July 14, 2012 Charlie Johnson

Publications

Names in bold are TxGen personnel – ready to support your next research project and/or grant. Journal Papers

2024

  •  Wardah K. Mustahsan, Yuya Liang, Abdul R. Mohammed, Charles D. Johnson, Endang M. Septiningsih, Lee Tarpley, Michael J. Thomson. Transcriptome profiling of two rice varieties reveals their molecular responses under high night-time temperature. Plos One Published: October 10, 2024
    https://doi.org/10.1371/journal.pone.0311746
  • Heidi M. Blank, Staci E. Hammer, Laurel Boatright, Courtney Roberts, Katarina E. Heyden, Aravindh Nagarajan, Mitsuhiro Tsuchiya, Marcel Brun, Charles D. Johnson, Patrick J. Stover, Raquel Sitcheran, Brian K. Kennedy, ProfileL. Garry Adams, Matt Kaeberlein, Martha S. Field, David W. Threadgill, Helene L. Andrews-Polymenis, Michael Polymenis. Late-life dietary folate restriction reduces biosynthetic processes without compromising healthspan in mice. Life Science Alliance 07/2024 doi: https://doi.org/10.1101/2024.01.12.575290  Preprint
  • Nancy H. Ing, Kranti Konganti, Noushin Ghaffar, Charles D. Johnson, David W. Forrest, Charles C. Love, Dickson D. Varner. Specific microRNAs in stallion spermatozoa are potential biomarkers of high functionality. Reproduction of Domestic Animals 15 July 2024 https://doi.org/10.1111/rda.14674
  • Alper Adak, Seth C. Murray, José I. Varela, Valentina Infant, Jennifer Wilker, Claudia Irene Calderón, Nithya Subramanian, Natalia de Leon, Jianming Yu, Matthew A. Stull, Marcel Brun, Joshua Hill, Charles D. Johnson, Oscar Riera-Lizarazu, William L. Rooney, Hongbin Zhang. Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize. Field Crops Research.
    Volume 311, 1 May 2024.  https://doi.org/10.1016/j.fcr.2024.109380
  • Henry L North, Zhen Fu, Richard Metz, Matt A Stull, Charles D Johnson, Xanthe Shirley, Kate Crumley, Dominic Reisig, David L Kerns, Todd Gilligan, Tom Walsh, Chris D Jiggins, Gregory A Sword Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea. Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae129, https://doi.org/10.1093/molbev/msae129

2023

  • Parker, K., Wang, Z., Dhakal, S., Yu, S., Rauf, Y., Baker, J. A., Baker, S., Ibrahim, A. M. H., Xue, Q., Wang, S., Johnson, C., & Liu, S. (2023) Multi-Trait Genomic Prediction of Baking Quality Traits for Synthetic Derived Hexaploid Wheat [Abstract]. ASA, CSSA, SSSA International Annual Meeting, St. Louis, MO. https://scisoc.confex.com/scisoc/2023am/meetingapp.cgi/Paper/150686
  • Liu, S., Wang, Z., Parker, K., Yu, S., Rauf, Y., Xue, Q., Dhakal, S., Rudd, J. C., Ibrahim, A. M. H., Baker, J. A., Baker, S., Wang, S., Johnson, C. (2023) Exploring Novel Genetic Alleles for Improving Wheat Yield and Resistances Using Genome-Wide Association Analyses and Genetic Prediction of Synthetic Derived Wheat Lines [Abstract]. ASA, CSSA, SSSA International Annual Meeting, St. Louis, MO. https://scisoc.confex.com/scisoc/2023am/meetingapp.cgi/Paper/151081
  • Alper Adak, Seth C. Murray, Claudia Irene Calderón, Valentina Infante, Jennifer Wilker, José I. Varela, Nithya Subramanian, Thomas Isakeit, Jean-Michel Ané, Jason Wallace, Natalia de Leon, Matthew A. Stull, Marcel Brun, Joshua Hill & Charles D. Johnson . Genetic mapping and prediction for novel lesion mimic in maize demonstrates quantitative effects from genetic background, environment and epistasis. Theor Appl Genet 136, 155 (2023). https://doi.org/10.1007/s00122-023-04394-y
  • Henry L. North, Zhen Fu, Richard Metz, Matt A. Stull, Charles D. Johnson, Xanthe Shirley, Kate Crumley, Dominic Reisig, David L. Kerns, Todd Gilligan, Tom Walsh, Chris D. Jiggins, Gregory A. Sword. Rapid evolution of pesticide resistance via adaptation and interspecific introgression in a major North American crop pest. bioRxiv 2023.10.04.560869; doi: https://doi.org/10.1101/2023.10.04.560869
  • Ranjita Thapa1, Rodante E. Tabien, Charles D. Johnson and Endang M. Septiningsih. Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 24, 185 (2023). https://doi.org/10.1186/s12864-023-09262-z
  • Cerit Mustafa, Zhen Wang, Mehmet Dogan, Shuhao Yu. Jorge L. Valenzuela-Antelo, Chenggen Chu, Shichen Wang, Qingwu Xue, Amir M. H. Ibrahim, Jackie C. Rudd, Richard Metz, Charles D. Johnson, Shuyu Liu. Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 × Gallagher. Agronomy 2023, 13(9), 2402; https://doi.org/10.3390/agronomy13092402
  • Kylie G. Bendele , Felix D. Guerrero , Kimberly H. Lohmeyer, Lane D. Foil , Richard P. Metz , Charles D. Johnson Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance. Data in Brief , ISSN 2352-3409,
    https://doi.org/10.1016/j.dib.2023.109272 online 30 May 2023
  • Ranjita Thapa, Rodante E. Tabien, Charles D. Johnson and Endang M. Septiningsih . Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 2023 https://doi.org/10.1186/s12864-023-09262

