D.
(2016).
Sequencing of RNA from stallion sperm identifies potential markers of fertility. Journal of Equine Veterinary Science.
43, s64-S64.
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Torres, M. F., Ghaffari, N., Buiate, E., Moore, N., Schwartz, S., Johnson, C. D., & Vaillancourt, L. J.
(2016).
A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC GENOMICS.
17(1), 202.
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Hurtado, L. A., De La Rosa-Reyna, X., Mateos, M., Shaver, D. J., Metz, R., Thiltges, J., ... Johnson, C.
(2016).
Short papers and notes. Gulf of Mexico Science.
33(2), 214-218.
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Halley, Y. A., Oldeschulte, D. L., Bhattarai, E. K., Hill, J., Metz, R. P., Johnson, C. D., ... Seabury, C. M.
(2015).
Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS ONE.
10(12), e0144913-e0144913.
-
SEQC/MAQC-III Consortium.
(2014).
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology.
32(9), 903-914.
-
Halley, Y. A., Dowd, S. E., Decker, J. E., Seabury, P. M., Bhattarai, E., Johnson, C. D., ... Seabury, C. M.
(2014).
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.
9(3), e90240-e90240.
-
Li, F., Cheng, C., Cui, F., de Oliveira, M., Yu, X., Meng, X., ... He, P.
(2014).
Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity. Cell Host and Microbe.
16(6), 748-758.
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Ghaffari, N., Yousefi, M. R., Johnson, C. D., Ivanov, I., & Dougherty, E. R.
(2013).
Modeling the next generation sequencing sample processing pipeline for the purposes of classification. BMC Bioinformatics.
14(1), 307.
-
Clavijo, A., Nikooienejad, A., Esfahani, M. S., Metz, R. P., Schwartz, S., Atashpaz-Gargari, E., ... Bounpheng, M.
(2013).
Identification and analysis of the first 2009 pandemic H1N1 influenza virus from U.S. feral swine. Zoonoses and Public Health.
60(5), 327-335.
-
Wang, Y., Ghaffari, N., Johnson, C. D., Braga-Neto, U. M., Wang, H., Chen, R., & Zhou, H.
(2011).
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics.
12 Suppl 10(Suppl 10), S5.
-
Shi, L., Campbell, G., Jones, W. D., Campagne, F., Wen, Z., Walker, S. J., ... MAQC Consortium.
(2010).
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology.
28(8), 827-838.
-
Ovcharenko, D., Kelnar, K., Johnson, C., Leng, N., & Brown, D.
(2007).
Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway. 67(22), 10782-10788.
-
Tadesse, M. G., He, Q., Carroll, R. J., & Ramos, K. S.
(2007).
Comparison of high-density short oligonucleotide microarray platforms. Current Bioinformatics.
2(3), 203-213.
-
Johnson, C. D., Esquela-Kerscher, A., Stefani, G., Byrom, M., Kelnar, K., Ovcharenko, D., ... Slack, F. J.
(2007).
The let-7 microRNA represses cell proliferation pathways in human cells. 67(16), 7713-7722.
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Bhattacherjee, V., Mukhopadhyay, P., Singh, S., Johnson, C., Philipose, J. T., Warner, C. P., Greene, R. M., & Pisano, M. M.
(2007).
Neural crest and mesoderm lineage-dependent gene expression in orofacial development. Differentiation.
75(5), 463-477.
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Johnson, C. D., Balagurunathan, Y., Dougherty, E. R., Afshari, C. A., He, Q., & Ramos, K. S.
(2007).
Insight into redox-regulated gene networks in vascular cells. Bioinformation.
1(10), 379-383.
-
MAQC Consortium, .., Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., ... Slikker, W.
(2006).
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology.
24(9), 1151-1161.
-
Shippy, R., Fulmer-Smentek, S., Jensen, R. V., Jones, W. D., Wolber, P. K., Johnson, C. D., ... Herman, D.
(2006).
Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nature Biotechnology.
24(9), 1123-1131.
-
Brun, M., Johnson, C. D., & Ramos, K. S.
