Genetic, Genomic and Network Biology
Genetic, Genomic and Network Biology - GGNB
Research using model organisms to study physiology in health and disease; quantitative, systems-based approaches to gain insight into the molecular, cellular and biochemical networks that underlie biological phenomena.
Faculty
Hubert Amrein, PhD
amrein@tamu.edu | 979.436.0799 | Office: MREB-II, 1348, Bryan Campus
Research Interest
Internal Nutrient Sensing; Brain-Gut Axis; Glucose Metabolism
Graduate Program Affiliation
- Medical Science PhD Program
- Interdisciplinary Graduate Program in Genetics
- Texas A&M University Institute for Neuroscience
Publications
- Miyamoto T, Amrein H. Neuronal Gluconeogenesis Regulates Systemic Glucose Homeostasis in Drosophila melanogaster. Curr Biol. 2019;29(8):1263-1272.e5. doi:10.1016/j.cub.2019.02.053
- Miyamoto T, Wright G, Amrein H. Nutrient sensors. Curr Biol. 2013;23(9):R369-R373. doi:10.1016/j.cub.2013.04.002
- Miyamoto T, Slone J, Song X, Amrein H. A fructose receptor functions as a nutrient sensor in the Drosophila brain. Cell. 2012;151(5):1113-1125. doi:10.1016/j.cell.2012.10.024
Helene Andrews-Polymenis, DVM, PhD
handrews@tamu.edu | 979.436.0340 | Office: MREB, 3008, Bryan Campus
Research Interest
Bacterial genetics and genomics, genetics of bacterial pathogens
Graduate Program Affiliation
Publications
- Elfenbein JR, Endicott-Yazdani T, Porwollik S, et al. Novel determinants of intestinal colonization of Salmonella enterica serotype typhimurium identified in bovine enteric infection. Infect Immun. 2013;81(11):4311-4320. doi:10.1128/IAI.00874-13
- Yang HJ, Bogomolnaya LM, Elfenbein JR, et al. Novel Two-Step Hierarchical Screening of Mutant Pools Reveals Mutants under Selection in Chicks. Infect Immun. 2016;84(4):1226-1238. Published 2016 Mar 24. doi:10.1128/IAI.01525-15
- Porwollik S, Santiviago CA, Cheng P, et al. Defined single-gene and multi-gene deletion mutant collections in Salmonella enterica sv Typhimurium. PLoS One. 2014;9(7):e99820. Published 2014 Jul 9. doi:10.1371/journal.pone.0099820
Vytas Bankaitis, PhD
vytas@tamu.edu | 979.436.0757 | Office: REYNOLDS 116 | Bryan Campus
Research Interest
Molecular & developmental genetics, lipid signaling, cancer biology, autism, chemical genetics
Graduate Program Affiliation
- Interdiscipilinary Graduate Program in Genetics
- Doctoral Program in Biochemistry and Biophysics
- Graduate Program in Chemistry
Publications
- Nile AH, Tripathi A, Yuan P, et al. PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nat Chem Biol. 2014;10(1):76-84. doi:10.1038/nchembio.1389
- Roy KR, Smith JD, Vonesch SC, et al. Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol. 2018;36(6):512-520. doi:10.1038/nbt.4137
- Wang Y, Yuan P, Grabon A, et al. Noncanonical regulation of phosphatidylserine metabolism by a Sec14-like protein and a lipid kinase. J Cell Biol. 2020;219(5):e201907128. doi:10.1083/jcb.201907128
Jeffrey Cirillo, PhD
jdcirillo@tamu.edu | 979.436.0343 | Office: MREB II | Bryan Campus
Research Interest
Susceptibility, resistance and protection network analyses
Graduate Program Affiliation
Publications
- DiNardo AR, Rajapakshe K, Nishiguchi T, et al. DNA hypermethylation during tuberculosis dampens host immune responsiveness. J Clin Invest. 2020;130(6):3113-3123. doi:10.1172/JCI134622
- DiNardo AR, Mace EM, Lesteberg K, et al. Schistosome Soluble Egg Antigen Decreases Mycobacterium tuberculosis-Specific CD4+ T-Cell Effector Function With Concomitant Arrest of Macrophage Phago-Lysosome Maturation. J Infect Dis. 2016;214(3):479-488. doi:10.1093/infdis/jiw156