2022

  • Ze-Tian Fang, Rajan Kapoor, Aniruddha Datta, Shuyu Liu, Matthew A. Stull, Paige G. Seitz, Charles D. Johnson, and Sakiko Okumoto. Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks Int. J. Mol. Sci. 2022, 23(20), 12660; https://doi.org/10.3390/ijms232012660
  • Bed Prakash Bhatta · Takshay Patel · Edgar Correa · Todd C. Wehner · Kevin M. Crosby ·Michael J. Thomson · Richard Metz · Shichen Wang · Marcel Brun · Charles D. Johnson · Subas Malla. Dissection of race 1 anthracnose resistance in a watermelon (Citrullus lanatus var. lanatus) biparental mapping population. Vol.: (0123456789) 1 3 Euphytica (2022) 218:157 https://doi.org/10.1007/s10681-022-03108-7
  • Kelsey Michelle Wells, Kai He, Aseem Pandey, Ana Cabello, Dongmei Zhang, Jing Yang, Gabriel Gomez, Yue Liu, Haowu Chang, Xueqiang Li, Hao Zhang, Xuehuang Feng, Luciana Fachini da Costa, Richard Metz, Charles D Johnson, Cameron Lee Martin, Jill Skrobarczyk, Luc R Berghman, Kristin L Patrick, Julian Leibowitz, Allison Ficht, Sing-Hoi Sze, Jianxun Song, Xiaoning Qian, Qing-Ming Qin, Thomas A Ficht, Paul de Figueiredo. Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife. 2022; 11: e73625. Published online 2022 May 19. doi: 10.7554/eLife.73625
  • Kelsey Michelle Wells, Kai He, Aseem Pandey, Ana Cabello, Dongmei Zhang, Jing Yang, Gabriel Gomez, Yue Liu, Haowu Chang, Xueqiang Li, Hao Zhang, Xuehuang Feng, Luciana Fachini da Costa,Richard Metz,Charles D Johnson, Cameron Lee Martin, Jill Skrobarczyk, Luc R Berghman,Kristin L Patrick,Julian Leibowitz, Allison Ficht, Sing-Hoi Sze,Jianxun Song,Xiaoning Qian,Qing-Ming Qin,Thomas A Ficht, and Paul de Figueiredo.  Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife. 2022; 11: e73625. Published online 2022 May 19. doi: 10.7554/eLife.73625
  • Chenggen Chu, Shichen Wang, Jackie C. Rudd, Amir M. H. Ibrahim, Qingwu Xue, Ravindra N. Devkota, Jason A. Baker, Shannon Baker, Bryan Simoneaux, Geraldine Opena, Haixiao Dong, Xiaoxiao Liu, Kirk E. Jessup, Ming-Shun Chen, Kele Hui, Richard Metz, Charles D. Johnson, Zhiwu S. Zhang & Shuyu Liu . Molecular Breeding volume 42, Article number: 18 (2022). A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding. volume 39 (3), in 2022. DOI https://doi.org/10.1007/s11032-022-01287-8

2021

  • C.L. Hunt, L. Yu, M. Cochran, J.-C. Liu, B. McCarl, C.D. Johnson, M. Brun & M. Berquist. A case study approach to high-containment laboratory workflows promoting sustainability, networking, and innovation. Scientific and Technical Review of the OIE. volume 39 (3), in 2021.
  • Chenggen Chu, Shichen Wang,, Li Paetzold, Zhen Wang, Kele Hui, Jackie C. Rudd, Qingwu Xue, Amir M. H. Ibrahim, Richard Metz, Charles D. Johnson, Charles M. Rush, Shuyu Liu. RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’ doi: https://doi.org/10.1038/s41598-021-83372-0
  • Felix D Guerrero, Noushin Ghaffari, Kylie G Bendele, Richard P Metz, C Michael Dickens, Philip D Blood, Jason Tidwell, Robert J Miller, Adalberto A Pérez de León, Pete D Teel, Charles D Johnson. Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus. Data In Brief. Volume 35, 2021, 106852, ISSN 2352-3409, https://doi.org/10.1016/j.dib.2021.106852

2020

  • C L Hunt, L Yu, M Cochran, J-C Liu, B Mccarl, C D Johnson, M Brun, M Berquist. A case study approach to high-containment laboratory workflows promoting sustainability, networking and innovation Rev Sci Tech. 2020 Jan;39(3):663-673. doi: 10.20506/rst.39.3.3169.
  • Yan Yang, Smit Dhakal, Chenggen Chu, Shichen Wang, Qingwu Xue, Jackie C. Rudd, Amir M.H. Ibrahim, Kirk Jessup, Jason Baker, Maria Pilar Fuentealba, Ravindra Devkota, Shannon Baker, Charles D. Johnson, Richard Metz, Shuyu Liu. Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112 doi: https://doi.org/10.1101/2020.07.27.222703 2020
  • Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan. Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”doi: https://doi.org/10.1101/810127 2020
  • Anne N Thorndike ,Jessica L McCurley ,Emily D Gelsomin ,Eric B Rimm,Yuchiao Chang,Bianca Porneala,Emma Anderson, Charles D. Johnson, Douglas E Levy. MP07: Automated, Personalized Feedback and Behavioral Nudges to Improve Workplace Food Choices and Prevent Weight Gain: Choosewell 365 Randomized Controlled Trial. 2 Mar 2020https://doi.org/10.1161/circ.141.suppl_1.MP07Circulation. 2020;141:AMP07
  • Christopher M Seabury, David L Oldeschulte, Eric K Bhattarai, Dhruti Legare, Pamela J Ferro, Richard P Metz, Charles D Johnson, Mitchell A Lockwood, Tracy A Nichols. Accurate Genomic Predictions for Chronic Wasting Disease in US White-Tailed Deer G3: Genes, Genomes, Genetics April 1, 2020 vol. 10 no. 4 1433-1441; https://doi.org/10.1534/g3.119.401002
  • Nancy H Ing, Kranti Konganti, Noushin Ghaffari, Charles D Johnson, David W Forrest, Charles C Love, Dickson D Varner. Identification and quantification of coding and long non‐coding RNAs in stallion spermatozoa separated by density 03 April 2020 https://doi.org/10.1111/andr.12791 Song, Q., Joshi, M., Wang, S. et al. Comparative Analysis of Root Transcriptome Profiles of Sesame (Sesamum indicum L.) in Response to Osmotic Stress. J Plant Growth Regul (2020). https://doi.org/10.1007/s00344-020-10230-0
  • Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M Visbisky, Scott L Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William KM Lai, Richard P Metz, Charles D Johnson, Sing-Hoi Sze, B Franklin Pugh, Bryce E Nickels, Craig D Kaplan. Genome Biol 21, 132 (2020). https://doi.org/10.1186/s13059-020-02040-0

