Publications

Publications from the Bioinformatics Core

  • Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Park Y, Rozas J, Benton R, Pedra JH, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun. 2016 Feb 9; 7:10507. doi: 10.1038/ncomms10507. PMID: 26856261.
  • Chowdhury B, Seetharam A, Wang Z, Liu Y, Lossie AC, Thimmapuram J, Irudayaraj J. A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells. PLoS One. 2016 Jan 28; 11(1):e0147514. doi: 10.1371/journal.pone.0147514. eCollection 2016. PMID: 26820575.
  • Widhalm JR, Gutensohn M, Yoo H, Adebesin F, Qian Y, Guo L, Jaini R, Lynch JH, McCoy RM, Shreve JT, Thimmapuram J, Rhodes D, Morgan JA, Dudareva N. Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network. Nat Commun. 2015 Sep 10; 6:8142. doi: 10.1038/ncomms9142. PMID: 26356302.
  • Ayyappan V, Kalavacharla V, Thimmapuram J, Bhide KP, Sripathi VR, Smolinski TG, Manoharan M, Thurston Y, Todd A, Kingham B. Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.). PLoS One. 2015 Jul 13; 10(7):e0132176. doi: 10.1371/journal.pone.0132176. eCollection 2015. PMID: 26167691.
  • Rajarapu SP, Shreve JT, Bhide KP, Thimmapuram J, Scharf ME. Metatranscriptomic profiles of Eastern subterranean termites, Reticulitermes flavipes (Kollar) fed on second generation feedstocks. BMC Genomics. 2015 Apr 22; 16:332. doi: 10.1186/s12864-015-1502-8. PMID: 25896921.
  • Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J. Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near-Isogenic Lines. The Plant Genome. 2015 March; 8:1-13. doi: 10.3835/plantgenome2014.09.0044.
  • Welkie D, Zhang X, Markville ML, Taylor R, Orr G, Jacobs J, Bhide K, Thimmapuram J, Gritsenko M, Mitchell H, Smith R, Sherman LA. Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle. BMC Genomics. 2014 Dec 29; 15(1):1185. [Epub ahead of print] PubMed PMID: 25547186.
  • Zhu Y, Schluttenhoffer CM, Wang P, Fu F, Thimmapuram J, Zhu JK, Lee SY, Yun DJ, Mengiste T. CYCLIN-DEPENDENT KINASE8 differentially regulates plant immunity to fungal pathogens through kinase-dependent and -independent functions in Arabidopsis. Plant Cell. 2014 Oct; 26(10):4149-70. doi: 10.1105/tpc.114.128611. Epub 2014 Oct 3. PubMed PMID: 25281690; PubMed Central PMCID: PMC4247566.
  • Penning BW, Sykes RW, Babcock NC, Dugard CK, Held MA, Klimek JF, Shreve JT, Fowler M, Ziebell A, Davis MF, Decker SR, Turner GB, Mosier NS, Springer NM, Thimmapuram J, Weil CF, McCann MC, Carpita NC. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. Plant Physiol. 2014 Jun 27; 165(4):1475-1487. [Epub ahead of print] PubMed PMID: 24972714; PubMed Central PMCID: PMC4119032.
  • Hung JE, Mill CP, Clifton SW, Magrini V, Bhide K, Francois JA, Ransome AE, Fulton L, Thimmapuram J, Wilson RK, Kappock TJ. Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate. Genome Announc. 2014 Jun 5; 2(3). pii: e00550-14. doi: 10.1128/genomeA.00550-14. PubMed PMID: 24903876; PubMed Central PMCID: PMC4047455.
  • Lai Z, Schluttenhofer CM, Bhide K, Shreve J, Thimmapuram J, Lee SY, Yun DJ, Mengiste T. MED18 interaction with distinct transcription factors regulates multiple plant functions. Nat Commun. 2014; 5:3064. doi: 10.1038/ncomms4064. PubMed PMID: 24451981.

Bioinformatics Core Acknowledged in

  • Freeman JL, Weber GJ, Sepulveda MS. Fishing for microRNAs in Toxicology. In microRNAs in Toxicology and Medicine, pp: 49-75, Edited by Sahu SC. 2014. Publ: John Wiley & Sons, Ltd.
  • Bonawitz ND, Kim JI, Tobimatsu Y, Ciesielski PN, Anderson NA, Ximenes E, Maeda J, Ralph J, Donohoe BS, Ladisch M, Chapple C. Disruption of Mediator rescues the stunted growth of a lignindeficient Arabidopsis mutant. Nature 509, 376–380 (15 May 2014) doi: 10.1038/nature13084
  • Jones-Hall YL, Kozik A, Nakatsu C. Ablation of Tumor Necrosis Factor is Associated with Decreased Inflammation and Alterations of the Microbiota in a Mouse Model of Inflammatory Bowel Disease. PloS One. 2015. 10(3):e0119441. doi: 10.1371/journal.pone.0119441. PMCID: PMC4361568.
  • Diaz-Valderrama JR, Aime MN. The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally. Heredity (Edinb). 2016 Mar 2. doi: 10.1038/hdy.2016.5.
  • Torres-Martínez L, Emery, NC. Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic. Conservation Genetics Resources. 2016. March 14; doi: 10.1007/s12686- 016-0524-0

Contact

Bioinformatics Core
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bioinformatics@purdue.edu
Phone: 765.496.6252
jyothit@purdue.edu

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