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Items: 46

1.

A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill.

Gillman JD, Biever JJ, Ye S, Spollen WG, Givan SA, Lyu Z, Joshi T, Smith JR, Fritschi FB.

BMC Res Notes. 2019 Aug 19;12(1):522. doi: 10.1186/s13104-019-4559-7.

2.

Draft Genome Sequence of Bradyrhizobium sp. Strain LVM 105, a Nitrogen-Fixing Symbiont of Chamaecrista fasciculata (Michx.) Greene.

Krishnan HB, Kim WS, Givan SA.

Microbiol Resour Announc. 2019 Apr 4;8(14). pii: e00132-19. doi: 10.1128/MRA.00132-19.

3.

Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome.

Ortega MT, Bivens NJ, Jogahara T, Kuroiwa A, Givan SA, Rosenfeld CS.

BMC Genomics. 2019 Jan 25;20(1):87. doi: 10.1186/s12864-019-5426-6.

4.

Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MMS, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

Genome Biol. 2018 Aug 23;19(1):122. doi: 10.1186/s13059-018-1508-z.

5.

The novel cyst nematode effector protein 30D08 targets host nuclear functions to alter gene expression in feeding sites.

Verma A, Lee C, Morriss S, Odu F, Kenning C, Rizzo N, Spollen WG, Lin M, McRae AG, Givan SA, Hewezi T, Hussey R, Davis EL, Baum TJ, Mitchum MG.

New Phytol. 2018 Jul;219(2):697-713. doi: 10.1111/nph.15179. Epub 2018 May 4.

6.

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut.

Ericsson AC, Gagliardi J, Bouhan D, Spollen WG, Givan SA, Franklin CL.

Sci Rep. 2018 Mar 6;8(1):4065. doi: 10.1038/s41598-018-21986-7.

7.

Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles.

Javurek AB, Suresh D, Spollen WG, Hart ML, Hansen SA, Ellersieck MR, Bivens NJ, Givan SA, Upendran A, Kannan R, Rosenfeld CS.

Sci Rep. 2017 Jun 6;7(1):2822. doi: 10.1038/s41598-017-02880-0.

8.

Hypothalamic transcriptomic alterations in male and female California mice (Peromyscus californicus) developmentally exposed to bisphenol A or ethinyl estradiol.

Johnson SA, Spollen WG, Manshack LK, Bivens NJ, Givan SA, Rosenfeld CS.

Physiol Rep. 2017 Feb;5(3). pii: e13133. doi: 10.14814/phy2.13133.

9.

Transcriptomic alterations in the brain of painted turtles (Chrysemys picta) developmentally exposed to bisphenol A or ethinyl estradiol.

Manshack LK, Conard CM, Bryan SJ, Deem SL, Holliday DK, Bivens NJ, Givan SA, Rosenfeld CS.

Physiol Genomics. 2017 Apr 1;49(4):201-215. doi: 10.1152/physiolgenomics.00103.2016. Epub 2017 Feb 3.

PMID:
28159858
10.

Bisphenol A (BPA) in the serum of pet dogs following short-term consumption of canned dog food and potential health consequences of exposure to BPA.

Koestel ZL, Backus RC, Tsuruta K, Spollen WG, Johnson SA, Javurek AB, Ellersieck MR, Wiedmeyer CE, Kannan K, Xue J, Bivens NJ, Givan SA, Rosenfeld CS.

Sci Total Environ. 2017 Feb 1;579:1804-1814. doi: 10.1016/j.scitotenv.2016.11.162. Epub 2016 Dec 6.

PMID:
27932218
11.

Effects of exposure to bisphenol A and ethinyl estradiol on the gut microbiota of parents and their offspring in a rodent model.

Javurek AB, Spollen WG, Johnson SA, Bivens NJ, Bromert KH, Givan SA, Rosenfeld CS.

Gut Microbes. 2016 Nov;7(6):471-485. Epub 2016 Sep 13.

12.

Consumption of a high-fat diet alters the seminal fluid and gut microbiomes in male mice.

