Research Articles

Osorio, D., Yu, X., Zhong, Y., Li, G., Serpedin, E., Huange, J. Z., & Cai, J. J. (2020). Single-Cell Expression Variability Implies Cell Function. Cells, 9(1), 14. https://doi.org/10.3390/cells9010014

Li, J., Yin, Y., & Zhang, M. (2020). GsmPlot: a web server to visualize epigenome data in NCBI. BMC Bioinformatics, 21(55). https://doi.org/10.1186/s12859-020-3386-0

Little, S. V., Hillhouse, A. E., & Lawhon, S. D. (2020). Whole-Genome Sequences of an Abortive Bacillus safensis Strain Isolated from a Mare’s Uterus. Microbiology Resource Announcements, 9(20). https://doi.org/10.1128/MRA.00342-20

Little, S. V., Hillhouse, A. E., & Lawhon, S. D. (2020). Genome Sequence of a Weissella confusa Strain Isolated from the First Reported Case of Neonatal Sepsis in an Equid. Microbiology Resource Announcements, 9(9). https://doi.org/10.1128/MRA.00066-20

Little, S. V., Hillhouse, A. E., & Lawhon, S. D. (2020). Draft Genome Sequence of Erysipelothrix rhusiopathiae, Isolated from a Canine Case of Diskospondylitis. Microbiology Resource Announcements, 9(26). https://doi.org/10.1128/MRA.00592-20

Yu, X., Kish, L., Seguin, J., & King, M. D. (2020). Ternary Fingerprints with Reference Odor for Fluctuation-Enhanced Sensing. Preprints. https://doi.org/10.20944/preprints202002.0151.v1

Medina-Perez, D. N., Wager, B., Troy, E., Gao, L., Norris, S. J., Lin, T., & Skare, J. T. (2020). The intergenic small non-coding RNA ittA is required for optimal infectivity and tissue tropism in Borrelia burgdorferi. PLoS Pathogens, 16(5). https://doi.org/10.1371/journal.ppat.1008423

Huang, G., Osorio, D., & Guan, J. (2020). Overdispersed gene expression in schizophrenia. Npj Schizophr, 6(9). https://doi.org/10.1038/s41537-020-0097-5

Yin, Y., Li, J., Lee, M., Zhao, S., Guo, L., & Sun, D. (2020). LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing. BioRxiv. https://doi.org/10.1101/2020.05.14.096461

Chakraborty, A., Scogin, C. K., Rizwan, K., Morley, T. S., & Rutkowski, J. M. (2020). Characterizing Lymphangiogenesis and Concurrent Inflammation in Adipose Tissue in Response to VEGF-D. Frontiers in Physiology, 11(363). https://doi.org/10.3389/fphys.2020.00363

Eldridge, R., Osorio, D., & Amstalden, K. (2020). Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Sci Rep, 10(7918). https://doi.org/10.1038/s41598-020-64862-z

Coleman, M. C., Whitfield-Cargile, C., Cohen, N. D., Goldsby, J. L., Davidson, L., Chamoun-Emanuelli, A. M., & Chapkin, R. S. (2020). Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome. PloS One, 15(3). https://doi.org/10.1371/journal.pone.0229797

Lugena, A. B., Zhang, Y., Menet, J. S., & Merlin, C. (2019). Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain. PLOS Genetics, 15(7), e1008265. https://doi.org/10/gf5kbg Download

Little, S. V., Bryan, L. K., Hillhouse, A. E., Konganti, K., & Lawhon, S. D. (2019). Whole-Genome Sequences of Staphylococcus pseudintermedius Isolates from Canine and Human Bacteremia Infections. Microbiology Resource Announcements, 8(28). https://doi.org/10/gf5kbm Download

Lunde‐Young, R., Ramirez, J., Naik, V., Orzabal, M., Lee, J., Konganti, K., Hillhouse, A., Threadgill, D., & Ramadoss, J. (2019). Hippocampal transcriptome reveals novel targets of FASD pathogenesis. Brain and Behavior, e01334. https://doi.org/10/gf5kbn Download

