Genomics Sequencing Center

Monson M.S., Settlage R.E., McMahon K.W., Mendoza K.M., Rawal S., El-Nezami H.S., Coulombe R.A., Reed K.M., Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo). PLoS One. 2014 Jun 30;9(6).

Dalloul R.A., Zimin A.V., Settlage R.E., Kim S., Reed K.M., Next-generation sequencing strategies for characterizing the turkey genome. Poult Sci. 2014 Feb;93(2):479-84.

Monson M.S., Settlage R.E., Mendoza K.M., Rawal S., El-Nezami H.S., Coulombe R.A., Reed K.M., Modulation of the spleen transcriptome in domestic turkey (Meleagris gallopavo) in response to aflatoxin B1 and probiotics. Immunogenetics. 2015 Mar;67(3):163-78.

Ding J, Reynolds LM, Zeller T, et al. Alterations of a Cellular Cholesterol Metabolism Network is a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. Diabetes. 2015; 64: 3464-74.

Liao X, Li S, Settlage RE, Sun S, Ren J, Reihl AM, Zhang H, Karyala SV, Reilly CM, Ahmed SA, Luo XM. (2015) Cutting Edge: Plasmacytoid Dendritic Cells in Late-Stage Lupus Mice Defective in Producing IFN-α. Journal of Immunology. 195:4578-4582.

Zhang H, Sparks JB, Karyala SV, Settlage R, Luo XM. (2014) Host adaptive immunity alters gut microbiota. ISME Journal 9(3):770-81.

Metch JW, Burrows ND, Murphy CJ,  Pruden A, Vikesland PJ. Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design. Nature. 2018

Reynolds LM, Ding J, Taylor JR, et al. Transcriptomic profiles of aging in purified human immune cells. BMC Genomics. 2015;16:333.  

Yi H, Breheny P, Imam N, Liu Y, Hoeschele I. Penalized multimarker vs. single-marker regression methods for genome-wide association studies of quantitative traits. Genetics. 2015; 199:205–222.

Liu Y, Ding J, Reynolds LM, et al. Methylomics of gene expression in human monocytes. Human Molecular Genetics. 2013:ddt356. 

Zhang H, Liao X, Sparks JB, Luo XM. (2014) Dynamics of gut microbiota in autoimmune lupus. Applied Environmental Microbiology 80(24):7551-60.

Mu Q, Zhang H, Luo XM (2015) SLE: Another Autoimmune Disorder Influenced by Microbes and Diet? Frontiers in Immunology doi: 10.3389/fimmu.2015.00608

Zhang H, Luo XM (2015) Control of commensal microbiota by the adaptive immune system. Gut Microbes 6(2):156-60.

Tae, H., Shallom, S., Settlage, R.E., Preston, D., Adams, L.G., Garner, H.R, Revised Genome Sequence of Brucella suis 1330. J. Bacteriology, 193(22), 2011, 6410.

Tae, H., Shallom, S., Settlage, R.E., Hawkins, G.N., Adams, L.G., Garner, H.R, Complete Genome Sequence of Brucella suis VBI22, Isolated from Bovine Milk. J. Bacteriology, 194(4), 2012, 910.

Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR. Genomics.  Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes. 2012 Nov;100(5):271-6.

Radakovits, R., Jinkerson, R.E., Fuerstenberg, S.I., Tae, H., Settlage, R.E., Boore, J.L., Posewitz, M.C, Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana, Nature Communications, 3:686, 2012.

Bavarva J.H., Tae H., Settlage R.E., Garner H.R., Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study. PLoS One. 2013 Jun 18;8(6):e67252.

Tae H., McMahon K.W., Settlage R.E., Bavarva J.H., Garner H.R., ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats. Bioinformatics. 2013 Jul 15;29(14):1734-41.

Zhang H., Wang H., Shepherd M., Wen K., Li G., Yang X., Kocher J., Giri-Rachman E., Dickerman A., Settlage R., Yuan L., Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs. Gut Pathog. 2014 Sep 9;6:39.

Jiang X., Peery A., Hall A.B., Sharma A., Chen X.G., Waterhouse R.M., Komissarov A., Riehle M.M., Shouche Y., Sharakhova M.V., Lawson D., Pakpour N., Arensburger P., Davidson V.L., Eiglmeier K., Emrich S., George P., Kennedy R.C., Mane S.P., Maslen G., Oringanje C., Qi Y., Settlage R., Tojo M., Tubio J.M., Unger M.F., Wang B., Vernick K.D., Ribeiro J.M., James A.A., Michel K., Riehle M.A., Luckhart S., Sharakhov I.V., Tu Z.., Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi. Genome Biol. 2014 Sep 23;15(9):459.