Javurek AB, Spollen WG, Johnson SA, Bivens NJ, Bromert KH, Givan SA, Rosenfeld CS.

Reprod Fertil Dev. 2017 Aug;29(8):1602-1612. doi: 10.1071/RD16119.

PMID:
27569192
13.

Corrigendum: Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status.

Javurek AB, Spollen WG, Mann Ali AM, Johnson SA, Lubahn DB, Bivens NJ, Bromert KH, Ellersieck MR, Givan SA, Rosenfeld CS.

Sci Rep. 2016 Apr 29;6:25216. doi: 10.1038/srep25216. No abstract available.

14.

Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status.

Javurek AB, Spollen WG, Ali AM, Johnson SA, Lubahn DB, Bivens NJ, Bromert KH, Ellersieck MR, Givan SA, Rosenfeld CS.

Sci Rep. 2016 Mar 14;6:23027. doi: 10.1038/srep23027. Erratum in: Sci Rep. 2016 Apr 29;6:25216.

15.

Intermittent severe hypoxia induces plasticity within serotonergic and catecholaminergic neurons in the neonatal rat ventrolateral medulla.

Givan SA, Cummings KJ.

J Appl Physiol (1985). 2016 Jun 1;120(11):1277-87. doi: 10.1152/japplphysiol.00048.2016. Epub 2016 Mar 10.

16.

Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle.

Williams M, Hoffman MD, Daniel JJ, Madren SM, Dhroso A, Korkin D, Givan SA, Jacobson SC, Brown PJ.

J Bacteriol. 2016 Feb 1;198(7):1149-59. doi: 10.1128/JB.00896-15.

17.

Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832T.

Daniel JJ, Givan SA, Brun YV, Brown PJ.

Genome Announc. 2015 Nov 19;3(6). pii: e01355-15. doi: 10.1128/genomeA.01355-15.

18.

Genome Sequences of Pseudoalteromonas Strains ATCC BAA-314, ATCC 70018, and ATCC 70019.

Givan SA, Zhou MY, Bromert K, Bivens N, Chapman LF.

Genome Announc. 2015 May 7;3(3). pii: e00390-15. doi: 10.1128/genomeA.00390-15.

19.

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.

Chettoor AM, Givan SA, Cole RA, Coker CT, Unger-Wallace E, Vejlupkova Z, Vollbrecht E, Fowler JE, Evans MM.

Genome Biol. 2014 Jul 31;15(7):414. doi: 10.1186/s13059-014-0414-2.

20.

Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci.

Creason AL, Vandeputte OM, Savory EA, Davis EW 2nd, Putnam ML, Hu E, Swader-Hines D, Mol A, Baucher M, Prinsen E, Zdanowska M, Givan SA, El Jaziri M, Loper JE, Mahmud T, Chang JH.

PLoS One. 2014 Jul 10;9(7):e101996. doi: 10.1371/journal.pone.0101996. eCollection 2014.

21.

Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ.

Genome Biol. 2014 Feb 27;15(2):R40. doi: 10.1186/gb-2014-15-2-r40. Erratum in: Genome Biol. 2018 Aug 23;19(1):122.

22.

Characterization of the rat developmental liver transcriptome.

Chapple RH, Tizioto PC, Wells KD, Givan SA, Kim J, McKay SD, Schnabel RD, Taylor JF.

Physiol Genomics. 2013 Apr 16;45(8):301-11. doi: 10.1152/physiolgenomics.00128.2012. Epub 2013 Feb 19.

23.

High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase.

Ditzler MA, Lange MJ, Bose D, Bottoms CA, Virkler KF, Sawyer AW, Whatley AS, Spollen W, Givan SA, Burke DH.

Nucleic Acids Res. 2013 Feb 1;41(3):1873-84. doi: 10.1093/nar/gks1190. Epub 2012 Dec 14.

24.

Computational analysis of RNA-seq.

Givan SA, Bottoms CA, Spollen WG.

Methods Mol Biol. 2012;883:201-19. doi: 10.1007/978-1-61779-839-9_16.

PMID:
22589136
25.

Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics.

Kimbrel JA, Givan SA, Temple TN, Johnson KB, Chang JH.

