July 14, 2012

Publications

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

2017

  • 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
  • Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, et al. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J. 2016; 86:195–207.  http://www.ncbi.nlm.nih.gov/pubmed/26945524

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.
  • Guttieri MJ, Baenziger PS, Frels K, Carver B, Arnall B, Wang S, et al. Prospects for Selecting Wheat with Increased Zinc and Decreased Cadmium Concentration in Grain. Crop Sci. 2015; 55:1712.  https://dl.sciencesocieties.org/publications/cs/abstracts/55/4/1712
  • Jordan KW, Wang S*(co-first), Lun Y, Gardiner L-J, MacLachlan R, Hucl P, et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 2015; 16:48. http://www.ncbi.nlm.nih.gov/pubmed/25886949
  • Tiwari VK, Wang S, Danilova T, Koo DH, Vrána J, Kubaláková M, et al. Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M(g) of Aegilops geniculata. Plant J. 2015; 84:733–46. http://www.ncbi.nlm.nih.gov/pubmed/26408103

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
  • Bruce M, Neugebauer KA, Joly DL, Migeon P, Cuomo CA, Wang S, et al. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Front. Plant Sci. 2014; 4:520. http://www.ncbi.nlm.nih.gov/pubmed/24454317
  • Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, et al. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol. J. 2014; 12:787–96. http://www.ncbi.nlm.nih.gov/pubmed/24646323
  • Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, et al. SNP Discovery for mapping alien introgressions in wheat. BMC Genomics. 2014; 15:273. http://www.ncbi.nlm.nih.gov/pubmed/24716476
  • Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, International Wheat Genome Sequencing Consortium (IWGSC), Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Číhalíková J, Dubská Z, Vrána J, Šperková R, Šimková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan P, Sharpe A, Klassen D, Edwards D, Batley J, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014; 345:1250091. http://www.ncbi.nlm.nih.gov/pubmed/25035498
  • International Wheat Genome Sequencing Consortium (IWGSC) – Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Cíhalíková J, Dubská Z, Vrána J, Sperková R, Simková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014; 345:1251788. http://www.ncbi.nlm.nih.gov/pubmed/25035500
  • Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, International Wheat Genome Sequencing Consortium (IWGSC), Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Číhalíková J, Dubská Z, Vrána J, Šperková R, Šimková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan P, Sharpe A, Klassen D, Edwards D, Batley J, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA.. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014; 345:1250092. http://www.ncbi.nlm.nih.gov/pubmed/25035499

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
  • Krasileva K V, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Wang S, et al. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol. 2013; 14:R66. http://www.ncbi.nlm.nih.gov/pubmed/23800085

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
  • Metz RP, Patterson JL, Wilson E. Vascular smooth muscle cells: isolation, culture, and characterization. Methods Mol Biol. 2012;843:169-76.

2011

  • Richardson WJ, Metz RP, Moreno MR, Wilson E, JE Moore, Jr. A Device to Study the Effects of Stretch Gradients on Cell Behavior. J Biomech Eng. 2011 Oct;133(10):101008. PMID: 22070333.
  • Scribner KC, Wellberg EA, Metz RP, Porter WW. Singleminded-2s (Sim2s) Promotes Delayed Involution of the Mouse Mammary Gland through Suppression of Stat3 and NF{kappa}B. Mol Endocrinol. 2011 Apr 25(4):635-44. PMID: 21292822.
  • 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
  • N. Ghaffari, I. Ivanov, X. Qian, and E. R. Dougherty, “A CoD-based Stationary Control Policy for Intervening in Large Gene Regulatory Networks”, BMC Bioinformatics, 12(Suppl 10):S10, 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
  • Nelson JC, Wang S, Wu Y, Li X, Antony G, White FF, et al. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics. 2011; 12:352. http://www.ncbi.nlm.nih.gov/pubmed/21736744
  • Wang S, Yang S, An B, Wang S, Yin Y, Lu Y, et al. Molecular dynamics analysis reveals structural insights into mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase. PLoS One. 2011; 6:e23342. http://www.ncbi.nlm.nih.gov/pubmed/21858078

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.
  • Qu X, Metz RP, Porter WW, Neuendorff N, Earnest BJ, Earnest DJ. The clock genes period 1 and period 2 mediate diurnal rhythms in dioxin-induced Cyp1A1 expression in the mouse mammary gland and liver. Toxicol Lett. 2010 Jun 16;196(1):28-32. PMID: 20371273
  • Wellberg E, Metz RP, Parker C, Porter WW. The bHLH/PAS transcription factor singleminded 2s promotes mammary gland lactogenic differentiation. Development.2010 Mar;137(6):945-52. PMID: 20150276.
  • X. Qian, N. Ghaffari, I. Ivanov, and E. R. Dougherty, “State Reduction for Network Intervention in Probabilistic Boolean Networks”, Bioinformatics, 26(24): 3098-3104, 2010.
  • N. Ghaffari, I. Ivanov, X. Qian, and E. R. Dougherty, “A CoD-Based Reduction Algorithm for Designing Stationary Control Policies on Boolean Networks”, Bioinformatics 26(12): 1556- 1563, 2010
  • Ivanov, P. Simeonov, N. Ghaffari, X. Qian, and E. R. Dougherty, “Selection Policy Induced Reduction Mappings for Boolean Networks”, IEEE Transactions on Signal Processing – TSP, 58(9), 4871-4882, 2010

