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

Research Interest

Internal Nutrient Sensing; Brain-Gut Axis; Glucose Metabolism

Graduate Program Affiliation

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

Complete Bibliography

Helene Andrews-Polymenis, DVM, PhD

handrews@tamu.edu | 979.436.0340 | Office: MREB, 3008

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

Complete Bibliography

Vytas Bankaitis, PhD

vytas@tamu.edu | 979.436.0757 | Office: REYNOLDS, 116

Research Interest

Molecular & developmental genetics, lipid signaling, cancer biology, autism, chemical genetics

Graduate Program Affiliation

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

Complete Bibliography

Jeffrey Cirillo, PhD

jdcirillo@tamu.edu | 979.436.0343 | Office: MREB II

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

Complete Bibliography

Shaunna Clark, PhD

slclark@tamu.edu | 979.436.0179 | Office: CB-1, 1410

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

Complete Bibliography

John Hettema, MD, PhD

hettema@tamu.edu | 804.516.3276

Research Interest

Psychiatric Genetic Association Studies

Graduate Program Affiliation

Publications

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
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
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

Complete Bibliography

Yun Huang, PhD

yun.huang@tamu.edu | 713.677.7484

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

Complete Bibliography

Jenny Hyde, PhD

jhyde@tamu.edu | 979.436.0872 | Office: MREB, 3002

Research Interest

Genetic mechanisms utilized by Borrelia burgdorferi

Graduate Program Affiliation

Interdisciplinary Graduate Program in Genetics

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

Complete Bibliography

Jun-yuan Ji, PhD

ji@tamu.edu | 979.436.0796 | Office: MREB-II

Research Interest

Developmental genetics

Graduate Program Affiliation

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

Complete Bibliography

Jason Karpac, PhD

karpac@tamu.edu | 979.436.0767 | Office: MREB-II, 4342

Research Interest

Functional and integrative genetics/genomics using Drosophila

Graduate Program Affiliation

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

Complete Bibliography

Julian Leibowitz, MD, PhD

jleibowitz@tamu.edu | 979.436.0313 | Office: MREB-II, 3224C

Research Interest

The role of various coronavirus and host genes in coronavirus replication and pathogenesis

Graduate Program Affiliation

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

Complete Bibliography

Alistair McGregor, PhD

mcgalistair2013@tamu.edu | 979.436.9400 | Office: MREB-II, 3348

Research Interest

Cytomegalovirus (CMV) viral genome and cellular response for virus tropism and congenital infection

Graduate Program Affiliation

Medical Science PhD Program

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

Complete Bibliography

Kristin Patrick, PhD

kpatrick03@tamu.edu | 979.436.0354 | Office: MREB, 3102

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

Complete Bibliography

Samba Reddy, PhD, RPh, FAAPS, FAAAS

sambareddy@tamu.edu | 919.539.8721 | Office: MREB, 2008

Research Interest

Epigenetics

Graduate Program Affiliation

Complete Bibliography

Dave Reiner, PhD

dreiner@tamu.edu | 713.677.7416 | Office: ALKEK, 916

Research Interest

Genome editing, CRISPR, penetrance

Graduate Program Affiliation

Medical Science PhD Program

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

Complete Bibliography

Irtisha Singh, PhD

isingh@tamu.edu | 646.574.2080 | Office: MREB-II

Research Interest

Gene regulation, transcription factors

Graduate Program Affiliation

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

Complete Bibliography

Raquel Sitcheran, PhD

sitcheran@tamu.edu | 979.436.0749 | Office: MREB-II, 4348

Research Interest

Genetic approaches to study NF-κB regulatory proteins in metabolism, development and cancer

Graduate Program Affiliation

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

Complete Bibliography

Jon Skare, PhD

jskare@tamu.edu | 979.436.0353 | Office: MREB, 3004

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

Complete Bibliography

Brad Verhulst

verhulst@tamu.edu | 979.436.9163 | Office: CB1, 1121

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

Complete Bibliography

Jun Wang, PhD

jwang188@tamu.edu | 979.436.0389 | Office: MREB, 2106

Research Interest

Optogenetics, chemognetics, viral genetics

Graduate Program Affiliation

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

Complete Bibliography

Robert Watson, PhD, MPH

robert.watson@tamu.edu | 979.436.0342 | Office: MREB, 3100

Research Interest

Genetic factors that alter susceptibility to intracellular bacterial infection

Graduate Program Affiliation

Interdisciplinary Graduate Program in Genetics

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

Complete Bibliography

Keith Young, PhD

kayoung@tamu.edu | 254.760.5568 | Office: MREB-II, 2310

Research Interest

Spatial transcriptomics, single cell sequencing, blood and brain genomics

Graduate Program Affiliation

Texas A&M University Institute for Neuroscience

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).

Complete Bibliography

Keywords: gene regulation, developmental genetics, bioinformatics, microbial and viral genetics, cancer genetics, epigenetics, polymorphism, multi genetic inheritance, mutations