(Cichocki et al., 2017) (Triff et al., 2013) (A. M. Hulse-Kemp, Lemm, et al., 2015) (Ing et al., 2016) Following are the articles published either through collaboration with Texas A&M Institute for Genome Sciences & Society (TIGSS), formerly Whole Systems Genomics Initiative (WSGI), or through providing computing resource and / or providing any help and assistance, both with analyses support or funding support. (Whitfield-Cargile et al., 2015)(Chávez-Galarza et al., 2013)(C. Brinkmeyer-Langford et al., 2013)(G. Wang, Yang, Brinkmeyer-Langford, & Cai, 2013)(Pechal et al., 2013)(Dawes et al., 2014)(Zoh et al., 2016)(Pinto et al., 2014)(Ence Yang et al., 2014)(A. M. Hulse-Kemp, Ashrafi, et al., 2015)(Fu, Tarone, & Sze, 2015)(J. M. Knight, Ivanov, & Dougherty, 2014)(Gang Wang, Yang, Smith, et al., 2014)(Truong, McCormick, Rooney, & Mullet, 2015)(E. Yang et al., 2013)(Gang Wang, Yang, Mandhan, Brinkmeyer-Langford, & Cai, 2014)(Amanda M Hulse-Kemp et al., 2014)(Zeng et al., 2015)(J. Knight, Ivanov, & Dougherty, 2013)(McCormick, Truong, & Mullet, 2015)(Konganti, Cai, Wang, & Yang, 2013)(Hoefler, Konganti, & Straight, 2013)(Guan et al., 2016)(Mccormick, Truong, & Mullet, 2016)(Mason et al., 2016)(C. L. Brinkmeyer-Langford, Guan, Ji, & Cai, 2016)(Johnson, Gaddis, Cairns, Lafon, & Krutovsky, 2016)(Forgacs, Wallen, Dobson, & Derr, 2016)(McQueen et al., 2016)(Ence Yang et al., 2016)(Lu et al., 2016)
Cichocki, J. A., Furuya, S., Konganti, K., Luo, Y.-S., McDonald, T. J., Iwata, Y., … Rusyn, I. (2017, February 1). Impact of Nonalcoholic Fatty Liver Disease on Toxicokinetics of Tetrachloroethylene in Mice. Journal of Pharmacology and Experimental Therapeutics. American Society for Pharmacology & Experimental Therapeutics (ASPET). https://doi.org/10.1124/jpet.116.238790
McQueen, C. M., Whitfield-Cargile, C. M., Konganti, K., Blodgett, G. P., Dindot, S. V., & Cohen, N. D. (2016, December).             TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-016-3345-3
Forgacs, D., Wallen, R. L., Dobson, L. K., & Derr, J. N. (2016, November 23). Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison. (Y. Bai, Ed.), PLOS ONE. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pone.0166081
Yang, Ence, Wang, G., Yang, J., Zhou, B., Tian, Y., & Cai, J. J. (2016, September 20). Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Human Molecular Genetics. Oxford University Press (OUP). https://doi.org/10.1093/hmg/ddw314
Lu, M., Krutovsky, K. V., Nelson, C. D., Koralewski, T. E., Byram, T. D., & Loopstra, C. A. (2016, September 13). Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-016-3081-8
Mccormick, R. F., Truong, S. K., & Mullet, J. E. (2016, August 15). 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture. Plant Physiology. American Society of Plant Biologists (ASPB). https://doi.org/10.1104/pp.16.00948
Mason, V. C., Li, G., Minx, P., Schmitz, J., Churakov, G., Doronina, L., … Murphy, W. J. (2016, August 10). Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates. Science Advances. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/sciadv.1600633
Brinkmeyer-Langford, C. L., Guan, J., Ji, G., & Cai, J. J. (2016, August 3). Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Frontiers in Aging Neuroscience. Frontiers Media SA. https://doi.org/10.3389/fnagi.2016.00183
Ing, N. H., Konganti, K., Ghaffari, N., Johnson, C. D., Forrest, D. W., Love, C. C., & Varner, D. D. (2016, August). Sequencing of RNA from stallion sperm identifies potential markers of fertility. Journal of Equine Veterinary Science. Elsevier BV. https://doi.org/10.1016/j.jevs.2016.06.026
Guan, J., Yang, E., Yang, J., Zeng, Y., Ji, G., & Cai, J. J. (2016, April 30). Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Human Genetics. Springer Nature. https://doi.org/10.1007/s00439-016-1673-7
Zoh, R. S., Mallick, B., Ivanov, I., Baladandayuthapani, V., Manyam, G., Chapkin, R. S., … Carroll, R. J. (2016, April 1). PCAN: Probabilistic correlation analysis of two non-normal data sets. Biometrics. Wiley-Blackwell. https://doi.org/10.1111/biom.12516
Johnson, J. S., Gaddis, K. D., Cairns, D. M., Lafon, C. W., & Krutovsky, K. V. (2016, March 3). Plant responses to global change: next generation biogeography. Physical Geography. Informa UK Limited. https://doi.org/10.1080/02723646.2016.1162597
Truong, S. K., McCormick, R. F., Rooney, W. L., & Mullet, J. E. (2015, August 31). Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.178608
Whitfield-Cargile, C. M., Cohen, N. D., Suchodolski, J., Chaffin, M. K., McQueen, C. M., Arnold, C. E., … Blodgett, G. P. (2015, August 25). Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals. (G. F. Browning, Ed.), PLOS ONE. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pone.0136586
Hulse-Kemp, A. M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D. D., … Stelly, D. M. (2015, April 22). Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3: Genes|Genomes|Genetics. Genetics Society of America. https://doi.org/10.1534/g3.115.018416