Zhang H., Sparks J.B., Karyala S.V., Settlage R., Luo X.M., Host adaptive immunity alters gut microbiota. ISME J. 2015 Mar;9(3):770-81.

Monson M.S., Settlage R.E., McMahon K.W., Mendoza K.M., Rawal S., El-Nezami H.S., Coulombe R.A., Reed K.M., Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo). PLoS One. 2014 Jun 30;9(6).

Dalloul R.A., Zimin A.V., Settlage R.E., Kim S., Reed K.M., Next-generation sequencing strategies for characterizing the turkey genome. Poult Sci. 2014 Feb;93(2):479-84.

Tae H., Kim D.Y., McCormick J., Settlage R.E., Garner H.R., Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs. Bioinformatics. 2014 Mar 1;30(5):652-9.

Monson M.S., Settlage R.E., Mendoza K.M., Rawal S., El-Nezami H.S., Coulombe R.A., Reed K.M., Modulation of the spleen transcriptome in domestic turkey (Meleagris gallopavo) in response to aflatoxin B1 and probiotics. Immunogenetics. 2015 Mar;67(3):163-78.

Zhang W., Kim S., Settlage R., McMahon W., Sumners L.H., Siegel P.B., Dorshorst B.J., Cline M.A., Gilbert E.R., Hypothalamic differences in expression of genes involved in monoamine synthesis and signaling pathways after insulin injection in chickens from lines selected for high and low body weight. Neurogenetics. 2015 Apr;16(2):133-44.

Zalenskaya I.A., Joseph T., Bavarva J., Yousefieh N., Jackson S.S., Fashemi T., Yamamoto H.S., Settlage R., Fichorova R.N., Doncel G.F., Gene Expression Profiling of Human Vaginal Cells In Vitro Discriminates Compounds with Pro-Inflammatory and Mucosa-Altering Properties: Novel Biomarkers for Preclinical Testing of HIV Microbicide Candidates. PLoS One. 2015 Jun 8;10(6).

Ding J, Reynolds LM, Zeller T, Müller C, Lohman K, Nicklas BJ, Kritchevsky SB, Huang Z, de la Fuente A, Soranzo N, Settlage RE, Chuang CC, Howard T, Xu N, Goodarzi MO, Chen YD, Rotter JI, Siscovick DS, Parks JS, Murphy S, Jacobs DR Jr, Post W, et al. Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. Diabetes. 2015 Oct;64(10):3464-74.

Hendrickson RC, Lee AY, Song Q, Liaw A, Wiener M, Paweletz CP, Seeburger JL, Li J, Meng F, Deyanova EG, Mazur MT, Settlage RE, Zhao X, Southwick K, Du Y, Holder  D, Sachs JR, Laterza OF, Dallob A, Chappell DL, Snyder K, Modur V, et al. High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of  Alzheimer's Disease in Human Cerebrospinal Fluid. PLoS One. 2015;10(8):e0135365.

Davis M, Jessee R, Close M, Fu X, Settlage R, Wang G, Cline MA, Gilbert ER. Fasting for 21days leads to changes in adipose tissue and liver physiology in juvenile checkered garter snakes (Thamnophis marcianus). Comp Biochem Physiol A Mol Integr Physiol. 2015 Sep 7;190:68-74. doi: 10.1016/j.cbpa.2015.09.001. [Epub ahead of print] PubMed [citation] PMID: 26358832

Liao X, Li S, Settlage RE, Sun S, Ren J, Reihl AM, Zhang H, Karyala SV, Reilly CM, Ahmed SA, Luo XM. Cutting Edge: Plasmacytoid Dendritic Cells in Late-Stage Lupus Mice Defective in Producing IFN-α.  J Immunol. 2015 Nov 15;195(10):4578-82. doi: 10.4049/jimmunol.1501157. Epub 2015 Oct 7.

Wang Z, Leary DH, Liu J, Settlage RE, Fears KP, North SH, Mostaghim A, Essock-Burns T, Haynes SE, Wahl KJ, Spillmann CM.  Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite.  BMC Genomics. 2015 Oct 24;16(1):859. doi: 10.1186/s12864-015-2076-1.

Zhan S, Merlin C, Boore JL, Reppert SM. The monarch butterfly genome yields insights into long-distance migration. Cell. 2011;147(5):1171–85.

