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A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells.

Chowdhury B, Seetharam A, Wang Z, Liu Y, Lossie AC, Thimmapuram J, Irudayaraj J.

PLoS One. 2016 Jan 28;11(1):e0147514. doi: 10.1371/journal.pone.0147514. eCollection 2016.


Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network.

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.

Nat Commun. 2015 Sep 10;6:8142. doi: 10.1038/ncomms9142.


Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.).

Ayyappan V, Kalavacharla V, Thimmapuram J, Bhide KP, Sripathi VR, Smolinski TG, Manoharan M, Thurston Y, Todd A, Kingham B.

PLoS One. 2015 Jul 13;10(7):e0132176. doi: 10.1371/journal.pone.0132176. eCollection 2015.


Metatranscriptomic profiles of Eastern subterranean termites, Reticulitermes flavipes (Kollar) fed on second generation feedstocks.

Rajarapu SP, Shreve JT, Bhide KP, Thimmapuram J, Scharf ME.

BMC Genomics. 2015 Apr 22;16:332. doi: 10.1186/s12864-015-1502-8.


Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle.

Welkie D, Zhang X, Markillie ML, Taylor R, Orr G, Jacobs J, Bhide K, Thimmapuram J, Gritsenko M, Mitchell H, Smith RD, Sherman LA.

BMC Genomics. 2014 Dec 29;15:1185. doi: 10.1186/1471-2164-15-1185.


CYCLIN-DEPENDENT KINASE8 differentially regulates plant immunity to fungal pathogens through kinase-dependent and -independent functions in Arabidopsis.

Zhu Y, Schluttenhoffer CM, Wang P, Fu F, Thimmapuram J, Zhu JK, Lee SY, Yun DJ, Mengiste T.

Plant Cell. 2014 Oct;26(10):4149-70. doi: 10.1105/tpc.114.128611. Epub 2014 Oct 3.


Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population.

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.

Plant Physiol. 2014 Jun 27;165(4):1475-1487. [Epub ahead of print]


Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate.

Hung JE, Mill CP, Clifton SW, Magrini V, Bhide K, Francois JA, Ransome AE, Fulton L, Thimmapuram J, Wilson RK, Kappock TJ.

Genome Announc. 2014 Jun 5;2(3). pii: e00550-14. doi: 10.1128/genomeA.00550-14.


MED18 interaction with distinct transcription factors regulates multiple plant functions.

Lai Z, Schluttenhofer CM, Bhide K, Shreve J, Thimmapuram J, Lee SY, Yun DJ, Mengiste T.

Nat Commun. 2014;5:3064. doi: 10.1038/ncomms4064.


Use of glucagon in relieving esophageal food bolus impaction in the era of eosinophilic esophageal infiltration.

Thimmapuram J, Oosterveen S, Grim R.

Dysphagia. 2013 Jun;28(2):212-6. doi: 10.1007/s00455-012-9434-9. Epub 2012 Dec 1.


The bench scientist's guide to statistical analysis of RNA-Seq data.

Yendrek CR, Ainsworth EA, Thimmapuram J.

BMC Res Notes. 2012 Sep 14;5:506. doi: 10.1186/1756-0500-5-506.


Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense).

Anderson JV, Doğramacı M, Horvath DP, Foley ME, Chao WS, Suttle JC, Thimmapuram J, Hernandez AG, Ali S, Mikel MA.

Funct Integr Genomics. 2012 Aug;12(3):515-31. doi: 10.1007/s10142-012-0280-5. Epub 2012 May 13.


Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle.

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.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):7693-8. doi: 10.1073/pnas.1114546109. Epub 2012 Apr 23.


Look before you eat: hazards of grilling.

Thimmapuram J, Oosterveen S.

Gastrointest Endosc. 2011 Dec;74(6):1399-400. doi: 10.1016/j.gie.2011.08.033. No abstract available.


Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing.

Kalavacharla V, Liu Z, Meyers BC, Thimmapuram J, Melmaiee K.

BMC Plant Biol. 2011 Oct 11;11:135. doi: 10.1186/1471-2229-11-135.


Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu WT.

PLoS One. 2011;6(9):e25263. doi: 10.1371/journal.pone.0025263. Epub 2011 Sep 23.


Mitochondrial small RNAs that are up-regulated in hippocampus during olfactory discrimination training in mice.

Smalheiser NR, Lugli G, Thimmapuram J, Cook EH, Larson J.

Mitochondrion. 2011 Nov;11(6):994-5. doi: 10.1016/j.mito.2011.08.014. Epub 2011 Sep 9.


Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.

Malik A, Korol A, Hübner S, Hernandez AG, Thimmapuram J, Ali S, Glaser F, Paz A, Avivi A, Band M.

PLoS One. 2011;6(8):e21227. doi: 10.1371/journal.pone.0021227. Epub 2011 Aug 12.


Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability.

Bushman BS, Larson SR, Tuna M, West MS, Hernandez AG, Vullaganti D, Gong G, Robins JG, Jensen KB, Thimmapuram J.

Theor Appl Genet. 2011 Jun;123(1):119-29. doi: 10.1007/s00122-011-1571-2. Epub 2011 Apr 5.


Esophageal Dieulafoy lesion: an unusual cause of GI bleeding.

Thimmapuram J, Shah M, Srour J.

Gastrointest Endosc. 2011 May;73(5):1055-6. doi: 10.1016/j.gie.2010.08.056. Epub 2010 Nov 9. No abstract available.

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