2009

  • X. Qian, I. Ivanov, N. Ghaffari, and E.R. Dougherty, “Intervention in gene regulatory networks via greedy control policies based on long-run behavior,” BMC Systems Biology, 3(61), 2009
  • Qu X, Metz RP, Porter WW, Cassone VM, Earnest DJ. Disruption of period gene expression alters the inductive effects of dioxin on the AhR signaling pathway in the mouse liver. Toxicol Appl Pharmacol. 2009 Feb 1;234(3):370-7. PMID: 19038280
  • Gustafson TL, Wellberg E, Laffin B, Schilling L, Metz RP, Zahnow CA, Porter WW. Ha-Ras transformation of MCF10A cells leads to repression of Singleminded-2s through NOTCH and C/EBPbeta. Oncogene. 2009 Mar 26;28(12):1561-8. PMID: 19169276
  • Wang S, Yang S, Yin Y, Guo X, Wang S, Hao D. An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome. Plant Mol. Biol. 2009; 69:167–78. http://www.ncbi.nlm.nih.gov/pubmed/18931920
  • Sun L, Wang S, Xi J, Yang S, Liu X, Chai X, et al. A fractionation procedure for identifying novel proteins induced by chill stress in Arabidopsis thaliana. Biotechnol. Lett. 2009; 31:1289–95. http://www.ncbi.nlm.nih.gov/pubmed/19347259
  • Wang S, Yang S, Yin Y, Xi J, Li S, Hao D. Molecular dynamics simulations reveal the disparity in specific recognition of GCC-box by AtERFs transcription factors super family in Arabidopsis. J. Mol. Recognit. 2009; 22:474–9. http://www.ncbi.nlm.nih.gov/pubmed/19533627
  • Yang S, Wang S, Liu X, Yu Y, Yue L, Wang X, et al. Four divergent Arabidopsis ethylene-responsive element-binding factor domains bind to a target DNA motif with a universal CG step core recognition and different flanking bases preference. FEBS J. 2009; 276:7177–86. http://www.ncbi.nlm.nih.gov/pubmed/19878300

2008

  • Laffin B, Wellberg E, Kwak HI, Burghardt RC, Metz RP, Gustafson T, Schedin P, Porter WW. Loss of singleminded-2s in the mouse mammary gland induces an epithelial-mesenchymal transition associated with up-regulation of slug and matrix metalloprotease 2. Mol Cell Biol. 2008 Mar;28(6):1936-46. PMID: 18160708.
  • Higgins KJ, Liu S, Abdelrahim M, Vanderlaag K, Liu X, Porter W, Metz R, Safe S. Vascular endothelial growth factor receptor-2 expression is down-regulated by 17beta-estradiol in MCF-7 breast cancer cells by estrogen receptor alpha/Sp proteins. Mol Endocrinol. 2008 Feb;22(2):388-402. PMID: 18006642.
  • C. Harris, N. Ghaffari, “Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning”, BMC Genomics, 9(Suppl 2):S7, 2008.

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)
  • Kwak HI, Gustafson T, Metz RP, Laffin B, Schedin P, Porter WW. Inhibition of breast cancer growth and invasion by single-minded 2s. Carcinogenesis. 2007 Feb;28(2):259-66. PMID: 16840439.
  • McDaniel SM, O’Neill C, Metz RP, Tarbutton E, Stacewicz-Sapuntzakis M, Heimendinger J, Wolfe P, Thompson H, Schedin P. Whole-food sources of vitamin A more effectively inhibit female rat sexual maturation, mammary gland development, and mammary carcinogenesis than retinyl palmitate. J Nutr. 2007 Jun;137(6):1415-22. PMID: 17513400.
  • Dash B, Metz R, Huebner HJ, Porter W, Phillips TD. Molecular characterization of two superoxide dismutases from Hydra vulgaris. Gene. 2007 Jan 31;387(1-2):93-108. PMID: 17150313.
  • Qu X, Metz RP, Porter WW, Cassone VM, Earnest DJ. Disruption of clock gene expression alters responses of the aryl hydrocarbon receptor signaling pathway in the mouse mammary gland. Mol Pharmacol. 2007 Nov;72(5):1349-58. PMID: 17715397.