Kang L., Settlage R., McMahon W., Michalak K., Tae H., Garner H.R., Stacy E., Price D. & Michalak P. 2015. Genomic signatures of speciation in sympatric and allopatric Hawaiian picture-winged Drosophila. Genome Biology, under revision.

Michalak K., Maciak S., Kim Y.B., Santopietro G., Oh J.H., Kang L., Garner H.R., & Michalak P. 20015. Nucleolar dominance and maternal control of 45S rDNA expression Proceedings of the Royal Society B: Biological Sciences, in press.

Philipson C.W., Bassaganya-Riera J., Viladomiu M., Kronsteiner B., Abedi V., Hoops S., Michalak P., Kang L., Girardin S.E. & Hontecillas R. 2015. Modeling the regulatory mechanisms by which NLRX1 modulates innate immune responses to Helicobacter pylori infection. PLoS One 10(9):e0137839.

Mechkarska M., Coquet L., Leprince J., Jouenne T., Vaudry H., Michalak K., Michalak P. &Conlon JM. 2014. Host-defense peptides from skin secretions of the octoploid frogs Xenopus vestitus and Xenopus wittei (Pipidae): Insights into evolutionary relationships. Comparative Biochemistry and Physiology – Part D Genomics Proteomics 11C: 20-28.

Kim Y.B., Oh J.H., McIver L.J., Rashkovetsky E., Michalak K., Garner H.R., Kang L., Nevo E., Korol A.B. & Michalak P. 2014. Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in ‘Evolution Canyon’, Israel. Proceedings of the National Academy of Sciences USA 111: 10630-10635.

Michalak K., Czesny S., Epifanio J., Snyder R.J., Schultz E.T., Velotta J.P., McCormick S.D., Brown B.L., Santopietro G., Michalak P. 2014. Beta-thymosin gene polymorphism associated with freshwater invasiveness of alewife (Alosa pseudoharengus). Journal of Experimental Zoology Part A: Ecological Genetics & Physiology 321: 233-240. [Cover]

Michalak P. 2014. Evidence for maternal imprinting of 45S ribosomal RNA genes in Xenopus hybrids. Development Genes & Evolution 224: 125-128.

Hübner S., Rashkovetsky E., Kim Y.B., Oh J.H., Michalak K., Weiner D., Korol A.B., Nevo E. & Michalak P. 2013. Genome differentiation of Drosophila melanogaster from a microclimate contrast in Evolution Canyon, Israel. Proceedings of the National Academy of Sciences USA 110: 21059-2164.

Viladomiu M., Hontecillas R., Pedragosa M., Michalak P., Michalak K., Guerrant R., Roche J., Warren C. & Bassaganya-Riera J. 2012. Modulation of immune responses to Clostridium difficile by peroxisome proliferator-activated receptor gamma and miRNA-146b. Journal of Immunology 2012, 188.

Zhang H, Wang H, Shepherd M, Wen K, Li G, et al. Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs. Gut Pathogens. 2014; 6:39.

Huang YW, Dickerman AW, Piñeyro P, Li L, Fang L, et al. Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States. mBio. 2013; 4(5):e00737-13.

Aulakh SS, Veilleux RE, Dickerman AW, Tang G, Flinn BS. Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. Plant Molecular Biology. 2014; 84(6):635-58.

Yuan L., Zhi. W., Karyala, S., Vikesland, P.J., Chen, X., Zhang, J. Lead toxicity to the performance, viability, and community composition of activated sludge microorganisms, Environ Sci Tech. 2015 Jan 20;49(2):824-30.

Cao, Z., Chen, C., He, B., Tan, K., & Lu, C. (2015). A microfluidic device for epigenomic profiling using 100 cells. Nature Methods. 2015 Oct;12(10):959-62

Stepherd, ML, Swecker, WS, Jensen, RV, Ponder, MA.  Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. FEMS Microbiol Lett. 2012, 326:62-8.

Holliday, JA,. Zhou, L. Bawa, R, Zhang, M, Oubida, RW., Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa. New Phytologist, 2015, doi: 10.1111/nph.13643. [Epub ahead of print].

Manrique-Carpintero, NC, Tokuhisa, JG, Ginzberg, I, Holliday, JA, Veilleux, RE.  Sequence diversity in coding regions of candidate genese in the glycoalkaloid biosynthetic pathway of wild potato species. G3, 2013, 3:1467-79.

Rodriques, RR, Pineda, RP, Barney, JN, Nilsen, ET., Barrett, JE, Williams, MA.  Plant invasions associated with change in root-zone microbial community structure and diversity. PLoS One, 2015 Oct 27;10(10):e0141424. doi: 10.1371/journal.pone.0141424. eCollection 2015.