- Christensen LM, Sule P, Cirillo SLG, et al. Legionnaires' Disease Mortality in Guinea Pigs Involves the p45 Mobile Genomic Element. J Infect Dis. 2019;220(10):1700-1710. doi:10.1093/infdis/jiz340
Shaunna Clark, PhD
slclark@tamu.edu | 979.436.0179 | Office: CB-1, 1410 | Bryan Campus
Research Interest
Genetic and epigenetic basis of addiction; Bioinformatics and software development
Graduate Program Affiliation
Publications
- Clark SL, Hattab MW, Chan RF, et al. A methylation study of long-term depression risk. Mol Psychiatry. 2020;25(6):1334-1343. doi:10.1038/s41380-019-0516-z
- Clark SL, Costin BN, Chan RF, et al. A Whole Methylome Study of Ethanol Exposure in Brain and Blood: An Exploration of the Utility of Peripheral Blood as Proxy Tissue for Brain in Alcohol Methylation Studies. Alcohol Clin Exp Res. 2018;42(12):2360-2368. doi:10.1111/acer.13905
- Clark SL, Aberg KA, Nerella S, et al. Combined Whole Methylome and Genomewide Association Study Implicates CNTN4 in Alcohol Use. Alcohol Clin Exp Res. 2015;39(8):1396-1405. doi:10.1111/acer.12790
John Hettema, MD, PhD
hettema@tamu.edu | 804.516.3276 | Bryan Campus
Research Interest
Psychiatric Genetic Association Studies
Graduate Program Affiliation
Publications
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Otowa T, Hek K, Lee M, et al. Meta-analysis of genome-wide association studies of anxiety disorders [published correction appears in Mol Psychiatry. 2016 Oct;21(10):1485]. Mol Psychiatry. 2016;21(10):1391-1399. doi:10.1038/mp.2015.197
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Hettema JM, Verhulst B, Chatzinakos C, et al. Genome-wide association study of shared liability to anxiety disorders in Army STARRS. Am J Med Genet B Neuropsychiatr Genet. 2020;183(4):197-207. doi:10.1002/ajmg.b.32776
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Purves KL, Coleman JRI, Meier SM, et al. A major role for common genetic variation in anxiety disorders [published online ahead of print, 2019 Nov 20]. Mol Psychiatry. 2019;10.1038/s41380-019-0559-1. doi:10.1038/s41380-019-0559-1
Yun Huang, PhD
yun.huang@tamu.edu | 713.677.7484 | Houston Campus
Research Interest
Epigenomic data analysis
Publications
- Li J, Wu X, Zhou Y, et al. Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC. Nucleic Acids Res. 2018;46(6):2883-2900. doi:10.1093/nar/gky063
- Lee M, Li J, Liang Y, et al. Engineered Split-TET2 Enzyme for Inducible Epigenetic Remodeling. J Am Chem Soc. 2017;139(13):4659-4662. doi:10.1021/jacs.7b01459
- Zhang X, Su J, Jeong M, et al. DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. Nat Genet. 2016;48(9):1014-1023. doi:10.1038/ng.3610
Jenny Hyde, PhD
jhyde@tamu.edu | 979.436.0872 | Office: MREB, 3002 | Bryan Campus
Research Interest
Genetic mechanisms utilized by Borrelia burgdorferi
Graduate Program Affiliation
Publications
- Ramsey ME, Hyde JA, Medina-Perez DN, et al. A high-throughput genetic screen identifies previously uncharacterized Borrelia burgdorferi genes important for resistance against reactive oxygen and nitrogen species. PLoS Pathog. 2017;13(2):e1006225. Published 2017 Feb 17. doi:10.1371/journal.ppat.1006225
- Hyde JA, Trzeciakowski JP, Skare JT. Borrelia burgdorferi alters its gene expression and antigenic profile in response to CO2 levels. J Bacteriol. 2007;189(2):437-445. doi:10.1128/JB.01109-06
- Hyde JA, Seshu J, Skare JT. Transcriptional profiling of Borrelia burgdorferi containing a unique bosR allele identifies a putative oxidative stress regulon. Microbiology. 2006;152(Pt 9):2599-2609. doi:10.1099/mic.0.28996-0