2019

2018

  • Jan E Janečka, Brian W Davis, Sharmila Ghosh, Nandina Paria, Pranab J Das, Ludovic Orlando, Mikkel Schubert, Martin K Nielsen, Tom AE Stout, Wesley Brashear, Gang Li, Charles D Johnson, Richard P Metz, Charles C Love, Dickson D Varner, Daniel W Bellott, William J Murphy, Bhanu P Chowdhary, Terje Raudsepp Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communicationsvolume 9, Article number: 2945 (2018)
  • NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner Functional RNAs in Stallion Sperm: Potential Indicators of Sperm Quality and Contributors to Fertility. Journal of Equine Veterinary Science. Volume 66, July 2018 https://doi.org/10.1016/j.jevs.2018.05.011
  • Brun M, Stull MA, Howard E, Hill J, Metz R, Johnson CD (2018) Comparison of MiSeq, iSeq and NovaSeq. In: Texas A&M AgriLife Genomics Bioinforma Serv, pp 2–4. . Comparison of MiSeq, iSeq and NovaSeq. 2018 https://www.txgen.tamu.edu/wp-content/uploads/2018/09/iSeq_MiSeq_NovaSeq-test_v03-1.pdf

2017

  • Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang, and Harold N. Trick Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017. 2 August 2017 18:572 https://doi.org/10.1186/s12864-017-3963-4 Link
  • David L. Oldeschulte, Yvette A. Halley, Miranda L. Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua Hill, Richard P. Metz, Charles D. Johnson, Dale Rollins, Markus J. Peterson, Derek M. Bickhart, Jared E. Decker, John F. Sewell and Christopher M. Seabury.  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  July 17, 2017; Link
  • Heidi M. Blank, Ricardo Perez, Chong He, Nairita Maitra, Richard Metz, Joshua Hill, Yuhong Lin, Charles D. Johnson, Vytas A. Bankaitis, Brian K. Kennedy, Rodolfo Aramayo and Michael Polymenis. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. 2017 DOI 10.15252/embj.201695050 | Published online 05.01.2017 The EMBO Journal (2017) e201695050 (Article ID: EMBJ788)

2016

  • Noushin Ghaffari, Jordi Abante, Raminder Singh, Philip D. Blood, Charles D. Johnson. Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data July 17 – 21, 2016 ISBN: 978-1-4503-4755-6
  • NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner. Sequencing of RNA from stallion sperm identifies potential markers of fertility. 2016 Journal of Equine Veterinary Science, S56eS82
  • Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson and Lisa J. Vaillancourt. Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC Genomics 201617:202. DOI:10.1186/s12864-016-2546-0. 8 March 2016

2015

  • Yvette A. Halley, David L. Oldeschulte, Eric K. Bhattarai, Joshua Hill, Richard P. Metz, Charles D. Johnson, Steven M. Presley, Rebekah E. Ruzicka, Dale Rollins, Markus J. Peterson, William J. Murphy, Christopher M. Seabury. (2015) Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS ONE 10(12): e0144913. doi: 10.1371/journal.pone.0144913
  • Ghaffari, N.; Arshad, O.A.; Jeong, H.; Thiltges, J.; Criscitiello, M.F.; Yoon, Byung-Jun; Datta, A.; Johnson, C.D., “Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline,” Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.PP, no.99, pp.1,1 doi: 10.1109/TCBB.2015.2446478
  • Masoud Toloue , Jan Risinger , Lindsey Renken , Josh Hill , Noushin Ghaffari , Richard P Metz , Charles D. Johnson , Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification – Mixed Species Plant and Animal Genome XXIII Conference 2015.

2014

  • 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. (2014) Nature Scientific Reports doi:10.1038/srep07081
  • Zhenqiang Su, Paweł P Łabaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Shi, Charles Wang, Gary P Schroth, Robert A Setterquist, John F Thompson, Wendell D Jones, 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, Scott S Auerbach, Wenjun Bao, Hans Binder, Thomas 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, Joaquin Dopazo, Tingting Du, Hong Fang, Yongxiang Fang, Mario Fasold, Anita Fernandez, Matthias Fischer, Pedro Furió-Tari, 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 Kleinjans, Samir Lababidi, Shawn Levy, Quan-Zhen Li, Li Li, Li Li, Peng Li, Yan Li, Haiqing Li, Jianying Li, Shiyong Li, Simon M Lin, Francisco J López, Xin Lu, Heng Luo, Xiwen Ma, Joseph Meehan, Dalila B Megherbi, Nan Mei, Bing Mu, Baitang Ning, Akhilesh Pandey, Javier Pérez-Florido, Roger G 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 Shah, Jie Shen, Todd M Smith, Oliver Stegle, Nancy Stralis-Pavese, Elia Stupka, Yutaka Suzuki, Lee T Szkotnicki, Matthew Tinning, Bimeng Tu, Joost van Delft, Alicia Vela-Boza, Elisa Venturini, Stephen J Walker, Liqing Wan, Wei Wang, Jinhui 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 K Zhang, Wenqian Zhang, Wenwei Zhang, Yanyan Zhang, Chen Zhao, Yuanting Zheng, Yiming Zhou, Paul Zumbo, Weida Tong, David P Kreil, Christopher E Mason & Leming Shi. 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
  • Madina, Bhaskara R., Vikas Kumar, Richard Metz, Blaine HM Mooers, Ralf Bundschuh, and Jorge Cruz-Reyes. “Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition.” RNA (2014)
  • 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. (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 DOI: 10.1371/journal.pone.0090240