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.
  • Metz RP, Qu X, Laffin B, Earnest D, Porter WW. Circadian clock and cell cycle gene expression in mouse mammary epithelial cells and in the developing mouse mammary gland. Dev Dyn. 2006 Jan;235(1):263-71. PMID: 16261617.
  • McDaniel SM, Rumer KK, Biroc SL, Metz RP, Singh M, Porter W, Schedin P. Remodeling of the mammary microenvironment after lactation promotes breast tumor cell metastasis. Am J Pathol. 2006 Feb;168(2):608-20. PMID: 16436674.
  • Metz RP, Kwak HI, Gustafson T, Laffin B, Porter WW. Differential transcriptional regulation by mouse single-minded 2s. J Biol Chem. 2006 Apr 21;281(16):10839-48. PMID: 16484282
  • Dash B, Metz R, Huebner HJ, Porter W, Phillips TD. Molecular characterization of phospholipid hydroperoxide glutathione peroxidases from Hydra vulgaris. Gene. 2006 Oct 15;381:1-12. PMID: 16919897.
  • Higgins KJ, Liu S, Abdelrahim M, Yoon K, Vanderlaag K, Porter W, Metz RP, Safe S. Vascular endothelial growth factor receptor-2 expression is induced by 17beta-estradiol in ZR-75 breast cancer cells by estrogen receptor alpha/Sp proteins. Endocrinology. 2006 Jul;147(7):3285-95. PMID: 16574784.

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

  • 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
  • Falahatpisheh M, Kerzee J, Metz R, Donnelly K, Ramos K. Inducible cytochrome P450 activities in renal glomerular mesangial cells: biochemical basis for antagonistic interactions among nephrocarcinogenic polycyclic aromatic hydrocarbons. J Carcinog. 2004 Aug 17;3(1):12. PMID: 15315710.

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
  • Metz RP, Kaeck M, Stacewicz-Sapuntzakis M, Mitrenga T, McCarty H, Schedin P. Adolescent vitamin A intake alters susceptibility to mammary carcinogenesis in the Sprague-Dawley rat. Nutr Cancer. 2002;42(1):78-90. PMID: 12235654.
  • Metz RP, Auyeung DJ, Kessler FK, Ritter JK. Involvement of hepatocyte nuclear factor 1 in the regulation of the UDP-glucuronosyltransferase 1A7 (UGT1A7) gene in rat hepatocytes. Mol Pharmacol. 2000 Aug;58(2):319-27. PMID: 10908299.
  • 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.
  • Metz RP, Ritter JK. Transcriptional activation of the UDP-glucuronosyltransferase 1A7 gene in rat liver by aryl hydrocarbon receptor ligands and oltipraz. J Biol Chem. 1998 Mar 6;273(10):5607-14. PMID: 9488689.
  • Grove AD, Kessler FK, Metz RP, Ritter JK. Identification of a rat oltipraz-inducible UDP-glucuronosyltransferase (UGT1A7) with activity towards benzo(a)pyrene-7,8-dihydrodiol. J Biol Chem. 1997 Jan 17;272(3):1621-7. PMID: 8999837.
  • 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

  • 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
  • R. Sotelo-Mundo, M. Criscitiello, S. Dindot, A. Ochoa-Leyva, A. Lopez-Zavala, N. Ghaffari, “Perspectives on the Impact of Next Generation Sequencing (NGS) Technologies on Shrimp Aquaculture,” FENACAM’15, Fortaleza, Brazil, 2015.
  • 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, NG:Noushin Ghaffari, RM: Rick Metz

  • 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.
  • N. Ghaffari, I. Ivanov, and E. R. Dougherty, “Intervention in Large Gene Regulatory Networks via A Novel Greedy Control Policy,” MCBIOS, College Station, TX, 2011.
  • N. Ghaffari, “Controlling Gene Regulatory Networks via a Greedy Approach: CoD-CP,” SRW, College Station, TX, 2011.
  • “Improved Transcriptome of the Whiteleg Shrimp (Litopenaeus Vannamei), a Dominant Crustacean in Global Seafood Mariculture,” the 39th Annual Eastern Fish Health Workshop (EFHW), April 2014 (NG)
  • 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

  • ECEN 489: At the Interface of Engineering and Life Sciences, “Next-generation Sequencing Technology and Applications,” February 2015 (NG)
  • Biochemical Genetics BICH 631, “Bioinformatics Introduction for Next-Generation Sequencing,” February 2014 (NG)
  • FSTC 619/POSC 619/SCSC 619/VTMI 619 Molecular Methods for Microbial Detection & Characterization, “Introduction to Next-Generation Sequencing: Bioinformatics,” October 2013 (NG)
  • 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)

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