Mol Plant Pathol. 2011 Aug;12(6):580-94. doi: 10.1111/j.1364-3703.2010.00694.x. Epub 2011 Jan 17.

26.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

27.

An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6.

Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH.

BMC Genomics. 2010 Sep 28;11:522. doi: 10.1186/1471-2164-11-522.

28.

MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana.

Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC.

Plant Cell. 2010 Apr;22(4):1074-89. doi: 10.1105/tpc.110.073999. Epub 2010 Apr 20.

29.

Genome-wide mapping of alternative splicing in Arabidopsis thaliana.

Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC.

Genome Res. 2010 Jan;20(1):45-58. doi: 10.1101/gr.093302.109. Epub 2009 Oct 26.

30.

Computational and analytical framework for small RNA profiling by high-throughput sequencing.

Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, Carrington JC.

RNA. 2009 May;15(5):992-1002. doi: 10.1261/rna.1473809. Epub 2009 Mar 23.

31.

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.

Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

PMID:
18419293
32.

The small genome of an abundant coastal ocean methylotroph.

Giovannoni SJ, Hayakawa DH, Tripp HJ, Stingl U, Givan SA, Cho JC, Oh HM, Kitner JB, Vergin KL, Rappé MS.

Environ Microbiol. 2008 Jul;10(7):1771-82. doi: 10.1111/j.1462-2920.2008.01598.x. Epub 2008 Apr 3.

PMID:
18393994
33.

Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, Givan SA, Yanovsky M, Hong F, Kay SA, Chory J.

PLoS Genet. 2008 Feb;4(2):e14. doi: 10.1371/journal.pgen.0040014.

34.
35.

Update of ASRP: the Arabidopsis Small RNA Project database.

Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD.

Nucleic Acids Res. 2008 Jan;36(Database issue):D982-5. Epub 2007 Nov 13.

36.

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data.

Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ.

Biol Direct. 2007 Nov 7;2:27.

37.

Polyphyletic photosynthetic reaction centre genes in oligotrophic marine Gammaproteobacteria.

Cho JC, Stapels MD, Morris RM, Vergin KL, Schwalbach MS, Givan SA, Barofsky DF, Giovannoni SJ.

Environ Microbiol. 2007 Jun;9(6):1456-63.

PMID:
17504483
38.

Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.

Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC.

Plant Cell. 2007 Mar;19(3):926-42. Epub 2007 Mar 30.

39.

High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC.

PLoS One. 2007 Feb 14;2(2):e219.

40.

Genome-wide profiling and analysis of Arabidopsis siRNAs.

Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC.

PLoS Biol. 2007 Mar;5(3):e57.

41.

Toxicogenomic profiling of the hepatic tumor promoters indole-3-carbinol, 17beta-estradiol and beta-naphthoflavone in rainbow trout.

Tilton SC, Givan SA, Pereira CB, Bailey GS, Williams DE.

Toxicol Sci. 2006 Mar;90(1):61-72. Epub 2005 Sep 28.

PMID:
16192472
42.

Use of a rainbow trout oligonucleotide microarray to determine transcriptional patterns in aflatoxin B1-induced hepatocellular carcinoma compared to adjacent liver.

Tilton SC, Gerwick LG, Hendricks JD, Rosato CS, Corley-Smith G, Givan SA, Bailey GS, Bayne CJ, Williams DE.

Toxicol Sci. 2005 Dec;88(2):319-30. Epub 2005 Sep 1.

PMID:
16141433
43.

Expression of Arabidopsis MIRNA genes.

Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC.

Plant Physiol. 2005 Aug;138(4):2145-54. Epub 2005 Jul 22.

44.

GTPase-activating proteins for Cdc42.

Smith GR, Givan SA, Cullen P, Sprague GF Jr.

Eukaryot Cell. 2002 Jun;1(3):469-80.

45.

Ctf3p, the Mis6 budding yeast homolog, interacts with Mcm22p and Mcm16p at the yeast outer kinetochore.

Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, Fields S, Davis TN, Hieter P.

Genes Dev. 2002 Jan 1;16(1):101-13.

46.

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