Hulse-Kemp, A. M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C. A., Scheffler, B. E., … Stelly, D. M. (2015, April 9). BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping. G3: Genes|Genomes|Genetics. Genetics Society of America. https://doi.org/10.1534/g3.115.017749
McCormick, R. F., Truong, S. K., & Mullet, J. E. (2015, February 13). RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK. G3: Genes|Genomes|Genetics. Genetics Society of America. https://doi.org/10.1534/g3.115.017012
Zeng, Y., Wang, G., Yang, E., Ji, G., Brinkmeyer-Langford, C. L., & Cai, J. J. (2015, January 24). Aberrant Gene Expression in Humans. (S. B. Montgomery, Ed.), PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004942
Fu, S., Tarone, A. M., & Sze, S.-H. (2015). Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. BMC Genomics. Springer Nature. https://doi.org/10.1186/1471-2164-16-s11-s5
Knight, J. M., Ivanov, I., & Dougherty, E. R. (2014, December). MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. BMC Bioinformatics. Springer Nature. https://doi.org/10.1186/s12859-014-0401-3
Yang, Ence, Chow, W.-N., Wang, G., Woo, P. C. Y., Lau, S. K. P., Yuen, K.-Y., … Cai, J. J. (2014, October 16). Signature Gene Expression Reveals Novel Clues to the Molecular Mechanisms of Dimorphic Transition in Penicillium marneffei. (P. M. Richardson, Ed.), PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004662
Wang, Gang, Yang, E., Smith, K. J., Zeng, Y., Ji, G., Connon, R., … Cai, J. J. (2014, September 11). Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Frontiers in Genetics. Frontiers Media SA. https://doi.org/10.3389/fgene.2014.00312
Wang, Gang, Yang, E., Mandhan, I., Brinkmeyer-Langford, C. L., & Cai, J. J. (2014, January 8). Population-level expression variability of mitochondrial DNA-encoded genes in humans. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/ejhg.2013.293
Pinto, M. A., Henriques, D., Chávez-Galarza, J., Kryger, P., Garnery, L., van der Zee, R., … Johnston, J. S. (2014, January). Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data. Journal of Apicultural Research. Informa UK Limited. https://doi.org/10.3896/ibra.
Hulse-Kemp, Amanda M, Ashrafi, H., Zheng, X., Wang, F., Hoegenauer, K. A., Maeda, A. B., … Stelly, D. M. (2014). Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics. Springer Nature. https://doi.org/10.1186/1471-2164-15-945
Dawes, M., Moore-Harrison, T., Hamilton, A. T., Ceaser, T., Kochan, K. J., Riggs, P. K., & Lightfoot, J. T. (2014). Differential Gene Expression in High- and Low-Active Inbred Mice. BioMed Research International. Hindawi Publishing Corporation. https://doi.org/10.1155/2014/361048
Wang, G., Yang, E., Brinkmeyer-Langford, C. L., & Cai, J. J. (2013, December 2). Additive, Epistatic, and Environmental Effects Through the Lens of Expression Variability QTL in a Twin Cohort. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.157503
Pechal, J. L., Crippen, T. L., Tarone, A. M., Lewis, A. J., Tomberlin, J. K., & Benbow, M. E. (2013, November 12). Microbial Community Functional Change during Vertebrate Carrion Decomposition. (C. Pan, Ed.), PLoS ONE. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pone.0079035
Chávez-Galarza, J., Henriques, D., Johnston, J. S., Azevedo, J. C., Patton, J. C., Muñoz, I., … Pinto, M. A. (2013, November 7). Signatures of selection in the Iberian honey bee ( Apis mellifera iberiensis ) revealed by a genome scan analysis of single nucleotide polymorphisms . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12537
Brinkmeyer-Langford, C., Rodrigues, A., Kochan, K. J., Haney, R., Rassu, F., Steelman, A. J., … Welsh, C. J. (2013, November 5). Consequences of perinatal bisphenol A exposure in a mouse model of multiple sclerosis. Autoimmunity. Informa Healthcare. https://doi.org/10.3109/08916934.2013.832220
Knight, J., Ivanov, I., & Dougherty, E. (2013, November). Bayesian multivariate Poisson model for RNA-seq classification. 2013 IEEE International Workshop on Genomic Signal Processing and Statistics. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/gensips.2013.6735946
Triff, K., Konganti, K., Gaddis, S., Zhou, B., Ivanov, I., & Chapkin, R. S. (2013, October 22). Genome-wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression. Physiological Genomics. American Physiological Society. https://doi.org/10.1152/physiolgenomics.00136.2013
Konganti, K., Cai, J., Wang, G., & Yang, E. (2013, September). SBEToolbox: A Matlab Toolbox for Biological Network Analysis. Evolutionary Bioinformatics. Libertas Academica, Ltd. https://doi.org/10.4137/ebo.s12012
Hoefler, B. C., Konganti, K., & Straight, P. D. (2013, August 1). De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomea.00535-13
Yang, E., Wang, G., Woo, P. C. Y., Lau, S. K. P., Chow, W.-N., Chong, K. T. K., … Cai, J. J. (2013, July 12). Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei. Eukaryotic Cell. American Society for Microbiology. https://doi.org/10.1128/ec.00159-13