2013

  • N Ghaffari, MR Youse, CD Johnson, I Ivanov, ER Dougherty, Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification BMC bioinformatics 14 (1), 307  2013
  • Joshua Hill, Thomas S. Edrington, Guy H. Loneragan, Sara H. Gragg, David J. Nisbet. “Rapid Detection of Salmonella in Bovine Lymph Nodes Using a Commercial Real-Time PCR System” Journal of Post Doctoral Research, Vol. 1, No. 2 Feb. 2013

2012

  • 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
  • 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

2011

  • 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
  • Paul A. Beare,Stacey D. Gilk, Charles L. Larson, Joshua Hill, Christopher M. Stead, Anders Omsland, Diane C. Cockrell, Dale Howe, Daniel E. Voth, and Robert A. Heinzen. “Dot/Icm Type IV Secretion System Requirements for Coxiella burnetii Growth in Human Macrophages” MBio. 2011 Sep 1;2(4):e00175-11. doi: 10.1128/mBio.00175-11
  • Omsland A, Beare PA, Hill J, Cockrell DC, Howe D, Hansen B, Samuel JE, Heinzen RA. “Isolation from Animal Tissue and Genetic Transformation of Coxiella burnetii Facilitated by an Improved Axenic Growth Medium” Appl Environ Microbiol. 2011 Jun;77(11):3720-5. Epub 2011 Apr 8
  • Hill J, Samuel JE.  Infection and Immunity. “Coxiella burnetii Acid Phosphatase Inhibits the Release of Reactive Oxygen Intermediates in Polymorphonuclear Leukocytes” 2011 Jan:79(1):414-420. doi:10.1128/IAI.01011-10

2010

  • Leming Shi, Gregory Campbell, Wendell D Jones, Fabien Campagne, Zhining Wen, Stephen J Walker, Zhenqiang Su, Tzu-Ming Chu, Federico M Goodsaid, Lajos Pusztai, John D Shaughnessy Jr, André Oberthuer, Russell S Thomas, Richard S Paules, Mark 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 Bylesjo, Minjun Chen, Jie Cheng, Jing Cheng, Jeff Chou, Timothy S Davison, Mauro Delorenzi, Youping Deng, Viswanath Devanarayan, David J Dix, Joaquin 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 Judson, Dilafruz Juraeva, Samir Lababidi, Christophe G Lambert, Li Li, Yanen Li, Zhen Li, Simon M Lin, Guozhen Liu, Edward K Lobenhofer, Jun Luo, Wen Luo, Matthew N McCall, Yuri Nikolsky, Gene A Pennello, Roger G 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 Li, 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, Kelci Miclaus, Richard A Moffitt, David Montaner, Piali Mukherjee, George J Mulligan, Padraic Neville, Tatiana Nikolskaya, Baitang Ning, Grier P Page, Joel 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 M 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 Thorn, Marina Tsyganova, Yaron Turpaz, Silvia C 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 Zhang, Min Zhang, Chen Zhao, Raj K Puri, Uwe Scherf, Weida Tong & Russell D Wolfinger. “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”. Natute Biotechnology, 24(9), 2010, pp 827-838X.

2007

  • Dmitriy Ovcharenko, Kevin Kelnar, Charles Johnson, Nan Leng, and David Brown. 2007 Genome scale microRNA and siRNA screens identify small RNA modulators of TRAIL-induced death receptor apoptosis pathway. Cancer Research Cancer Research 67: 10782-10788
  • 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
  • Vasker Bhattacherjee, Partha Mukhopadhyay, Saurabh Singh, Charles Johnson, John T. Philipose, Courtney P. Warner, Robert M. Greene, M. Michele Pisano (2007) Neural crest and mesoderm lineage-dependent gene expression in orofacial development Differentiation 75 (5), 463–477.
  • 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 2007. Bioinformation 1(10)

2006

  • 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. Nature Biotechnology. 2006 Sep 8;24(9):1151-1161
  • 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. Nature Biotechnology. 2006 Sep;24(9):1123-31.

2005

  • Thackaberry EA, Jiang Z, Johnson CD, Ramos KS, Walker MK. Toxicogenomic Profile of 2,3,7,8-Tetrachlorodibenzo-p-dioxin in the Murine Fetal Heart: Modulation of Cell Cycle and Extracellular Matrix Genes. Toxicol Sci. 2005 PMID: 16120747
  • Partridge CR, Williams ES, Barhoumi R, Tadesse MG, Johnson CD, Lu KP, Meininger GA, Wilson E, Ramos KS. Novel genomic targets in oxidant-induced vascular injury. J Mol Cell Cardiol. 2005 Jun;38(6):983-96. Epub 2005 Apr 19. PMID: 15910882
  • Partridge CR, Johnson CD, Ramos KS. In vitro models to evaluate acute and chronic injury to the heart and vascular systems. Toxicol In Vitro. 2005 Aug;19(5):631-44. Review. PMID: 15893448
  • Ward DM, Vaughn MB, Shiflett SL, White PL, Pollock AL, Hill J, Schnegelberger R, Sundquist WI, Kaplan J. “The role of LIP5 and CHMP5 in multivesicluar body formation in HIV-1 budding mammalian cells” J Biol Chem. 2005 Mar 18;280(11):10548-55. doi: 10.1074/jbc.M413734200