Lu, M., Loopstra, C. A., & Krutovsky, K. V. (2019). Detecting the genetic basis of local adaptation in loblolly pine ( Pinus taeda L.) using whole exome‐wide genotyping and an integrative landscape genomics analysis approach. Ecology and Evolution. https://doi.org/10/gf5kbh Download

Lewis, L., Borowa-Mazgaj, B., de Conti, A., Chappell, G. A., Luo, Y.-S., Bodnar, W., Konganti, K., Wright, F. A., Threadgill, D. W., Chiu, W. A., Pogribny, I. P., & Rusyn, I. (2019). Population-Based Analysis of DNA Damage and Epigenetic Effects of 1,3-Butadiene in the Mouse. Chemical Research in Toxicology. https://doi.org/10/gf5kbq Download

Batool, M., Hillhouse, A. E., Ionov, Y., Kochan, K. J., Mohebbi, F., Stoica, G., Threadgill, D. W., Zelikovsky, A., Waghela, S. D., Wiener, D. J., & Rogovskyy, A. S. (2019). New Zealand White Rabbits Effectively Clear Borrelia burgdorferi B31 despite the Bacterium's Functional vlsE Antigenic Variation System. Infection and Immunity, 87(7). https://doi.org/10/gf5k55

Little, S. V., Bryan, L. K., Hillhouse, A. E., Cohen, N. D., & Lawhon, S. D. (2019). Characterization of agr Groups of Staphylococcus pseudintermedius Isolates from Dogs in Texas. MSphere, 4(2). https://doi.org/10/gf5kbj Download

Orzabal, M. R., Lunde-Young, E. R., Ramirez, J. I., Naik, V. D., Hillhouse, A., Konganti, K., Threadgill, D. W., & Ramadoss, J. (2019). Gestational binge alcohol-induced alterations in maternal uterine artery transcriptome. Reproductive Toxicology, 87, 42–49. https://doi.org/10/gf5kbp

Therrien, D. A., Taylor, M., Gill, J., & Riggs, P. (2019). Genome Sequencing of Non-Pathogenic E. coli Approved as Pathogen Surrogates. Meat and Muscle Biology, 1(3). https://doi.org/10.221751/rmc2017.127

Zou, D., Ganugula, R., Arora, <, Nabity, M. B., Sheikh-Hamad, D., & Kumar, M. R. (2019). Oral delivery of nanoparticle urolithin A normalizes cellular stress and improves survival in mouse model of cisplatin-induced AKI. American Journal of Physiology-Renal Physiology, 317(5), F1255–F1264. https://doi.org/10.1152/ajprenal.00346.2019

Chakraborty, A., Barajas, S., Lammoglia, G. M., Reyna, A. J., Morley, T. S., Johnson, J. A., & Rutkowski, J. M. (2019). Vascular endothelial growth factor–D (VEGF-D) overexpression and lymphatic expansion in murine adipose tissue improves metabolism in obesity. The American Journal of Pathology, 189(4), 924–939. https://doi.org/10.1016/j.ajpath.2018.12.008

Khan, S. A., Eggleston, H., Myles, K. M., Andelman, Z. N., & Huang, J. Z. (2019). Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. G3: Genes, Genomes, Genetics, 9(7), 2363–2373. https://doi.org/10.1534/g3.119.400340

Song, J., Logeswaran, D., Castillo-Gonzalez, C., Li, Y., Bose, S., Aklilu, B., & Shippen, D. E. (2019). The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans. Proceedings of the National Academy of Sciences, 116(49), 2354224542–2354224550. https://doi.org/10.1073/pnas.1915312116

Zhang, K., Kuraparthy, V., & Fang, H. (2019). High-density linkage map construction and QTL analyses for fiber quality, yield and morphological traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.). BMC Genomics, 20(889). https://doi.org/10.1186/s12864-019-6214-z

