Publications

2019

Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, et al. 2019. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol. 17(1):92.

Nieman DC, Simonson A, Sakaguchi CA, Sha W, Blevins T, Hattabaugh J, Kohlmeier M. 2019. Acute Ingestion of a Mixed Flavonoid and Caffeine Supplement Increases Energy Expenditure and Fat Oxidation in Adult Women: A Randomized, Crossover Clinical Trial. Nutrients. 11(11).

Curry JM, Besmer DM, Erick TK, Steuerwald N, Das Roy L, Grover P, Rao S, Nath S, Ferrier JW, Reid RW, Mukherjee P. 2019. Indomethacin enhances anti-tumor efficacy of a MUC1 peptide vaccine against breast cancer in MUC1 transgenic mice. PLoS ONE. 14(11):e0224309.

Lin JP, Tsai MH, Kroh A, Trautman A, Machado DJ, Chang LY, Reid R, Lin KT, Bronstein O, Lee SJ, Janies D. 2019. The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida). Genomics.

Trujillo-Gonzalez I, Friday WB, Munson CA, Bachleda A, Weiss ER, Alam NM, Sha W, Zeisel SH, Surzenko N. 2019. Low availability of choline in utero disrupts development and function of the retina. FASEB J. 33(8):9194-9209.

Nieman DC, Gillitt ND, Sha W. 2019. Identification of a select metabolite panel for measuring metabolic perturbation in response to heavy exertion. Metabolomics. 14(11):147.

2018

Jay JJ, Sanders A, Reid RW, Brouwer CR. 2018. Connecting nutrition composition measures to biomedical research. BMC Res Notes. 11(1):883.

Brunner Huber LR, Smith K, Sha W, Vick T. 2018. Interbirth Interval and Pregnancy Complications and Outcomes: Findings from the Pregnancy Risk Assessment Monitoring System. J Midwifery Womens Health. 63(4):436-445.

Jacob Machado D, Janies D, Brouwer C, Grant T. 2018. A new strategy to infer circularity applied to four new complete frog mitogenomes. Ecol Evol. 8(8):4011-4018.

Brunner Huber LR, Smith K, Sha W, Zhao L, Vick T. 2018. Factors associated with pregnancy intention among women who have experienced a short birth interval: findings from the 2009 to 2011 Mississippi and 2009 Tennessee Pregnancy Risk Assessment Monitoring System. Ann Epidemiol. 28(6):372-376.

Luo W, Zhang C, Jiang YH, Brouwer CR. 2018. Systematic reconstruction of autism biology from massive genetic mutation profiles. Sci Adv. 4(4):e1701799.

Nieman DC, Gillitt ND, Sha W, Esposito D, Ramamoorthy S. 2018. Metabolic recovery from heavy exertion following banana compared to sugar beverage or water only ingestion: A randomized, crossover trial. PLoS ONE. 13(3):e0194843.

2017

Ouellette LA, Reid RW, Blanchard SG, Brouwer CR. 2017. LinkageMapView - Rendering High Resolution Linkage and QTL Maps. Bioinformatics.

Winglee K, Howard AG, Sha W, Gharaibeh RZ, Liu J, Jin D, Fodor AA, Gordon-Larsen P. 2017. Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. Microbiome. 5(1):121.

Luo Y, Reid R, Freese D, Li C, Watkins J, Shi H, Zhang H, Loraine A, Song BH. 2017. Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato. Sci Rep. 7(1):9624.

Linchangco GV, Foltz DW, Reid R, Williams J, Nodzak C, Kerr AM, Miller AK, Hunter R, Wilson NG, Nielsen WJ, et al. 2017. The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics. Mol. Phylogenet. Evol. 115:161-170.

Zhang B, Mao YS, Diermeier SD, Novikova IV, Nawrocki EP, Jones TA, Lazar Z, Tung CS, Luo W, Eddy SR, et al. 2017. Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Rep. 19(8):1723-1738.

Luo W, Pant G, Bhavnasi YK, Blanchard SG, Brouwer C. 2017. Pathview Web: user friendly pathway visualization and data integration. Nucleic Acids Res. 45(W1):W501-W508.