Jun-yuan Ji, PhD
ji@tamu.edu | 979.436.0796 | Office: MREB-II, | Bryan Campus
Research Interest
Developmental genetics
Graduate Program Affiliation
- Interdisciplinary Graduate Program in Genetics
- Texas A&M University Interdisciplinary Faculty of Toxicology
Publications
- Xie XJ, Hsu FN, Gao X, et al. CDK8-Cyclin C Mediates Nutritional Regulation of Developmental Transitions through the Ecdysone Receptor in Drosophila [published correction appears in PLoS Biol. 2015 Aug;13(8):e1002250]. PLoS Biol. 2015;13(7):e1002207. Published 2015 Jul 29. doi:10.1371/journal.pbio.1002207
Jason Karpac, PhD
karpac@tamu.edu | 979.436.0767 | Office: MREB-II, 4342 | Bryan Campus
Research Interest
Functional and integrative genetics/genomics using Drosophila
Graduate Program Affiliation
- Medical Science PhD Program
- Interdisciplinary Graduate Program in Genetics
- Biomedical Sciences Graduate Program
Publications
- Zhao X, Karpac J. Muscle Directs Diurnal Energy Homeostasis through a Myokine-Dependent Hormone Module in Drosophila. Curr Biol. 2017;27(13):1941-1955.e6. doi:10.1016/j.cub.2017.06.004
- Zhao X, Li X, Shi X, Karpac J. Diet-MEF2 interactions shape lipid droplet diversification in muscle to influence Drosophila lifespan. Aging Cell. 2020;19(7):10.1111/acel.13172. doi:10.1111/acel.13172
- Mlih M, Khericha M, Birdwell C, West AP, Karpac J. A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis. PLoS Biol. 2018;16(7):e2005796. Published 2018 Jul 23. doi:10.1371/journal.pbio.2005796
Julian Leibowitz, MD, PhD
jleibowitz@tamu.edu | 979.436.0313 | Office: MREB-II, 3224C | Bryan Campus
Research Interest
The role of various coronavirus and host genes in coronavirus replication and pathogenesis
Graduate Program Affiliation
- Medical Science PhD Program
- Interdisciplinary Graduate Program in Genetics
- Texas A&M University Institute for Neuroscience
Publications
- Parr RL, Fung L, Reneker J, Myers-Mason N, Leibowitz JL, Levy G. Association of mouse fibrinogen-like protein with murine hepatitis virus-induced prothrombinase activity. J Virol. 1995;69(8):5033-5038. doi:10.1128/JVI.69.8.5033-5038.1995
- Yang D, Leibowitz JL. The structure and functions of coronavirus genomic 3' and 5' ends. Virus Res. 2015;206:120-133. doi:10.1016/j.virusres.2015.02.025
- Leibowitz JL, Srinivasa R, Williamson ST, et al. Genetic determinants of mouse hepatitis virus strain 1 pneumovirulence. J Virol. 2010;84(18):9278-9291. doi:10.1128/JVI.00330-10
Alistair McGregor, PhD
mcgalistair2013@tamu.edu | 979.436.9400 | Office: MREB-II, 3348 |Bryan Campus
Research Interest
Cytomegalovirus (CMV) viral genome and cellular response for virus tropism and congenital infection
Graduate Program Affiliation
Publications
- Coleman S, Choi KY, Root M, McGregor A. A Homolog Pentameric Complex Dictates Viral Epithelial Tropism, Pathogenicity and Congenital Infection Rate in Guinea Pig Cytomegalovirus. PLoS Pathog. 2016;12(7):e1005755. Published 2016 Jul 7. doi:10.1371/journal.ppat.1005755
- Choi KY, El-Hamdi NS, McGregor A. Requirements for guinea pig cytomegalovirus tropism and antibody neutralization on placental amniotic sac cells. J Gen Virol. 2020;101(4):426-439. doi:10.1099/jgv.0.001394
- Coleman S, Choi KY, McGregor A. Cytomegalovirus UL128 homolog mutants that form a pentameric complex produce virus with impaired epithelial and trophoblast cell tropism and altered pathogenicity in the guinea pig. Virology. 2017;509:205-221. doi:10.1016/j.virol.2017.06.008
Kristin Patrick, PhD
kpatrick03@tamu.edu | 979.436.0354 | Office: MREB, 3102 | Bryan Campus