Janga, M. R., Pandeya, D., Campbell, L. M., Konganti, K., Villafuerte, S. T., Puckhaber, L., Pepper, A., Stipanovic, R. D., Scheffler, J. A., & Rathore, K. S. (2018). Genes regulating gland development in the cotton plant. Plant Biotechnology Journal. https://doi.org/10/gft2nc

Furuya, S., Cichocki, J. A., Konganti, K., Dreval, K., Uehara, T., Katou, Y., Fukushima, H., Kono, H., Pogribny, I. P., Argemi, J., Bataller, R., & Rusyn, I. (2018). Histopathological and Molecular Signatures of a Mouse Model of Acute-on-Chronic Alcoholic Liver Injury Demonstrate Concordance With Human Alcoholic Hepatitis. Toxicological Sciences. https://doi.org/10/gft2m9

Grady, S. T., Watts, A. E., Thompson, J. A., Penedo, M. C. T., Konganti, K., & Hinrichs, K. (2018). Effect of intra-ovarian injection of mesenchymal stem cells in aged mares. Journal of Assisted Reproduction and Genetics. https://doi.org/10/gft2nb

Konganti, K., Ehrlich, A., Rusyn, I., & Threadgill, D. W. (2018). gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population. G3&#58; Genes|Genomes|Genetics, g3.200230.2018. https://doi.org/10/gd2zzm

Garbutt, T. A., Konneker, T. I., Konganti, K., Hillhouse, A. E., Swift-Haire, F., Jones, A., Phelps, D., Aylor, D. L., & Threadgill, D. W. (2018). Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus. Scientific Reports, 8(1). https://doi.org/10/gft2nd

Venkatratnam, A., House, J. S., Konganti, K., McKenney, C., Threadgill, D. W., Chiu, W. A., Aylor, D. L., Wright, F. A., & Rusyn, I. (2018). Population-based dose–response analysis of liver transcriptional response to trichloroethylene in mouse. Mammalian Genome, 1–14. https://doi.org/10/gc7wsh

Mahan, A. L., Murray, S. C., & Klein, P. E. (2018). Four-Parent Maize (FPM) Population: Development and Phenotypic Characterization. Crop Science, 58(3), 1106–1117. https://doi.org/10/gd2zzp

Lightfoot, J. T., De Geus, E. J., Booth, F. W., Bray, M. S., Den Hoed, M., Kaprio, J., Kelly, S. A., Pomp, D., Saul, M. C., & Thomis, M. A. (2018). Biological/genetic regulation of physical activity level: consensus from GenBioPAC. Medicine & Science in Sports & Exercise, 50(4), 863–873. https://doi.org/10/gc9x9k Download Download

Barrington, W. T., Wulfridge, P., Wells, A. E., Rojas, C. M., Howe, S. Y., Perry, A., Hua, K., Pellizzon, M. A., Hansen, K. D., & Voy, B. H. (2018). Improving metabolic health through precision dietetics in mice. Genetics, 208(1), 399–417. https://doi.org/10/gcs3f2

Beytebiere, J. R., Trott, A. J., Greenwell, B., Osborne, C. A., Vitet, H. M., Spence, J., Yoo, S.-H., Chen, Z., Takahashi, J. S., & Ghaffari, N. (2018). Tissue-specific BMAL1 cistromes reveal that enhancer-enhancer interactions regulate rhythmic transcription. BioRxiv, 319319. https://doi.org/10/gd2zzr Download

Trott, A. J., & Menet, J. S. (2018). Regulation of circadian clock transcriptional output by CLOCK: BMAL1. PLoS Genetics, 14(1), e1007156. https://doi.org/10/gcs7d2

Rogovskyy, A. S., Lawhon, S., Kuczmanski, K., Gillis, D. C., Wu, J., Hurley, H., Rogovska, Y. V., Konganti, K., Yang, C.-Y., & Duncan, K. (2018). Phenotypic and genotypic characteristics of Trueperella pyogenes isolated from ruminants. Journal of Veterinary Diagnostic Investigation, 30(3), 348–353. https://doi.org/10/gdkq48