Mitchell EL, Davis AT, Brass K, Dendinger M, Barner R, Gharaibeh R, Fodor AA, Kavanagh K. 2017. Reduced Intestinal Motility, Mucosal Barrier Function, and Inflammation in Aged Monkeys. J Nutr Health Aging. 21(4):354-361.

2016

Lambirth KC, Whaley AM, Schlueter JA, Piller KJ, Bost KL. 2016. Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max. Int J Plant Genomics. 2016:1562041.

Nieman DC, Sha W, Pappan KL. 2016. IL-6 Linkage to Exercise-Induced Shifts in Lipid-Related Metabolites: A Metabolomics-Based Analysis. J. Proteome Res. 16(2):970-977.

Chaffin AS, Huang YF, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, et al. 2016. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. Plant Genome. 9(2).

Zhu Y, Wang P, Sha W, Sang S. 2016. Urinary Biomarkers of Whole Grain Wheat Intake Identified by Non-targeted and Targeted Metabolomics Approaches. Sci Rep. 6:36278.

Reid RW, Luo Y, Yan S, Miller TE, Song BH. 2016. Transcriptome Dataset of Halophyte Beach Morning Glory, a Close Wild Relative of Sweet Potato. Front Plant Sci. 7:1267.

Jay JJ, Brouwer C. 2016. Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine. PLoS ONE. 11(8):e0160519.

Cialdella-Kam L, Nieman DC, Knab AM, Shanely RA, Meaney MP, Jin F, Sha W, Ghosh S. 2016. A Mixed Flavonoid-Fish Oil Supplement Induces Immune-Enhancing and Anti-Inflammatory Transcriptomic Changes in Adult Obese and Overweight Women-A Randomized Controlled Trial. Nutrients. 8(5).

Clouse RM, Linchangco GV, Kerr AM, Reid RW, Janies DA. 2016. Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. R Soc Open Sci. 2(12):150377.

Bubier JA, Wilcox TD, Jay JJ, Langston MA, Baker EJ, Chesler EJ. 2016. Cross-Species Integrative Functional Genomics in GeneWeaver Reveals a Role for Pafah1b1 in Altered Response to Alcohol. Front Behav Neurosci. 10:1.

Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA. 2016. EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics. 17:48.

2015

Lambirth KC, Whaley AM, Schlueter JA, Bost KL, Piller KJ. 2015. CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing. Genom Data. 6:175-81.

Nieman DC, Gillitt ND, Sha W, Meaney MP, John C, Pappan KL, Kinchen JM. 2015. Metabolomics-Based Analysis of Banana and Pear Ingestion on Exercise Performance and Recovery. J. Proteome Res. 14(12):5367-77.

Muhlebach MS, Sha W. 2015. Lessons learned from metabolomics in cystic fibrosis. Mol Cell Pediatr. 2(1):9.

Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ. 2015. A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq. BMC Biotechnol. 15:89.

Ray A, Basu S, Gharaibeh RZ, Cook LC, Kumar R, Lefkowitz EJ, Walker CR, Morrow CD, Franklin CL, Geiger TL, et al. 2015. Gut Microbial Dysbiosis Due to Helicobacter Drives an Increase in Marginal Zone B Cells in the Absence of IL-10 Signaling in Macrophages. J. Immunol. 195(7):3071-85.

Brown AF, Yousef GG, Reid RW, Chebrolu KK, Thomas A, Krueger C, Jeffery E, Jackson E, Juvik JA. 2015. Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms. Theor. Appl. Genet. 128(7):1431-47.

Gupta V, Estrada AD, Blakley I, Reid R, Patel K, Meyer MD, Andersen SU, Brown AF, Lila MA, Loraine AE. 2015. RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. Gigascience. 4:5.

2014

Nieman DC, Scherr J, Luo B, Meaney MP, Dréau D, Sha W, Dew DA, Henson DA, Pappan KL. 2014. Influence of pistachios on performance and exercise-induced inflammation, oxidative stress, immune dysfunction, and metabolite shifts in cyclists: a randomized, crossover trial. PLoS ONE. 9(11):e113725.