2004

2003-1996

  • 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
  • Garcia MR, Amstalden M, Williams SW, Johnson CD, Nizielski SE, Keisler DH, and Williams GL. Leptin and pubertal development in heifers: relationship of ob gene expression to circulating leptin as measured by heterologous radioimmunoassay. 1999. Biol. Reprod. 60 (Suppl. 1): 253.
  • Johnson, C. D., and Decoteau D. R. 1996. Nitrogen and potassium fertility affects Jalapeno pepper plant growth, pod yield, and pungency. HortScience 31:1119-1123.
  • Johnson, J.R., and Johnson C.D. 1993. Cash In On New Markets For Collards.  American Vegetable Grower. 1:34-26.
  • Johnson, J.R., and Johnson C.D. 1992. Two Zesty Alternatives to Bell Pepper.  American Vegetable Grower. 5:24-27.

Book Chapters

Patents (US and EU)

  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; MIR-200 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2009 EP Patent 2,076,599
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; MIR-143 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION   2009 EP Patent 2,094,848
  • Byrom, M.; Johnson, C.D.; Brown, D.; Bader, A.G.; MIRNA REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION   2009  EP Patent 2,102,341
  • Byrom, M.; Patrawala, L.; Johnson, C.D.; Brown, D.; Bader, A.G.; miR-16 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2009 EP Patent 2,102,342
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; MIR-20 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION   2009  EP Patent 2,104,734
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; MIR-21 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION   2009  EP Patent 2,104,735
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; MIR-126 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2009  EP Patent 2,104,736
  • Johnson, C.D.; Byrom, M.; Bader, A.G.; Slack, F.J.; Brown, D.; Ovcharenko, D.; Kelnar, K.;  FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS  2009    EP Patent 2,104,737
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; Patrawala, L.; 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   2010 EP Patent 2,145,001
  • Bader, A.G.; Patrawala, L.; Byrom, M.; Johnson, C.D.; Brown, D.;  MIR-34 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2010 EP Patent 2,167,138
  • Ovcharenko, D.; Johnson, C.D.; Bader, A.G.; Brown, D.;  miR-10 Regulated Genes and Pathways as Targets for Therapeutic Intervention  2008 US Patents 20090192114
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; mir-21 Regulated genes and pathways as targets for therapeutic intervention  2008 US Patents 20090192102
  • Bader, A.G.; Patrawala, L.; Wiggins, J.F.; Byrom, M.W.; Johnson, C.D.; Brown, D.; miR-34 Regulated Genes and Pathways as Targets for Therapeutic Intervention 2008 US Patents 20090227533
  • Johnson, C.D.; Byrom, M.W.; Bader, A.G.; Slack, F.J.; Brown, D.; FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS 2007  Patent: 20120282696, Granted 2012
  • Byrom, M.W.; Patrawala, L.; Johnson, C.D.; Brown, D.; Bader, A.G.; miR-16 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION  2007  US Patents 20090175827
  • Bader, A.G.; Byrom, M.; Johnson, C.D.; Brown, D.; miR-20 Regulated Genes and Pathways as Targets for Therapeutic Intervention  2008 US Patents 20090163434
  • Bader, A.G.; Byrom, M.W.; Patrawala, L.; Johnson, C.D.; Brown, D.; 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   2008 US Patents 20090131356
  • Bader, A.G.; Byrom, M.W.; Johnson, C.D.; Brown, D.; miR-143 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION   2008  US Patents 20090232893
  • Bader, A.G.; Byrom, M.W.; Patrawala, L.; Johnson, C.D.; Brown, D.; miR-126 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2008 US Patents
  • Johnson, Charles D; Byrom, Mike W; Bader, Andreas G; Slack, Frank J; Brown, David; Ovcharenko, Dmitriy; Kelnar, Kevin; Johnson; D., Charles;  UNCTIONS AND TARGETS OF LET-7 MICRO RNAS 2012 US Patent 20,120,282,696
  • Johnson, Charles D; Byrom, Mike; Bader, Andreas G; Slack, Frank J; Brown, David; Ovcharenko, Dmitriy; Kelnar, Kevin; Asuragen, INC.; Yale University, Inc.; FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS 2009 EP Patent 2,104,737
  • Bader, Andreas G; Byrom, Mike W; Johnson, Charles D; Brown, David; miR-200 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION 2008 US Patent App. 12/124,394
  • Bader, Andreas G; Byrom, Mike W; Johnson, Charles D; Brown, David; Mir-143 regulated genes and pathways as targets for therapeutic intervention 2008       US Patent App. 12/125,412
  • Bader, Andreas G; Byrom, Mike W; Patrawala, Lubna; Johnson, Charles D; Brown, David;             miR-126 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION     2008 US Patent App. 12/125,675
  • Bader, Andreas G; Patrawala, Lubna; Wiggins, Jason F; Byrom, Mike W; Johnson, Charles D; Brown, David;       Mir-34 regulated genes and pathways as targets for therapeutic intervention 2008 US Patent App. 12/134,932
  • Ovcharenko, Dmitriy; Johnson, Charles D; Bader, Andreas G; Brown, David; miR-10 Regulated Genes and Pathways as Targets for Therapeutic Intervention 2008       US Patent App. 12/340,329
  • BADER, Andreas; BYROM, Mike; JOHNSON, Charles; BROWN, David; PATRAWALA, Lubna; ASURAGEN, INC.; BADER; Andreas; G.; BYROM; 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 2008 WO Patent 2,008,036,776

