Publications

Publications from the Bioinformatics Core

  • Bailey TW, Dos Santos AP, do Nascimento NC, Xie S, Thimmapuram J, Sivasankar MP, Cox A, . RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge. BMC Genomics. 2020 Dec 11;21(1):888. doi: 10.1186/s12864-020-07301-7. PubMed PMID: 33308144.
  • Abdelrazek S, Choudhari S, Thimmapuram J, Simon P, Colley M, Mengiste T, Hoagland L, . Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype. Sci Rep. 2020 Aug 13;10(1):13685. doi: 10.1038/s41598-020-70683-x. PubMed PMID: 32792547.
  • Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson S, Riva A, Settles ML, Thimmapuram J, Levine SS, . Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. J Biomol Tech. 2020 Jul;31(2):66-73. doi: 10.7171/jbt.20-3102-005. PubMed PMID: 32382253.
  • Kumuthini J, Chimenti M, Nahnsen S, Peltzer A, Meraba R, McFadyen R, Wells G, Taylor D, Maienschein-Cline M, Li JL, Thimmapuram J, Murthy-Karuturi R, Zass L, . Ten simple rules for providing effective bioinformatics research support. PLoS Comput Biol. 2020 Mar;16(3):e1007531. doi: 10.1371/journal.pcbi.1007531. PubMed PMID: 32214318.
  • McCauley CL, McAdam SAM, Bhide K, Thimmapuram J, Banks JA, Young BG, . Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application. J Exp Bot. 2020 Jun 22;71(12):3701-3709. doi: 10.1093/jxb/eraa124. PubMed PMID: 32161961.
  • Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS, . Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech. 2020 Jul;31(2):47-56. doi: 10.7171/jbt.20-3102-001. PubMed PMID: 31966025.
  • Penning BW, Shiga TM, Klimek JF, SanMiguel PJ, Shreve J, Thimmapuram J, Sykes RW, Davis MF, McCann MC, Carpita NC, . Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. BMC Genomics. 2019 Oct 29;20(1):785. doi: 10.1186/s12864-019-6117-z. PubMed PMID: 31664907.
  • Ayyappan V, Sripathi VR, Kalavacharla VK, Saha MC, Thimmapuram J, Bhide KP, Fiedler E, . Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics. 2019 Aug 22;20(1):667. doi: 10.1186/s12864-019-6038-x. PubMed PMID: 31438854.
  • McCoy RM, Utturkar SM, Crook JW, Thimmapuram J, Widhalm JR, . The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut. Hortic Res. 2018;5():67. doi: 10.1038/s41438-018-0067-5. PubMed PMID: 30393541.
  • Murgia MV, Bell-Sakyi L, de la Fuente J, Kurtti TJ, Makepeace BL, Mans B, McCoy KD, Munderloh U, Plantard O, Rispe C, Valle MR, Tabor A, Thangamani S, Thimmapuram J, Hill CA, . Meeting the challenge of tick-borne disease control: A proposal for 1000 Ixodes genomes. Ticks Tick Borne Dis. 2019 Jan;10(1):213-218. doi: 10.1016/j.ttbdis.2018.08.009. PubMed PMID: 30266208.
  • Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS, . Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics. 2018 Mar 15;19(1):199. doi: 10.1186/s12864-018-4585-1. PubMed PMID: 29703133.
  • Dworkin M, Xie S, Saha M, Thimmapuram J, Kalavacharla VK, . Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq. BMC Genomics. 2017 Nov 7;18(1):851. doi: 10.1186/s12864-017-4218-0. PubMed PMID: 29115936.
  • Huang X, Zhang S, Li K, Thimmapuram J, Xie S, Wren J, . ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data. Bioinformatics. 2018 Feb 15;34(4):708-709. doi: 10.1093/bioinformatics/btx633. PubMed PMID: 29087450.
  • Ponniah SK, Thimmapuram J, Bhide K, Kalavacharla VK, Manoharan M, . Comparative analysis of the root transcriptomes of cultivated sweetpotato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don). BMC Plant Biol. 2017 Jan 13;17(1):9. doi: 10.1186/s12870-016-0950-x. PubMed PMID: 28086804.
  • Ayyappan V, Saha MC, Thimmapuram J, Sripathi VR, Bhide KP, Fiedler E, Hayford RK, Kalavacharla VK, . Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass. Plant Cell Rep. 2017 Jan;36(1):129-150. doi: 10.1007/s00299-016-2065-0. PubMed PMID: 27812750.
  • Hong Y, Thimmapuram J, Zhang J, Collings CK, Bhide K, Schmidt K, Ebner PD, . The impact of orally administered phages on host immune response and surrounding microbial communities. Bacteriophage. 2016 Jul-Sep;6(3):e1211066. . PubMed PMID: 27738553.
  • 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 SMS, 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 CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, 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. PubMed 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;11(1):e0147514. doi: 10.1371/journal.pone.0147514. PubMed 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. PubMed 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;10(7):e0132176. doi: 10.1371/journal.pone.0132176. PubMed 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. PubMed 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. Plant Genome. 2015 Mar;8(1):eplantgenome2014.09.0044. doi: 10.3835/plantgenome2014.09.0044. PubMed PMID: 33228285.
  • Welkie D, Zhang X, Markillie ML, Taylor R, Orr G, Jacobs J, Bhide K, Thimmapuram J, Gritsenko M, Mitchell H, Smith RD, 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():1185. doi: 10.1186/1471-2164-15-1185. 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. PubMed PMID: 25281690.