(2005).
Clustering: Revealing intrinsic dependencies in microarray data. Eurasip Book Series on Signal Processing and Communications.
2, 129-162.
-
Thackaberry, E. A., Jiang, Z., Johnson, C. D., Ramos, K. S., & Walker, M. K.
(2005).
Toxicogenomic profile of 2,3,7,8-tetrachlorodibenzo-p-dioxin in the murine fetal heart: modulation of cell cycle and extracellular matrix genes. TOXICOLOGICAL SCIENCES.
88(1), 231-241.
-
Partridge, C. R., Johnson, C. D., & Ramos, K. S.
(2005).
In vitro models to evaluate acute and chronic injury to the heart and vascular systems. Toxicology in Vitro.
19(5), 631-644.
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Partridge, C. R., Williams, E. S., Barhoumi, R., Tadesse, M. G., Johnson, C. D., Lu, K. P., ... Ramos, K. S.
(2005).
Novel genomic targets in oxidant-induced vascular injury. Journal of Molecular and Cellular Cardiology.
38(6), 983-996.
-
Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpisheh, M. H., Brun, M., Walker, M. K., Dougherty, E. R., & Ramos, K. S.
(2004).
Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environmental Health Perspectives.
112(4), 403-412.
-
Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpisheh, M. H., Brun, M., Walker, M. K., Dougherty, E. R., & Ramos, K. S.
(2004).
Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environmental Health Perspectives.
-
Johnson, C. D., Balagurunathan, Y., Lu, K. P., Tadesse, M., Falahatpisheh, M. H., Carroll, R. J., ... Ramos, K. S.
(2003).
Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiological Genomics.
13(3), 263-275.
-
Johnson, C. D., & Decoteau, D. R.
(1996).
Nitrogen and potassium fertility affects Jalapeno pepper plant growth, pod yield, and pungency. Hortscience.
31(7), 1119-1123.
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Moraghan, T., Antoniucci, D. M., Grenert, J. P., Sieck, G. C., Johnson, C., Miller, V. M., & Fitzpatrick, L. A.
(1996).
Differential response in cell proliferation to beta estradiol in coronary arterial vascular smooth muscle cells obtained from mature female versus male animals. ENDOCRINOLOGY.
137(11), 5174-5177.
-
Wells, K. M., He, K., Pandey, A., Cabello, A., Zhang, D., Yang, J., ... de Figueiredo, P.
Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife.
11, e73625.
-
Blank, H. M., Hammer, S. E., Boatright, L., Roberts, C., Heyden, K. E., Nagarajan, A., ... Polymenis, M.
Late-life dietary folate restriction reduces biosynthesis without compromising healthspan in mice. Life Science Alliance.
-
Ghaffari, N., Sanchez-Flores, A., Doan, R., Garcia-Orozco, K. D., Chen, P. L., Ochoa-Leyva, A., ... Criscitiello, M. F.
Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Scientific Reports.
4(1), 7081.
-
Doan, R., Cohen, N. D., Sawyer, J., Ghaffari, N., Johnson, C. D., & Dindot, S. V.
Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC GENOMICS.
13(1), 78.
-
Adak, A., Murray, S. C., Varela, J. I., Infante, V., Wilker, J., Caldern, C. I., ... Zhang, H.
(2024).
Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize. Field Crops Research.
311, 109380-109380.
-
chapter
-
Davison, T. S., Johnson, C. D., & Andruss, B. F.
(2006).
Analyzing micro-RNA expression using microarrays. METHODS IN ENZYMOLOGY.
DNA MICROARRAYS, PART B: DATABASES AND STATISTICS.
(pp. 14-34).
Elsevier.
-
Davison, T. S., Johnson, C. D., & Andruss, B. F.
(2006).
Analyzing micro-RNA expression using microarrays. METHODS IN ENZYMOLOGY.
DNA MICROARRAYS, PART B: DATABASES AND STATISTICS.
(pp. 14-34).
Elsevier.
-
conference paper
-
Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of Race 1 Anthracnose Resistance in a Watermelon (Citrullus lanatus var. lanatus) Biparental Mapping Population. Hortscience.