Conference Abstracts & White Papers

  • Fifth SC Workshop on Best Practices for HPC Training and Education 2019
  • Plant and Animal Genomic. PerkinElmer WorkShop 2019
  • Plant and Animal Genomie Abstract 2019
  • AGBT 2018 LIMS Poster
  • D. Cocom Basto, N. Ghaffari, and C. D. Johnson, “Sequencing Technologies and Their Applications ”, CANIETI Summer Program , College Station, TX, 2016
  • N. H. Ing, K. Konganti, N. Ghaffari, C. D. Johnson, D. W. Forrest, C. C. Love, and D. D. Varner, “Sequencing of RNA from stallion spermatozoa identifies potential markers of fertility”, 7th International Symposium on Stallion Reproduction, Champaign, IL, 2016
  • N. Ghaffari, J. Abante, R. Singh, P. D. Blood, and C. D. Johnson, “Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data”, XSEDE16, Miami, FL, 2016
  • J. Abante, N. Ghaffari, C. D. Johnson, and A. Datta, “Using Hidden Markov Models to Analyze Next-Generation Sequencing Data”, ENG-LIFE 2016, College Station, TX, 2016
  • A-S C. Hieke, N. Ghaffari, C. D. Johnson, and S. D. Pillai, “Transcriptomic Responses of Salmonella Typhimurium after Exposure to Lethal Doses of Electron Beam and Gamma Radiation”, Advances in Genome Biology and Technology (AGBT), Orlando, FL, 2016
  • H. Jeong, O. Arshad, N. Ghaffari, J. Thiltges, P. Blood, M. Criscitiello, B-J Yoon, A. Datta and C. D. Johnson, “Comparative De novo Transcriptome Assemblies for Pacific Whiteleg Shrimp Empowered by XSEDE,” XSEDE15, St. Louis, MO, 2015.
  • J. Risinger, L. Renken, J. Hill, N. Ghaffari, R. P. Metz, C. D. Johnson, and M. M. Toloue, “Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification”, PAG XXII, San Diego, CA, 2015.
  • Johnson, CD. 1st annual ARC metagenomics of soil conference, South Africa
  • N. Ghaffari, O. A. Arshad, H. Jeong, J. Thiltges, M. F. Criscitielloz, B-J. Yoon, A. Datta, and C. D. Johnson, “De Novo Transcriptome Assemblies and Annotation for Pacific Whiteleg Shrimp.” Genomic Signal Processing and Statistics (GENSIPS’14) conference, Atlanta, GA, 2014.
  • M. Torres, N. Ghaffari, E. Buiate, S. Schwartz, C. D. Johnson, and L. Vaillancourt, “Understanding Hemibiotrophy in Colletotrichum Graminicola,” Second International Symposium on Microbiology and Biotechnology, Brazil, pp. 115-124, 2013.
  • M. P. McLeod, A. Golovko, N. Ghaffari, E. A. Gargari, H. Guo, C. D. Johnson, S. H. Safe, I. Jutooru, and B. Morpurgo, “A Gene Trap Resource to Characterize Cancer-Related lncRNAs in C57BL/6 ES Cells & Mice,” 3rd Annual Advances in Oncology: From Clinical Science to Clinical Practice, Houston, TX, 2012.
  • N. Ghaffari, M. R. Yousefi, C. D. Johnson, I. Ivanov, and E. R. Dougherty, “Classification and Feature Selection Approaches for Next Generation Sequencing,” BioC2012, Seattle, WA, 2012.
  • R. Doan, N. Cohen, J. Sawyer, N. Ghaffari, C. D. Johnson, and S. V. Dindot, “Whole-Genome Analysis of a Quarter Horse Mare,” Plant and Animal Genome XX Conference, San Diego, CA, 2012.
  • A Gene Trap Resource to Characterize Cancer-related lncRNAs in C57BL/6 ES Cells & Mice
  • A.E. Szafranska, M. Doleshal, B. Cannon, L. Elizondo, J. Ehardt, M. Wilson, B. Choudhury, C.D. Johnson and S. Hunicke-Smith.  2007. Exploration of microRNA Expression Profiling in Fixed Archived Tissues: Lung Cancer Pilot Study
  • Jason Wiggins, Dmitriy Ovcharenko, Kevin Kelnar, Jaclyn Shingara, Charles D. Johnson, David Brown, and Andreas G. Bader. 2007. microRNAs in the Treatment of Cancer
  • Jin Xu, Timothy S. Davison and Charles D. Johnson.  2006 RANOVA: A New Method of Detecting Differentially Expressed Genes through Probe Level Data from Oligonucleotide Arrays.  International Biometric Society of Eastern North American Region.
  • Johnson C.D., Li Y., Wilson M., Davison, T.S., 2006. PowerAssist™: A Microarray QC Tool. Discovery to Diagnostics.
  • Whitley, P., Moturi, S., Santiago J., Agarwal, S., San Jose, C., Johnson, C., Wilson M., Setterquist R., 2005. A service for gene expression profiling form Globin-depleted whole blood RNA, Microarray’s in Medicine.
