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Items: 34

1.

Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.

Jang H, Woo J, Lee Y, Negrete F, Finkelstein S, Chase HR, Addy N, Ewing L, Beaubrun JJG, Patel I, Gangiredla J, Eshwar A, Jaradat ZW, Seo K, Shabarinath S, Fanning S, Stephan R, Lehner A, Tall BD, Gopinath GR.

Stand Genomic Sci. 2018 Nov 29;13:35. doi: 10.1186/s40793-018-0339-6. eCollection 2018.

2.

RNA Sequencing-Based Transcriptional Overview of Xerotolerance in Cronobacter sakazakii SP291.

Srikumar S, Cao Y, Yan Q, Van Hoorde K, Nguyen S, Cooney S, Gopinath GR, Tall BD, Sivasankaran SK, Lehner A, Stephan R, Fanning S.

Appl Environ Microbiol. 2019 Jan 23;85(3). pii: e01993-18. doi: 10.1128/AEM.01993-18. Print 2019 Feb 1.

PMID:
30446557
3.

Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis.

Carter L, Chase HR, Gieseker CM, Hasbrouck NR, Stine CB, Khan A, Ewing-Peeples LJ, Tall BD, Gopinath GR.

Int J Food Microbiol. 2018 Nov 2;284:31-39. doi: 10.1016/j.ijfoodmicro.2018.06.016. Epub 2018 Jun 27.

4.

Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments.

Jang H, Addy N, Ewing L, Jean-Gilles Beaubrun J, Lee Y, Woo J, Negrete F, Finkelstein S, Tall BD, Lehner A, Eshwar A, Gopinath GR.

Genome Announc. 2018 Apr 12;6(15). pii: e00223-18. doi: 10.1128/genomeA.00223-18.

5.

A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes.

Gopinath GR, Cinar HN, Murphy HR, Durigan M, Almeria M, Tall BD, DaSilva AJ.

Gut Pathog. 2018 Apr 10;10:15. doi: 10.1186/s13099-018-0242-0. eCollection 2018.

6.

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples.

Gopinath GR, Chase HR, Gangiredla J, Eshwar A, Jang H, Patel I, Negrete F, Finkelstein S, Park E, Chung T, Yoo Y, Woo J, Lee Y, Park J, Choi H, Jeong S, Jun S, Kim M, Lee C, Jeong H, Fanning S, Stephan R, Iversen C, Reich F, Klein G, Lehner A, Tall BD.

Gut Pathog. 2018 Mar 10;10:11. doi: 10.1186/s13099-018-0238-9. eCollection 2018.

7.

Detection of Salmonella enterica subsp. enterica Serovar Cubana from Naturally Contaminated Chick Feed.

Benahmed F, Wang H, Beaubrun JJ, Gopinath GR, Cheng CM, Hanes DE, Hammack TS, Rasmussen M, Davidson MK.

J Food Prot. 2017 Nov;80(11):1815-1820. doi: 10.4315/0362-028X.JFP-16-344. Erratum in: J Food Prot. 2018 Feb;81(2):170.

PMID:
28981377
8.

Draft Genome Sequence of Cronobacter sakazakii GP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato's Rhizoplane/Rhizosphere Continuum.

Chase HR, Eberl L, Stephan R, Jeong H, Lee C, Finkelstein S, Negrete F, Gangiredla J, Patel I, Tall BD, Gopinath GR, Lehner A.

Genome Announc. 2017 Aug 3;5(31). pii: e00723-17. doi: 10.1128/genomeA.00723-17.

9.

Comparative Genomic Characterization of the Highly Persistent and Potentially Virulent Cronobacter sakazakii ST83, CC65 Strain H322 and Other ST83 Strains.

Chase HR, Gopinath GR, Eshwar AK, Stoller A, Fricker-Feer C, Gangiredla J, Patel IR, Cinar HN, Jeong H, Lee C, Negrete F, Finkelstein S, Stephan R, Tall BD, Lehner A.

Front Microbiol. 2017 Jun 26;8:1136. doi: 10.3389/fmicb.2017.01136. eCollection 2017.

10.

Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology.