S290-S291.
-
Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of Race 1 Anthracnose Resistance in a Watermelon (Citrullus lanatus var. lanatus) Biparental Mapping Population. Hortscience.
S229-S230.
-
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.
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 and Developmental Biology - Animal.
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. 1-4.
-
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 Pacific Whiteleg Shrimp. 1342-1343.
-
Atashpaz-Gargari, E., Esfahani, M. S., Metz, R., & Johnson, C. D.
(2012).
OBGene: Optimal Barcode Generator for NGS Experiments. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
90-94.
-
Nikooienejad, A., Metz, R., Yoon, B., & Johnson, C. D.
(2012).
Fast DNA Barcode Generating Algorithm Using Radix Coding Method. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
26-30.
-
Wilson, M., Leng, N., Sah, S., Sekinger, E., Fletcher, F., & Johnson, C.
(2006).
A high-density MicroRNA array for analyzing the expression of 15,090 verified and predicted small, non-coding RNAs. Blood.
132B-132B.
-
Ramos, K. S., Johnson, C. D., Falahatpisheh, M. H., Thomas, T., Beremand, P., Tadesse, M., ... Dougherty, R.
(2003).
Application of clustering methodologies to the analysis of altered cellular phenotypes induced by oxidative stress. TOXICOLOGICAL SCIENCES.
223-223.
-
Ramos, K. S., & Walker, C. L.
(2003).
Beyond genomics: Image analysis and computational biology. TOXICOLOGICAL SCIENCES.
223-223.
-
Falahatpisheh, M. H., Johnson, C. D., Tadesse, M. G., & Ramos, K. S.
(2003).
Chemical disruption of global gene expression during nephrogenesis: Role of aryl hydrocarbon receptor. TOXICOLOGICAL SCIENCES.
96-96.
-
Walker, M. K., Johnson, C. D., Tadesse, M., Ramos, K. S., Steele, I. D., & Thackaberry, E. A.
(2003).
Dioxin induces growth arrest and reduces cell cycle gene expression in the fetal murine heart. TOXICOLOGICAL SCIENCES.
231-231.
-
Johnson, C. D., Balagurunathan, Y., Tadesse, M., Falahatpisheh, M. H., Dougherty, E. R., Walker, M. K., & Ramos, K. S.
(2003).
From "omics" to insight: The use of a novel computational approach to study genegene interactions. TOXICOLOGICAL SCIENCES.
93-93.
-
Partridge, C. R., Williams, E. S., Lu, K. P., Chao, S., Johnson, C. D., Barhoumi, R., ... Ramos, K. S.
(2003).
Genomic and immunofluorescence analysis of interactive gene networks in oxidant induced atherogenesis. TOXICOLOGICAL SCIENCES.
95-95.
-
Garcia, M. R., Amstalden, M., Williams, S. W., Johnson, C. D., Nizielski, S. E., Keisler, D. H., & Williams, G. L.
(1999).
Leptin and pubertal development in heifers: Relationship of ob gene expression to circulating leptin as measured by heterologous radioimmunoassay. Biology of Reproduction.
253-253.
-
Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of Race 1 Anthracnose Resistance in a Watermelon (Citrullus lanatus var. lanatus) Biparental Mapping Population. Hortscience.
S290-S291.
-
institutional repository document
-
Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of Race 1 Anthracnose Resistance in a Watermelon (Citrullus lanatus var. lanatus) Biparental Mapping Population
-
Balasubramanian, S., Curtis-Robles, R., Chirra, B., Auckland, L. D., Mai, A., Bocanegra-Garcia, V., ... Hamer, S. A.
(2021).
Characterization of Triatomine Bloodmeal Sources Using Direct Sanger Sequencing and Amplicon Deep Sequencing Methods
-
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
-
Chu, C., Wang, S., Rudd, J. C., Ibrahim, A., Xue, Q., Devkota, R. N., ... Liu, S.
(2021).