  • Johnson, C.D., Thomas, T.L., Ramos, K.S. 2004 A genomic model of benzo(a)pyrene induced atherogenesis.  Annual Meeting of Society of Toxicology. Falahatpisheh, M.H., Johnson, C.D., Ramos, K.S. 2004.  Transcriptional profiles following ligand-activated Ahr signaling in the developing kidney:  A role for Wt1 and IGF signaling.  Annual Meeting of Society of Toxicology.
  • Falahatpisheh, M.H., Johnson, C.D., Ramos, K.S. 2004.  Transcriptional profiles following ligand-activated Ahr signaling in the developing kidney:  A role for Wt1 and IGF signaling.  Annual Meeting of Society of Biochemistry.
  • 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 gene-gene interactions. TOXICOL SCI 72 (1): 449 Suppl.
  • Walker M. K., C.D. Johnson, M. Tadesse, K.S. Ramos, I.D. Steele, E.A. Thackaberry. 2003. Dioxin induces growth arrest and reduces cell cycle gene expression in the fetal murine heart. TOXICOL SCI 72 (1): 1124 Suppl..
  • Ramos, K.S., Johnson, C.D., Falahatpisheh, M.H., Tadesse, M., Thomas, T., Beremand, P., . Lu, K.P, Balagurunathan, Y., Afshari, C.A., Dougherty, E.R.. 2003. Application of clustering methodologies to the analysis of altered cellular phenotypes induced by oxidative stress. TOXICOL SCI 72 (1): 1084 Suppl.
  • Partridge, C.R., E.S. Williams, K.P. Lu, S. Chao, C.D. Johnson, R. Mouneimni, G.A. Meininger, E. Wilson, and K.S. Ramos. 2003. Genomic and immunofluorescence analysis of interactive gene networks in oxidant-induced atherogenesis. TOXICOL SCI 72 (1): 459 Suppl. S
  • 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. TOXICOL SCI 72 (1): 464 Suppl.
  • Partridge C.R., Lu K.P., Johnson C.D., Williams E.S., Meininger G.A., Wilson E., Ramos K.S. 2002. Transcriptome analysis of vascular tissue following oxidative injury. Annual Meeting of American Physiological Society.
  • Johnson C.D., Lu K.P., Beremand P.D., Thomas T.L., Ramos K.S. 2002. Global gene expression profiles in chemical atherogenesis. Annual Meeting of Society of Toxicology.
  • Falahatpisheh, M.H, Johnson, C.D, Ramos K.S. 2002. Global gene expression profiles in disrupted nephrogenesis. Gordon Research Conference
  • Partridge, C.R., E.S. Williams, K.P. Lu, S. Chao, C.D. Johnson, R. Mouneimni, G.A. Meininger, E. Wilson, and K.S. Ramos. 2002. Genomic and immunofluorescence analysis of interactive gene networks in oxidant-induced atherogenesis. Annual Meeting of Gulf Coast Society of Toxicology
  • Johnson C.D., Lu K. P., Afshari C.A., Balagurunathan Y., Dougherty E.R., Ramos K.S.. 2001.  Global response of SMC to oxidative stress.  Symposium on Gene Expression and Proteomics in Environmental Health Sciences.
  • Nizielski S.E., Seo J., Koppanur R., Johnson C.D. 1999.  Divergent effects of insulin-like growth factor-I (IGF-I) and growth hormone (GH) on the expression of adipogenic markers in brown vs. white adipose tissue of rats.  Annual Meeting of North American Association for the Study of Obesity.
  • Nizielski, S. E. and Johnson C.D. 1997.  Expression of a bovine growth hormone (bGH) transgene increases brown adipose tissue (BAT) mass: Involvement of C/EBP-g and PPAR-a.  Annual Meeting of North American Association for the Study of Obesity.
  • Hamilton, B. K., Pike L. M., Yoo K. S., Johnson C. D. 1994.  The effects of soil type, sulfur fertility, and harvest date on the pungency of TG1015Y onions.  Annual Meeting of American Society for Horticultural Science.
  •  Johnson, C. D., Johnson J. R., Decoteau D. R. 1992.  Nitrogen and potassium fertility of Jalapeno pepper during plant development and affects plant growth and fruit yield and pungency.  Annual Meeting of American Society for Horticultural Science.
  • Johnson, J.R., and Johnson C.D. 1992.  Habanero Pepper: World’s Hottest Pepper Comes to South Carolina.   Clemson University Vegetable Report .
  • Johnson, J.R., and Johnson C.D.  1992. Nitrogen Fertility and Cultivar Influence Collard Yield and Leaf Nitrogen Content.  Clemson University Vegetable Report.