Tall BD, Gangiredla J, Grim CJ, Patel IR, Jackson SA, Mammel MK, Kothary MH, Sathyamoorthy V, Carter L, Fanning S, Iversen C, Pagotto F, Stephan R, Lehner A, Farber J, Yan QQ, Gopinath GR.

Microarrays (Basel). 2017 Mar 4;6(1). pii: E6. doi: 10.3390/microarrays6010006. Review.

11.

Analysis and Characterization of Proteins Associated with Outer Membrane Vesicles Secreted by Cronobacter spp.

Kothary MH, Gopinath GR, Gangiredla J, Rallabhandi PV, Harrison LM, Yan QQ, Chase HR, Lee B, Park E, Yoo Y, Chung T, Finkelstein SB, Negrete FJ, Patel IR, Carter L, Sathyamoorthy V, Fanning S, Tall BD.

Front Microbiol. 2017 Feb 9;8:134. doi: 10.3389/fmicb.2017.00134. eCollection 2017.

12.

Draft Genome Sequences of Enterotoxigenic Bacillus cereus Strains Obtained from Powdered Infant Formula.

Carter L, Chase HR, Choi H, Jun S, Park J, Jeong S, Kim M, Han K, Lee C, Jeong H, Finkelstein S, Negrete F, Cinar HN, Tall BD, Gopinath GR.

Genome Announc. 2017 Feb 23;5(8). pii: e01644-16. doi: 10.1128/genomeA.01644-16.

13.

Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions.

Cinar HN, Qvarnstrom Y, Wei-Pridgeon Y, Li W, Nascimento FS, Arrowood MJ, Murphy HR, Jang A, Kim E, Kim R, da Silva A, Gopinath GR.

Parasit Vectors. 2016 Nov 29;9(1):611.

14.

Genome Sequences of Malonate-Positive Cronobacter sakazakii Serogroup O:2, Sequence Type 64 Strains CDC 1121-73 and GK1025, Isolated from Human Bronchial Wash and a Powdered Infant Formula Manufacturing Plant.

Chase HR, Gopinath GR, Gangiredla J, Patel IR, Kothary MH, Carter L, Sathyamoorthy V, Lee B, Park E, Yoo YJ, Chung TJ, Choi H, Jun S, Park J, Jeong S, Kim M, Reich F, Klein G, Tall BD.

Genome Announc. 2016 Nov 10;4(6). pii: e01072-16. doi: 10.1128/genomeA.01072-16.

15.

Diverse profiles of N-acyl-homoserine lactones in biofilm forming isolates of Cronobacter sakazakii.

Tall BD, Chase HR, Gopinath GR.

Virulence. 2017 Apr 3;8(3):246-247. doi: 10.1080/21505594.2016.1240861. Epub 2016 Sep 27. No abstract available.

16.

Purification and Characterization of a Rabbit Serum Factor That Kills Listeria Species and Other Foodborne Bacterial Pathogens.

Kothary MH, Franco AA, Tall BD, Gopinath GR, Datta AR.

Foodborne Pathog Dis. 2016 Aug;13(8):441-7. doi: 10.1089/fpd.2015.2109. Epub 2016 Jul 25.

PMID:
27455064
17.

Linking Genomo- and Pathotype: Exploiting the Zebrafish Embryo Model to Investigate the Divergent Virulence Potential among Cronobacter spp.

Eshwar AK, Tall BD, Gangiredla J, Gopinath GR, Patel IR, Neuhauss SC, Stephan R, Lehner A.

PLoS One. 2016 Jun 29;11(6):e0158428. doi: 10.1371/journal.pone.0158428. eCollection 2016.

18.

Genome Sequence of Cronobacter sakazakii Serogroup O:4, Sequence Type 4 Strain CDC 2009-03746, Isolated from a Fatal Case of Infantile Meningitis.

Grim CJ, Gopinath GR, Jarvis KG, Sathyamoorthy V, Trach LH, Chase HR, Tall BD.

Genome Announc. 2015 May 21;3(3). pii: e00492-15. doi: 10.1128/genomeA.00492-15.

19.

Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

Tall BD, Gangiredla J, Gopinath GR, Yan Q, Chase HR, Lee B, Hwang S, Trach L, Park E, Yoo Y, Chung T, Jackson SA, Patel IR, Sathyamoorthy V, Pava-Ripoll M, Kotewicz ML, Carter L, Iversen C, Pagotto F, Stephan R, Lehner A, Fanning S, Grim CJ.