Research Interest
Global regulation of pre-mRNA splicing and systems biology of host-pathogen interactions
Graduate Program Affiliation
Publications
- West KO, Scott HM, Torres-Odio S, West AP, Patrick KL, Watson RO. The Splicing Factor hnRNP M Is a Critical Regulator of Innate Immune Gene Expression in Macrophages. Cell Rep. 2019;29(6):1594-1609.e5. doi:10.1016/j.celrep.2019.09.078
- Patrick KL, Wojcechowskyj JA, Bell SL, et al. Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Cell Syst. 2018;7(3):323-338.e6. doi:10.1016/j.cels.2018.06.010
- Patrick KL, Ryan CJ, Xu J, et al. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. PLoS Genet. 2015;11(3):e1005074. Published 2015 Mar 31. doi:10.1371/journal.pgen.1005074
Samba Reddy, PhD, RPh, FAAPS, FAAAS
sambareddy@tamu.edu | 919.539.8721 | Office: MREB, 2008 | Bryan Campus
Research Interest
Epigenetics
Graduate Program Affiliation
Dave Reiner, PhD
dreiner@tamu.edu | 713.677.7416 | Office: ALKEK, 916 | Houston Campus
Research Interest
Genome editing, CRISPR, penetrance
Graduate Program Affiliation
Publications
- Dickinson DJ, Ward JD, Reiner DJ, Goldstein B. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods. 2013;10(10):1028-1034. doi:10.1038/nmeth.2641
Irtisha Singh, PhD
isingh@tamu.edu | 646.574.2080 | Office: MREB-II |Bryan Campus
Research Interest
Gene regulation, transcription factors
Graduate Program Affiliation
- Medical Science PhD Program
- Interdisciplinary Graduate Program in Genetics
- Texas A&M University Institute for Neuroscience
Publications
- Singh I, Lee SH, Sperling AS, et al. Widespread intronic polyadenylation diversifies immune cell transcriptomes. Nat Commun. 2018;9(1):1716. Published 2018 Apr 30. doi:10.1038/s41467-018-04112-z
- Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Affinity regression predicts the recognition code of nucleic acid-binding proteins. Nat Biotechnol. 2015;33(12):1242-1249. doi:10.1038/nbt.3343
- Han YC, Vidigal JA, Mu P, et al. An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron. Nat Genet. 2015;47(7):766-775. doi:10.1038/ng.3321
Raquel Sitcheran, PhD
sitcheran@tamu.edu | 979.436.0749 | Office: MREB-II, 4348 | Bryan Campus
Research Interest
Genetic approaches to study NF-κB regulatory proteins in metabolism, development and cancer
Graduate Program Affiliation
- Medical Science PhD Program
- Interdisciplinary Graduate Program in Genetics
- Texas A&M University Institute for Neuroscience
Publications
- Jung JU, Ravi S, Lee DW, et al. NIK/MAP3K14 Regulates Mitochondrial Dynamics and Trafficking to Promote Cell Invasion. Curr Biol. 2016;26(24):3288-3302. doi:10.1016/j.cub.2016.10.009
- Duran CL, Lee DW, Jung JU, et al. NIK regulates MT1-MMP activity and promotes glioma cell invasion independently of the canonical NF-κB pathway. Oncogenesis. 2016;5(6):e231. Published 2016 Jun 6. doi:10.1038/oncsis.2016.39
- Cherry EM, Lee DW, Jung JU, Sitcheran R. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) promotes glioma cell invasion through induction of NF-κB-inducing kinase (NIK) and noncanonical NF-κB signaling. Mol Cancer. 2015;14(1):9. Published 2015 Jan 27. doi:10.1186/s12943-014-0273-1
Jon Skare, PhD
jskare@tamu.edu | 979.436.0353 | Office: MREB, 3004 |Bryan Campus
Research Interest
Transcriptomic and proteomic analysis of Lyme disease spirochetes; emphasis on regulatory schemes
Graduate Program Affiliation
Publications
- Medina-Pérez DN, Wager B, Troy E, et al. The intergenic small non-coding RNA ittA is required for optimal infectivity and tissue tropism in Borrelia burgdorferi. PLoS Pathog. 2020;16(5):e1008423. Published 2020 May 4. doi:10.1371/journal.ppat.1008423