A New Strategy for Using Historical Imbalanced Yield Data to Conduct Genome-Wide Association Studies and Develop Genomic Prediction Models for Wheat Breeding
-
Chu, C., Wang, S., Rudd, J. C., Ibrahim, A., Xue, Q., Devkota, R. N., ... Liu, S.
(2021).
A New Strategy for Using Historical Imbalanced Yield Data to Conduct Genome-Wide Association Studies and Develop Genomic Prediction Models for Wheat Breeding
-
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.
-
Bhatta, B. P., Patel, T., Correa, E., Wehner, T. C., Crosby, K. M., Thomson, M. J., ... Malla, S.
(2022).
Dissection of Race 1 Anthracnose Resistance in a Watermelon (Citrullus lanatus var. lanatus) Biparental Mapping Population
-
patent
-
Johnson, C. D., Byron, M. W., Bader, A. G., Slack, F. J., Brown, D., Ovcharenko, D., & Kelnar, K.
(2012).
Functions and targets of let-7 micro rnas
-
Bader, A. G., Patrawala, L., Wiggins, J. F., Byrom, M. W., Johnson, C., & Brown, D.
(2009).
miR-34 Regulated Genes and Pathways as Targets for Therapeutic Intervention
-
Ovcharenko, D., Johnson, C. D., Bader, A. G., & Brown, D.
(2009).
miR-10 Regulated Genes and Pathways as Targets for Therapeutic Intervention
-
Bader, A. G., Byrom, M., Johnson, C., & Brown, D.
(2009).
mir-21 Regulated genes and pathways as targets for therapeutic intervention
-
Bader, A. G., Byrom, M. W., Johnson, C. D., & Brown, D.
(2009).
miR-143 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
-
Byrom, M. W., Patrawala, L., Johnson, C. D., Brown, D., & Bader, A. G.
(2009).
miR-16 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
-
Bader, A. G., Byrom, M., Johnson, C. D., & Brown, D.
(2009).
miR-20 Regulated Genes and Pathways as Targets for Therapeutic Intervention
-
Bader, A. G., Byrom, M. W., Patrawala, L., Johnson, C. D., & Brown, D.
(2009).
miR-126 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
-
Bader, A. G., Byrom, M. W., Patrawala, L., Johnson, C. D., & Brown, D.
(2009).
miR-15, miR-26, miR-31, miR-145, miR-147, miR-188, miR-215, miR-216, miR-331, mmu-miR-292-3P REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
-
Johnson, C. D., Byron, M. W., Bader, A. G., Slack, F. J., Brown, D., Ovcharenko, D., & Kelnar, K.
(2012).
Functions and targets of let-7 micro rnas
Research
principal investigator on
co-principal investigator on
- SG: Collaborative Research: Evolution and Speciation in Afromontane and Alpine Grasshoppers in Southern Africa awarded by National Science Foundation - (Arlington, Virginia, United States) 2017 - 2020
- Transcriptional regulation of differentiation gene expression awarded by National Institute of Child Health and Human Development - (Bethesda, Maryland, United States) 2016 - 2020
- SEQUENCING, CHARACTERIZATION AND FUNCTIONAL ANALYSIS OF THE HORSE Y CHROMOSOME awarded by United States Food and Drug Administration - (Silver Spring, Maryland, United States) 2011 - 2013
Teaching
teaching activities
- BIOT684 Directed Prof Internship Instructor
- BIOT685 Directed Studies Instructor
- GENE685 Directed Studies Instructor
Background
education and training
- Ph.D. in Agronomy, Texas A&M University - (College Station, Texas, United States) 2000
- M.S. in Horticulture, Clemson University - (Clemson, South Carolina, United States) 1993
- B.S. in Soil and Crop Science, Texas A&M University - (College Station, Texas, United States) 1988
- University of Louisville - (Louisville, Kentucky, United States) , Postdoctoral Training 2004
awards and honors
Contact
first name
- Charles
has last name
- Johnson
mailing address
-
Texas A&M Agrilife Research
Genomics & Bioinformatics Services
2125 TAMU
College Station, TX 77843-2125
USA
Other
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- Charlie@ag.tamu.edu