White Papers

  • Robert Setterquist, Mike Wilson, Charles Johnson, Shika Agarwal, Sharmili Moturi. Synthesize High Yields of Biotinylated aRNA. Ambion TechNote 12(3) page 17-18
  • Penn Whitley, Sharmili Moturi, Jose Santiago, Charles Johnson, Robert Setterquist. Improved Microarray Sensitivity using Whole Blood RNA Samples. Ambion, Inc. TechNote 12(3) page 20-22
  • Charlie Johnson, Robert Setterquist, Sharmili Moturi, Charmaine San Jose, Penn Whitley. Increase Signal and Detect More Genes on Affymetrix® Arrays Ambion, Inc. TechNote 12(4) page 28-29

Invited Talks/ lectures (CJ:Charles Johnson

  • Charles D. Johnson Revitty workshop 2024
  • Charles D. Johnson Illumina Workshop at PAG 2024
  • Charle D. Johnson Revitty workshop 2023
  • Marcel Brun EMBL 2023
  • Charles D. Johnson AGBT-AG 2022
  • Charles D. Johnson PAG 2022
  • Charles D. Johnson GenomeWeb July 2020
  • Charles D. Johnson Lexogen 2020
  • Charles D. Johnson PerkinElmer 2020
  • Joshua Hill ABRF 2020
  • Charles D. Johnson AGBT 2020
  • Charles D. Johnson PAG 2020
  • Charles D. Johnson TxGen Grand Opening 2019
  • Charles Johnson, H. Jeong, O. Arshad, N. Ghaffari, J. Thiltges, P. Blood, M. Criscitiello, B-J Yoon, A. Datta and C. D. Johnson, “Comparative De novo Transcriptome Assemblies for Pacific Whiteleg Shrimp Empowered by XSEDE”, Submitted to XSEDE15.
  • J. Risinger, L. Renken, J. Hill, N. Ghaffari, R. P. Metz, C. D. Johnson, and M. M. Toloue, “Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification”, PAG XXII, San Diego, CA, 2015.
  • Johnson, CD. 1st annual ARC metagenomics of soil conference, South Africa
  • N. Ghaffari, O. A. Arshad, H. Jeong, J. Thiltges, M. F. Criscitielloz, B-J. Yoon, A. Datta, and C. D. Johnson, “De Novo Transcriptome Assemblies and Annotation for Pacific Whiteleg Shrimp.” Genomic Signal Processing and Statistics (GENSIPS’14) conference, Atlanta, GA, 2014.
  • M. Torres, N. Ghaffari, E. Buiate, S. Schwartz, C. D. Johnson, and L. Vaillancourt, “Understanding Hemibiotrophy in Colletotrichum Graminicola,” Second International Symposium on Microbiology and Biotechnology, Brazil, pp. 115-124, 2013.
  • M. P. McLeod, A. Golovko, N. Ghaffari, E. A. Gargari, H. Guo, C. D. Johnson, S. H. Safe, I. Jutooru, and B. Morpurgo, “A Gene Trap Resource to Characterize Cancer-Related lncRNAs in C57BL/6 ES Cells & Mice,” 3rd Annual Advances in Oncology: From Clinical Science to Clinical Practice, Houston, TX, 2012.
  • N. Ghaffari, M. R. Yousefi, C. D. Johnson, I. Ivanov, and E. R. Dougherty, “Classification and Feature Selection Approaches for Next Generation Sequencing,” BioC2012, Seattle, WA, 2012.
  • R. Doan, N. Cohen, J. Sawyer, N. Ghaffari, C. D. Johnson, and S. V. Dindot, “Whole-Genome Analysis of a Quarter Horse Mare,” Plant and Animal Genome XX Conference, San Diego, CA, 2012.
  • The Genomics Symposium at Hermosillo and Ciudad Obregon, Mexico, “Assembling the Genome and Transcriptome of the Whiteleg Shrimp,” May 2013 (NG)
  • AgriLife Amarillo REC (CJ, RM, SS) 2013 AgriLife Lubbock REC (CJ, RM, SS) 2013, AgriLife Weslaco REC (CJ) 2013

TAMU College Station guest lecturer

  • FSTC 619/POSC 619/SCSC 619/VTMI 619 Molecular Methods for Microbial Detection & Characterization, “Introduction to Next-Generation Sequencing,” October 2013 (CJ)
  • VTMI 689-600 Special Topics in Microbial Bioinformatics, “Next Generation Sequencing Technology Analysis”, March 2013 (NG, RM)
  • ECEN “Introduction to NGS” September 2015 (CJ), 2016, 2017 (NG)
  • Biochem 6XX class “Introduction to Genomic Technology” 2011, 2012, 2013, 2014, 2016, 2017 (CJ)

News Reports

AgriLife News

Acknowlegements or paper we generated data for

Illumina sponsored GenomeWeb talk. The talk focused on the application of high-performance computing into our genotyping pipeline. We are the first agriculture focused NGS lab to have an Illumina DREGEN system for sequence data processing. The DRAGEN is part of our low cost WGS genotyping product line. https://www.dropbox.com/s/gg4gqa5dl0slr28/GenomeWebJohnson09Jul2020Final.pdf?dl=0

Our Magic DRAGEN: A Sequencing Lab Case Study on Accelerated Bioinformatics Illumina’s website

Link to  GenomeWeb talk: https://event.on24.com/eventRegistration/EventLobbyServlet?target=reg20.jsp&partnerref=site&eventid=2385462&sessionid=1&key=7E57E485A9C95FC64EFB71433ED19BB7&regTag=&sourcepage=register

AGBT2020 Illumina video feature the TxGen laboratory and Charlie Johnson https://www.youtube.com/watch?v=v39FGRRRxXA

Illumina Story
https://www.illumina.com/science/customer-stories/icommunity-customer-interviews-case-studies/johnson-agrilife-interview-ag-novaseq.html

Texas A&M Deploys DRAGEN: First American Academic Institution Install for Agricultural Applications https://www.illumina.com/company/news-center/feature-articles/texas-a-m-deploys-dragen-for-agricultural-applications-.html

Agriculture Throughout the World is Benefiting from the Latest NGS Technologies https://www.illumina.com/science/customer-stories/icommunity-customer-interviews-case-studies/johnson-agrilife-interview-ag-novaseq.html

Advancing Agricultural Genomics with Low-Cost NGS Genotyping. PerkinElmer featured my lab in their Agricultural marketing. https://perkinelmer-appliedgenomics.com/2020/04/24/ngs-genotyping-for-agrigenomics/

Slides for a cooperate values and technology at the PerkinElmer Worldwide sales meeting in 2020. 800 participants. Keynote speaker. https://www.dropbox.com/s/6rvat4ne7pjyku0/PerkinElmerSales2020v2%20Leadership.pdf?dl=0 
AGBT AG 2022

Illumina sponsored YouTube Videos Sequencing Complex Plant Genomes at Texas A&M AgriLife https://www.youtube.com/watch?v=eecnhlhAn9w/

NovaSeq 6000 Sequencing System | Empowering Agrigenomics Across the Globe https://www.youtube.com/watch?v=UfBR6FJnQ_o

Using the iSeq™ 100 Sequencing System for Quality Control https://www.youtube.com/watch?v=btlh3Xvrhyo

Preview: Using the iSeq™ 100 Sequencing System for Quality Control https://www.youtube.com/watch?v=dlYAh8XFyD8

Greater Good Initiative | Awarding agricultural research https://www.youtube.com/watch?v=wSFtVRHe5-k

Illumina links:
https://archive.ph/MIMEh
https://archive.ph/6xlRs
https://archive.ph/udP23
https://archive.ph/dYsJW
https://archive.ph/3e7yE
https://archive.ph/6m6AJ
https://archive.ph/WGqp8
https://archive.ph/MZKfx
https://archive.ph/u4ujV
https://archive.ph/xDfVn