- Phelan JP, Kern A, Ramsey ME, et al. Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector. PLoS Pathog. 2019;15(5):e1007644. Published 2019 May 14. doi:10.1371/journal.ppat.1007644
- Ramsey ME, Hyde JA, Medina-Perez DN, et al. A high-throughput genetic screen identifies previously uncharacterized Borrelia burgdorferi genes important for resistance against reactive oxygen and nitrogen species. PLoS Pathog. 2017;13(2):e1006225. Published 2017 Feb 17. doi:10.1371/journal.ppat.1006225
Brad Verhulst
verhulst@tamu.edu | 979.436.9163 | Office: CB1, 1121| Bryan Campus
Research Interest
Analysis of human genetic data for psychiatric disorders
Publications
- Verhulst B, Maes HH, Neale MC. GW-SEM: A Statistical Package to Conduct Genome-Wide Structural Equation Modeling. Behav Genet. 2017;47(3):345-359. doi:10.1007/s10519-017-9842-6
- Verhulst B, Neale MC, Kendler KS. The heritability of alcohol use disorders: a meta-analysis of twin and adoption studies. Psychol Med. 2015;45(5):1061-1072. doi:10.1017/S0033291714002165
- Hettema JM, Verhulst B, Chatzinakos C, et al. Genome-wide association study of shared liability to anxiety disorders in Army STARRS. Am J Med Genet B Neuropsychiatr Genet. 2020;183(4):197-207. doi:10.1002/ajmg.b.32776
Jun Wang, PhD
jwang188@tamu.edu | 979.436.0389 | Office: MREB, 2106 |Bryan Campus.
Research Interest
Optogenetics, chemognetics, viral genetics
Graduate Program Affiliation
- Medical Science PhD Program
- Texas A&M University Institute for Neuroscience
- Texas A&M University Interdisciplinary Faculty of Toxicology
Publications
- Roltsch Hellard E, Binette A, Zhuang X, et al. Optogenetic control of alcohol-seeking behavior via the dorsomedial striatal circuit. Neuropharmacology. 2019;155:89-97. doi:10.1016/j.neuropharm.2019.05.022
- Cheng Y, Huang CCY, Ma T, et al. Distinct Synaptic Strengthening of the Striatal Direct and Indirect Pathways Drives Alcohol Consumption. Biol Psychiatry. 2017;81(11):918-929. doi:10.1016/j.biopsych.2016.05.016
- Lu J, Cheng Y, Wang X, et al. Alcohol intake enhances glutamatergic transmission from D2 receptor-expressing afferents onto D1 receptor-expressing medium spiny neurons in the dorsomedial striatum. Neuropsychopharmacology. 2019;44(6):1123-1131. doi:10.1038/s41386-019-0332-9
Robert Watson, PhD, MPH
robert.watson@tamu.edu | 979.436.0342 | Office: MREB, 3100|Bryan Campus.
Research Interest
Genetic factors that alter susceptibility to intracellular bacterial infection
Graduate Program Affiliation
Publications
- Weindel CG, Bell SL, Vail KJ, West KO, Patrick KL, Watson RO. LRRK2 maintains mitochondrial homeostasis and regulates innate immune responses to Mycobacterium tuberculosis. Elife. 2020;9:e51071. Published 2020 Feb 14. doi:10.7554/eLife.51071
- Patrick KL, Wojcechowskyj JA, Bell SL, et al. Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Cell Syst. 2018;7(3):323-338.e6. doi:10.1016/j.cels.2018.06.010
Keith Young, PhD
kayoung@tamu.edu | 254.760.5568 | Office: MREB-II, 2310|Bryan Campus
Research Interest
Spatial transcriptomics, single cell sequencing, blood and brain genomics
Graduate Program Affiliation
Publications
- Nievergelt, C.M., Maihofer, A.X., Klengel, T. et al.International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci. Nat Commun 10, 4558 (2019).
Keywords: gene regulation, developmental genetics, bioinformatics, microbial and viral genetics, cancer genetics, epigenetics, polymorphism, multi genetic inheritance, mutations