Stokell JR, Gharaibeh RZ, Hamp TJ, Zapata MJ, Fodor AA, Steck TR. 2014. Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period. J. Clin. Microbiol. 53(1):237-47.

Aniket , Reid R, Hall B, Marriott I, El-Ghannam A. 2014. Early osteoblast responses to orthopedic implants: Synergy of surface roughness and chemistry of bioactive ceramic coating. J Biomed Mater Res A. 103(6):1961-73.

Arthur JC, Gharaibeh RZ, Mühlbauer M, Perez-Chanona E, Uronis JM, McCafferty J, Fodor AA, Jobin C. 2014. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat Commun. 5:4724.

Brown AF, Yousef GG, Chebrolu KK, Byrd RW, Everhart KW, Thomas A, Reid RW, Parkin IA, Sharpe AG, Oliver R, et al. 2014. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets. Theor. Appl. Genet. 127(9):2051-64.

Reid RW, Brouwer CR, Jackson EW, Lila MA. 2014. A need for a transdisciplinary environment: the Plant Pathways Elucidation Project. Trends Plant Sci. 19(8):485-7.

Hanna EM, Hamp TJ, McKillop IH, Bahrani-Mougeot F, Martinie JB, Horton JM, Sindram D, Gharaibeh RZ, Fodor AA, Iannitti DA. 2014. Comparison of culture and molecular techniques for microbial community characterization in infected necrotizing pancreatitis. J. Surg. Res. 191(2):362-9.

Gruber HE, Sha W, Brouwer CR, Steuerwald N, Hoelscher GL, Hanley EN. 2014. A novel catechol-O-methyltransferase variant associated with human disc degeneration. Int J Med Sci. 11(7):748-53.

Knab AM, Nieman DC, Gillitt ND, Shanely RA, Cialdella-Kam L, Henson D, Sha W, Meaney MP. 2014. Effects of a freeze-dried juice blend powder on exercise-induced inflammation, oxidative stress, and immune function in cyclists. Appl Physiol Nutr Metab. 39(3):381-5.

2013

Nieman DC, Shanely RA, Luo B, Dew D, Meaney MP, Sha W. 2013. A commercialized dietary supplement alleviates joint pain in community adults: a double-blind, placebo-controlled community trial. Nutr J. 12(1):154.

Shanely RA, Nieman DC, Knab AM, Gillitt ND, Meaney MP, Jin F, Sha W, Cialdella-Kam L. 2013. Influence of vitamin D mushroom powder supplementation on exercise-induced muscle damage in vitamin D insufficient high school athletes. J Sports Sci. 32(7):670-9.

Sun X, Luo W, Tan X, Li Q, Zhao Y, Zhong W, Sun X, Brouwer C, Zhou Z. 2013. Increased plasma corticosterone contributes to the development of alcoholic fatty liver in mice. Am. J. Physiol. Gastrointest. Liver Physiol. 305(11):G849-61.

Arthur JC, Gharaibeh RZ, Uronis JM, Perez-Chanona E, Sha W, Tomkovich S, Mühlbauer M, Fodor AA, Jobin C. 2013. VSL#3 probiotic modifies mucosal microbial composition but does not reduce colitis-associated colorectal cancer. Sci Rep. 3:2868.

Sha W, Martins AM, Laubenbacher R, Mendes P, Shulaev V. 2013. The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PLoS ONE. 8(9):e74939.

Joseloff E, Sha W, Bell SC, Wetmore DR, Lawton KA, Milburn MV, Ryals JA, Guo L, Muhlebach MS. 2013. Serum metabolomics indicate altered cellular energy metabolism in children with cystic fibrosis. Pediatr. Pulmonol. 49(5):463-72.

McCafferty J, Mühlbauer M, Gharaibeh RZ, Arthur JC, Perez-Chanona E, Sha W, Jobin C, Fodor AA. 2013. Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. ISME J. 7(11):2116-25.

Kavanagh K, Wylie AT, Tucker KL, Hamp TJ, Gharaibeh RZ, Fodor AA, Cullen JM. 2013. Dietary fructose induces endotoxemia and hepatic injury in calorically controlled primates. Am. J. Clin. Nutr. 98(2):349-57.