McQueen, C. M., Schmitt, E. E., Sarkar, T. R., Elswood, J., Metz, R. P., Earnest, D., Rijnkels, M., & Porter, W. W. (2018). PER2 regulation of mammary gland development. Development, 145(6), dev157966. https://doi.org/10/gc87nk

Konganti, K., Guerrero, F. D., Schilkey, F., Ngam, P., Jacobi, J. L., Umale, P. E., de Leon, A. A. P., & Threadgill, D. W. (2018). A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination. G3: Genes, Genomes, Genetics, 8(5), 1675–1686. https://doi.org/10/gd2zzn

Lee, M. O., Dobson, L., Davis, B. W., Skow, L., Derr, J., & Womack, J. E. (2018). Genomic Structure and Tissue Expression of the NK-lysin Gene Family in Bison. Journal of Heredity. https://doi.org/10/gdwzpb

Hillman, P. R., Christian, S. G., Doan, R., Cohen, N. D., Konganti, K., Douglas, K., Wang, X., Samollow, P. B., & Dindot, S. V. (2017). Genomic imprinting does not reduce the dosage of UBE3A in neurons. Epigenetics & Chromatin, 10(1), 27. https://doi.org/10/f967mn

Cichocki, J. A., Furuya, S., Konganti, K., Luo, Y.-S., McDonald, T. J., Iwata, Y., Chiu, W. A., Threadgill, D. W., Pogribny, I. P., & Rusyn, I. (2017). Impact of nonalcoholic fatty liver disease on toxicokinetics of tetrachloroethylene in mice. Journal of Pharmacology and Experimental Therapeutics, 361(1), 17–28. https://doi.org/10/f9459s

Venkatratnam, A., Furuya, S., Kosyk, O., Gold, A., Bodnar, W., Konganti, K., Threadgill, D. W., Gillespie, K. M., Aylor, D. L., Wright, F. A., & others. (2017). Editor’s Highlight: Collaborative Cross Mouse Population Enables Refinements to Characterization of the Variability in Toxicokinetics of Trichloroethylene and Provides Genetic Evidence for the Role of PPAR Pathway in Its Oxidative Metabolism. Toxicological Sciences, 158(1), 48–62. https://doi.org/10/gbqbh4

Triff, K., McLean, M. W., Konganti, K., Pang, J., Callaway, E., Zhou, B., Ivanov, I., & Chapkin, R. S. (2017). Assessment of histone tail modifications and transcriptional profiling during colon cancer progression reveals a global decrease in H3K4me3 activity. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1863(6), 1392–1402. https://doi.org/10/gbm8nx

Sze, S.-H., Pimsler, M. L., Tomberlin, J. K., Jones, C. D., & Tarone, A. M. (2017). A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics, 18(4), 387. https://doi.org/10/gd2z2b

Cichocki, J. A., Furuya, S., Luo, Y.-S., Iwata, Y., Konganti, K., Chiu, W. A., Threadgill, D. W., Pogribny, I. P., & Rusyn, I. (2017). Nonalcoholic fatty liver disease is a susceptibility factor for perchloroethylene-induced liver effects in mice. Toxicological Sciences, 159(1), 102–113. https://doi.org/10/gd2zzq

Guada, M., Ganugula, R., Vadhanam, M., & Kumar, M. N. R. (2017). Urolithin A mitigates cisplatin-induced nephrotoxicity by inhibiting renal inflammation and apoptosis in an experimental rat model. Journal of Pharmacology and Experimental Therapeutics, 363(1), 58–65. https://doi.org/10/gbzzdx

Johnson, J. S., Chhetri, P. K., Krutovsky, K. V., & Cairns, D. M. (2017). Growth and Its Relationship to Individual Genetic Diversity of Mountain Hemlock (Tsuga mertensiana) at Alpine Treeline in Alaska: Combining Dendrochronology and Genomics. Forests, 8(11), 418. https://doi.org/10/gcqhjs

Johnson, J. S., Gaddis, K. D., Cairns, D. M., Konganti, K., & Krutovsky, K. V. (2017). Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change. American Journal of Botany, 104(3), 439–450. https://doi.org/10/f928sv Download