Front Pediatr. 2015 Apr 30;3:36. doi: 10.3389/fped.2015.00036. eCollection 2015.

20.

Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain.

Yan Q, Wang J, Gangiredla J, Cao Y, Martins M, Gopinath GR, Stephan R, Lampel K, Tall BD, Fanning S.

Appl Environ Microbiol. 2015 Jul;81(13):4388-402. doi: 10.1128/AEM.00359-15. Epub 2015 Apr 24.

21.

Draft Genome Sequences of Streptococcus bovis Strains ATCC 33317 and JB1.

Benahmed FH, Gopinath GR, Harbottle H, Cotta MA, Luo Y, Henderson C, Teri P, Soppet D, Rasmussen M, Whitehead TR, Davidson M.

Genome Announc. 2014 Oct 9;2(5). pii: e01012-14. doi: 10.1128/genomeA.01012-14.

22.

Cronobacter: an emergent pathogen causing meningitis to neonates through their feeds.

Tall BD, Chen Y, Yan Q, Gopinath GR, Grim CJ, Jarvis KG, Fanning S, Lampel KA.

Sci Prog. 2014;97(Pt 2):154-72.

PMID:
25108996
24.

Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Cubana Strains Isolated from Agricultural Sources.

Benahmed FH, Gopinath GR, Wang H, Jean-Gilles Beaubrun J, Grim C, Cheng CM, McClelland M, Ayers S, Abbott J, Desai P, Frye JG, Weinstock G, Hammack TS, Hanes DE, Rasmussen MA, Davidson MK.

Genome Announc. 2014 Jan 23;2(1). pii: e01184-13. doi: 10.1128/genomeA.01184-13.

25.

Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder.

Grim CJ, Gopinath GR, Mammel MK, Sathyamoorthy V, Trach LH, Chase HR, Tall BD, Fanning S, Stephan R.

Genome Announc. 2013 Dec 12;1(6). pii: e01038-13. doi: 10.1128/genomeA.01038-13.

26.

Genome Sequence of Enterobacter turicensis Strain 610/05 (LMG 23731), Isolated from Fruit Powder.

Stephan R, Grim CJ, Gopinath GR, Mammel MK, Sathyamoorthy V, Trach LH, Chase HR, Fanning S, Tall BD.

Genome Announc. 2013 Dec 26;1(6). pii: e00996-13. doi: 10.1128/genomeA.00996-13.

27.

Genome Sequences of Two Enterobacter pulveris Strains, 601/05T (=LMG 24057T =DSM 19144T) and 1160/04 (=LMG 24058 =DSM 19146), Isolated from Fruit Powder.

Gopinath GR, Grim CJ, Tall BD, Mammel MK, Sathyamoorthy V, Trach LH, Chase HR, Fanning S, Stephan R.

Genome Announc. 2013 Dec 5;1(6). pii: e00991-13. doi: 10.1128/genomeA.00991-13.

28.

Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility.

Yan Q, Power KA, Cooney S, Fox E, Gopinath GR, Grim CJ, Tall BD, McCusker MP, Fanning S.

Front Microbiol. 2013 Sep 2;4:256. doi: 10.3389/fmicb.2013.00256. eCollection 2013.

29.

The Rat Genome Database (RGD): developments towards a phenome database.

de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D485-91.

30.

Reactome: a knowledgebase of biological pathways.

Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D428-32.

31.

The Genome Knowledgebase: a resource for biologists and bioinformaticists.

Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D'Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L.

Cold Spring Harb Symp Quant Biol. 2003;68:237-43. No abstract available.

PMID:
15338623
32.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

33.

Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data.

Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ.

Genome Res. 2004 Apr;14(4):651-60.

34.

Identification of rat mammary tumor-1 gene (RMT-1), which is highly expressed in rat mammary tumors.

Chiou S, Yoo J, Loh KC, Guzman RC, Gopinath GR, Rajkumar L, Chou YC, Yang J, Popescu NC, Nandi S.

Cancer Lett. 2001 Dec 10;174(1):45-55.

PMID:
11675151

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