  • 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 Aug;165(4):1475-1487. . PubMed PMID: 24972714.
  • 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.
  • 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.
  • Yendrek CR, Ainsworth EA, Thimmapuram J, . The bench scientist's guide to statistical analysis of RNA-Seq data. BMC Res Notes. 2012 Sep 14;5():506. doi: 10.1186/1756-0500-5-506. PubMed PMID: 22980220.
  • Anderson JV, Doğramacı M, Horvath DP, Foley ME, Chao WS, Suttle JC, Thimmapuram J, Hernandez AG, Ali S, Mikel MA, . Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense). Funct Integr Genomics. 2012 Aug;12(3):515-31. doi: 10.1007/s10142-012-0280-5. PubMed PMID: 22580957.
  • Larkin DM, Daetwyler HD, Hernandez AG, Wright CL, Hetrick LA, Boucek L, Bachman SL, Band MR, Akraiko TV, Cohen-Zinder M, Thimmapuram J, Macleod IM, Harkins TT, McCague JE, Goddard ME, Hayes BJ, Lewin HA, . Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc Natl Acad Sci U S A. 2012 May 15;109(20):7693-8. doi: 10.1073/pnas.1114546109. PubMed PMID: 22529356.
  • Kalavacharla V, Liu Z, Meyers BC, Thimmapuram J, Melmaiee K, . Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol. 2011 Oct 11;11():135. doi: 10.1186/1471-2229-11-135. PubMed PMID: 21985325.
  • Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu WT, . Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS One. 2011;6(9):e25263. doi: 10.1371/journal.pone.0025263. PubMed PMID: 21966473.
  • Smalheiser NR, Lugli G, Thimmapuram J, Cook EH, Larson J, . Mitochondrial small RNAs that are up-regulated in hippocampus during olfactory discrimination training in mice. Mitochondrion. 2011 Nov;11(6):994-5. doi: 10.1016/j.mito.2011.08.014. PubMed PMID: 21925291.
  • Malik A, Korol A, Hübner S, Hernandez AG, Thimmapuram J, Ali S, Glaser F, Paz A, Avivi A, Band M, . Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns. PLoS One. 2011;6(8):e21227. doi: 10.1371/journal.pone.0021227. PubMed PMID: 21857902.
  • Bushman BS, Larson SR, Tuna M, West MS, Hernandez AG, Vullaganti D, Gong G, Robins JG, Jensen KB, Thimmapuram J, . Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability. Theor Appl Genet. 2011 Jun;123(1):119-29. doi: 10.1007/s00122-011-1571-2. PubMed PMID: 21465186.
  • Smalheiser NR, Lugli G, Thimmapuram J, Cook EH, Larson J, . Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training. RNA. 2011 Jan;17(1):166-81. doi: 10.1261/rna.2123811. PubMed PMID: 21045079.
  • Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small BC, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu Z, Catfish Genome Consortium., . Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010 Jan 22;11(1):R8. doi: 10.1186/gb-2010-11-1-r8. PubMed PMID: 20096101.
  • Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA, . Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One. 2009 Aug 14;4(8):e6650. doi: 10.1371/journal.pone.0006650. PubMed PMID: 19680555.
  • Ergen NZ, Thimmapuram J, Bohnert HJ, Budak H, . Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integr Genomics. 2009 Aug;9(3):377-96. doi: 10.1007/s10142-009-0123-1. PubMed PMID: 19330365.
  • Horvath DP, Chao WS, Suttle JC, Thimmapuram J, Anderson JV, . Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.). BMC Genomics. 2008 Nov 12;9():536. doi: 10.1186/1471-2164-9-536. PubMed PMID: 19014493.
  • Bushman BS, Larson SR, Mott IW, Cliften PF, Wang RR, Chatterton NJ, Hernandez AG, Ali S, Kim RW, Thimmapuram J, Gong G, Liu L, Mikel MA, . Development and annotation of perennial Triticeae ESTs and SSR markers. Genome. 2008 Oct;51(10):779-88. doi: 10.1139/G08-062. PubMed PMID: 18923529.
  • Kaur P, Larson SR, Shaun Bushman B, Wang RR, Mott IW, Hole D, Thimmapuram J, Gong G, Liu L, . Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates. Funct Integr Genomics. 2008 Nov;8(4):375-86. doi: 10.1007/s10142-008-0085-8. PubMed PMID: 18543009.
  • Wechter WP, Levi A, Harris KR, Davis AR, Fei Z, Katzir N, Giovannoni JJ, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V, Trebitsh T, . Gene expression in developing watermelon fruit. BMC Genomics. 2008 Jun 5;9():275. doi: 10.1186/1471-2164-9-275. PubMed PMID: 18534026.
  • Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M, . The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856. PubMed PMID: 18432245.
  • Replogle K, Arnold AP, Ball GF, Band M, Bensch S, Brenowitz EA, Dong S, Drnevich J, Ferris M, George JM, Gong G, Hasselquist D, Hernandez AG, Kim R, Lewin HA, Liu L, Lovell PV, Mello CV, Naurin S, Rodriguez-Zas S, Thimmapuram J, Wade J, Clayton DF, . The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics. 2008 Mar 18;9():131. doi: 10.1186/1471-2164-9-131. PubMed PMID: 18366674.
  • Yu Q, Hou S, Feltus FA, Jones MR, Murray JE, Veatch O, Lemke C, Saw JH, Moore RC, Thimmapuram J, Liu L, Moore PH, Alam M, Jiang J, Paterson AH, Ming R, . Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J. 2008 Jan;53(1):124-32. . PubMed PMID: 17973896.
  • Thimmapuram J, Duan H, Liu L, Schuler MA, . Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome. RNA. 2005 Feb;11(2):128-38. . PubMed PMID: 15659355.

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