Luo W, Brouwer C. 2013. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 29(14):1830-1.

Stokell JR, Gharaibeh RZ, Steck TR. 2013. Rapid emergence of a ceftazidime-resistant Burkholderia multivorans strain in a cystic fibrosis patient. J. Cyst. Fibros. 12(6):812-6.

Garhyan J, Gharaibeh RZ, McGee S, Gibas CJ. 2013. The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization. BMC Res Notes. 6:72.

Corbin KD, Abdelmalek MF, Spencer MD, da Costa KA, Galanko JA, Sha W, Suzuki A, Guy CD, Cardona DM, Torquati A, et al. 2013. Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis. FASEB J. 27(4):1674-89.

2012

Cialdella-Kam L, Nieman DC, Sha W, Meaney MP, Knab AM, Shanely RA. 2012. Dose-response to 3 months of quercetin-containing supplements on metabolite and quercetin conjugate profile in adults. Br. J. Nutr. 109(11):1923-33.

Knab AM, Nieman DC, Gillitt ND, Shanely RA, Cialdella-Kam L, Henson DA, Sha W. 2012. Effects of a flavonoid-rich juice on inflammation, oxidative stress, and immunity in elite swimmers: a metabolomics-based approach. Int J Sport Nutr Exerc Metab. 23(2):150-60.

Mazurek A, Luo W, Krasnitz A, Hicks J, Powers RS, Stillman B. 2012. DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells. Cancer Discov. 2(9):812-25.

Nieman DC, Gillitt ND, Henson DA, Sha W, Shanely RA, Knab AM, Cialdella-Kam L, Jin F. 2012. Bananas as an energy source during exercise: a metabolomics approach. PLoS ONE. 7(5):e37479.

Jin F, Nieman DC, Sha W, Xie G, Qiu Y, Jia W. 2012. Supplementation of milled chia seeds increases plasma ALA and EPA in postmenopausal women. Plant Foods Hum Nutr. 67(2):105-10.

Knab AM, Nieman DC, Sha W, Broman-Fulks JJ, Canu WH. 2012. Exercise frequency is related to psychopathology but not neurocognitive function. Med Sci Sports Exerc. 44(7):1395-400.

2011

Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L. 2011. Visualizing the drug target landscape. Drug Discov. Today. 17 Suppl:S3-15.

Shanely RA, Nieman DC, Henson DA, Jin F, Knab AM, Sha W. 2011. Inflammation and oxidative stress are lower in physically fit and active adults. Scand J Med Sci Sports. 23(2):215-23.

Luo W, Friedman MS, Hankenson KD, Woolf PJ. 2011. Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Syst Biol. 5:82.

Knab AM, Shanely RA, Jin F, Austin MD, Sha W, Nieman DC. 2011. Quercetin with vitamin C and niacin does not affect body mass or composition. Appl Physiol Nutr Metab. 36(3):331-8.

Nieman DC, Henson DA, Sha W. 2011. Ingestion of micronutrient fortified breakfast cereal has no influence on immune function in healthy children: a randomized controlled trial. Nutr J. 10:36.

Rossmann MP, Luo W, Tsaponina O, Chabes A, Stillman B. 2011. A common telomeric gene silencing assay is affected by nucleotide metabolism. Mol. Cell. 42(1):127-36.

Cortes DF, Sha W, Hower V, Blekherman G, Laubenbacher R, Akman S, Torti SV, Shulaev V. 2011. Differential gene expression in normal and transformed human mammary epithelial cells in response to oxidative stress. Free Radic. Biol. Med. 50(11):1565-74.

Powell R, Hudson LC, Lambirth KC, Luth D, Wang K, Bost KL, Piller KJ. 2011. Recombinant expression of homodimeric 660 kDa human thyroglobulin in soybean seeds: an alternative source of human thyroglobulin. Plant Cell Rep. 30(7):1327-38.

Knab AM, Shanely RA, Corbin KD, Jin F, Sha W, Nieman DC. 2011. A 45-minute vigorous exercise bout increases metabolic rate for 14 hours. Med Sci Sports Exerc. 43(9):1643-8.

Gharaibeh RZ, Fodor AA, Gibas CJ. 2011. Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. PLoS ONE. 5(12):e14464.

2010

Spencer MD, Hamp TJ, Reid RW, Fischer LM, Zeisel SH, Fodor AA. 2010. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology. 140(3):976-86.

Nieman DC, Henson DA, Austin MD, Sha W. 2010. Upper respiratory tract infection is reduced in physically fit and active adults. Br J Sports Med. 45(12):987-92.

Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, Depamphilis CW, Ma H. 2010. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biol. 11(10):R101.

Gharaibeh RZ, Newton JM, Weller JW, Gibas CJ. 2010. Application of equilibrium models of solution hybridization to microarray design and analysis. PLoS ONE. 5(6):e11048.

Fischer LM, da Costa KA, Galanko J, Sha W, Stephenson B, Vick J, Zeisel SH. 2010. Choline intake and genetic polymorphisms influence choline metabolite concentrations in human breast milk and plasma. Am. J. Clin. Nutr. 92(2):336-46.

Jin F, Nieman DC, Shanely RA, Knab AM, Austin MD, Sha W. 2010. The variable plasma quercetin response to 12-week quercetin supplementation in humans. Eur J Clin Nutr. 64(7):692-7.

Sha W, da Costa KA, Fischer LM, Milburn MV, Lawton KA, Berger A, Jia W, Zeisel SH. 2010. Metabolomic profiling can predict which humans will develop liver dysfunction when deprived of dietary choline. FASEB J. 24(8):2962-75.

2009

Tripathi AK, Sha W, Shulaev V, Stins MF, Sullivan DJ. 2009. Plasmodium falciparum-infected erythrocytes induce NF-kappaB regulated inflammatory pathways in human cerebral endothelium. Blood. 114(19):4243-52.

Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG, Chervitz SA, Harmon C, Loraine AE. 2009. Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics. 10:266.

Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. 2009. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics. 25(20):2730-1.

Barnes MR, Harland L, Foord SM, Hall MD, Dix I, Thomas S, Williams-Jones BI, Brouwer CR. 2009. Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. Nat Rev Drug Discov. 8(9):701-8.

Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. 2009. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics. 10:161.

2008

Reid RW, Fodor AA. 2008. Determining gene expression on a single pair of microarrays. BMC Bioinformatics. 9:489.

Luo W, Hankenson KD, Woolf PJ. 2008. Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics. 9:467.

Gharaibeh RZ, Fodor AA, Gibas CJ. 2008. Background correction using dinucleotide affinities improves the performance of GCRMA. BMC Bioinformatics. 9:452.

Koussevitzky S, Suzuki N, Huntington S, Armijo L, Sha W, Cortes D, Shulaev V, Mittler R. 2008. Ascorbate peroxidase 1 plays a key role in the response of Arabidopsis thaliana to stress combination. J. Biol. Chem. 283(49):34197-203.

Luo W, Shitaye H, Friedman M, Bennett CN, Miller J, Macdougald OA, Hankenson KD. 2008. Disruption of cell-matrix interactions by heparin enhances mesenchymal progenitor adipocyte differentiation. Exp. Cell Res. 314(18):3382-91.

2007

Martins AM, Sha W, Evans C, Martino-Catt S, Mendes P, Shulaev V. 2007. Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae. Yeast. 24(3):181-8.

2006

Sioson AA, Mane SP, Li P, Sha W, Heath LS, Bohnert HJ, Grene R. 2006. The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison. BMC Bioinformatics. 7:215.

Fujita K, Forsyth M, MacFarlane DR, Reid RW, Elliott GD. 2006. Unexpected improvement in stability and utility of cytochrome c by solution in biocompatible ionic liquids. Biotechnol. Bioeng. 94(6):1209-13.

2003

Mendes P, Sha W, Ye K. 2003. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics. 19 Suppl 2:ii122-9.

Sha W, Moore J, Chen K, Lassaletta AD, Yi CS, Tyson JJ, Sible JC. 2003. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl. Acad. Sci. U.S.A. 100(3):975-80.