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Items: 42

1.

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation.

Ibraim IC, Parise MTD, Parise D, Sfeir MZT, de Paula Castro TL, Wattam AR, Ghosh P, Barh D, Souza EM, Góes-Neto A, Gomide ACP, Azevedo V.

BMC Genomics. 2019 Aug 20;20(1):663. doi: 10.1186/s12864-019-6018-1.

2.

Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina.

Gagetti P, Wattam AR, Giacoboni G, De Paulis A, Bertona E, Corso A, Rosato AE.

BMC Vet Res. 2019 Jul 27;15(1):264. doi: 10.1186/s12917-019-1990-x.

3.

Whole genome sequence analysis of NDM-1, CMY-4, and SHV-12 coproducing Salmonella enterica serovar Typhimurium isolated from a case of fatal burn wound infection.

Banerjee K, Sekar P, Krishnan P, Wattam AR, Roy S, Hays JP, Menezes GA.

Infect Drug Resist. 2018 Nov 28;11:2491-2495. doi: 10.2147/IDR.S167027. eCollection 2018.

4.

Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis.

Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V.

PLoS One. 2018 Nov 12;13(11):e0207304. doi: 10.1371/journal.pone.0207304. eCollection 2018.

5.

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems.

Imchen M, Kumavath R, Barh D, Vaz A, Góes-Neto A, Tiwari S, Ghosh P, Wattam AR, Azevedo V.

Sci Rep. 2018 Jul 25;8(1):11187. doi: 10.1038/s41598-018-29521-4.

6.

Cell Division in genus Corynebacterium: protein-protein interaction and molecular docking of SepF and FtsZ in the understanding of cytokinesis in pathogenic species.

Oliveira AF Jr, Folador EL, Gomide ACP, Goes-Neto A, Azevedo VAC, Wattam AR.

An Acad Bras Cienc. 2018 Aug;90(2 suppl 1):2179-2188. doi: 10.1590/0001-3765201820170385. Epub 2018 Feb 15.

7.

Author Correction: Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P, Viana M, Wattam AR.

Sci Rep. 2018 Jan 4;8(1):165. doi: 10.1038/s41598-017-18550-0.

8.

Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.

Wattam AR, Brettin T, Davis JJ, Gerdes S, Kenyon R, Machi D, Mao C, Olson R, Overbeek R, Pusch GD, Shukla MP, Stevens R, Vonstein V, Warren A, Xia F, Yoo H.

Methods Mol Biol. 2018;1704:79-101. doi: 10.1007/978-1-4939-7463-4_4. Review.

PMID:
29277864
9.

Comparative Genomics for Prokaryotes.

Setubal JC, Almeida NF, Wattam AR.

Methods Mol Biol. 2018;1704:55-78. doi: 10.1007/978-1-4939-7463-4_3. Review.

PMID:
29277863
10.

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species.

Oliveira A, Oliveira LC, Aburjaile F, Benevides L, Tiwari S, Jamal SB, Silva A, Figueiredo HCP, Ghosh P, Portela RW, De Carvalho Azevedo VA, Wattam AR.

Front Microbiol. 2017 Oct 12;8:1937. doi: 10.3389/fmicb.2017.01937. eCollection 2017. Review.

11.

PATRIC as a unique resource for studying antimicrobial resistance.

Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.

Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. [Epub ahead of print]

PMID:
28968762
12.

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P, Viana M, Wattam AR.

Sci Rep. 2017 Aug 18;7(1):8859. doi: 10.1038/s41598-017-09254-6. Erratum in: Sci Rep. 2018 Jan 4;8(1):165.

13.

Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.

Viana MVC, Figueiredo H, Ramos R, Guimarães LC, Pereira FL, Dorella FA, Selim SAK, Salaheldean M, Silva A, Wattam AR, Azevedo V.

PLoS One. 2017 Apr 26;12(4):e0176347. doi: 10.1371/journal.pone.0176347. eCollection 2017.

14.

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts.

Al Dahouk S, Köhler S, Occhialini A, Jiménez de Bagüés MP, Hammerl JA, Eisenberg T, Vergnaud G, Cloeckaert A, Zygmunt MS, Whatmore AM, Melzer F, Drees KP, Foster JT, Wattam AR, Scholz HC.

Sci Rep. 2017 Mar 16;7:44420. doi: 10.1038/srep44420.

15.

Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart.

Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR.

Genome Announc. 2017 Mar 2;5(9). pii: e01687-16. doi: 10.1128/genomeA.01687-16.

16.

Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog.

Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR.

Genome Announc. 2017 Feb 23;5(8). pii: e01688-16. doi: 10.1128/genomeA.01688-16.

17.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.

Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

18.

Antimicrobial Resistance Prediction in PATRIC and RAST.

Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R.

Sci Rep. 2016 Jun 14;6:27930. doi: 10.1038/srep27930.

19.

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.

Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H.

Front Microbiol. 2016 Feb 8;7:118. doi: 10.3389/fmicb.2016.00118. eCollection 2016.

20.

The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.

Tufariello JM, Kerantzas CA, Vilchèze C, Calder RB, Nordberg EK, Fischer JA, Hartman TE, Yang E, Driscoll T, Cole LE, Sebra R, Maqbool SB, Wattam AR, Jacobs WR Jr.

MBio. 2015 Nov 17;6(6):e01313-15. doi: 10.1128/mBio.01313-15.

21.

Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing.

Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan D.

J Bacteriol. 2015 Nov 9;198(3):427-35. doi: 10.1128/JB.00711-15. Print 2016 Feb 1.

22.

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F.

Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365.

23.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B.

Bioinformatics. 2015 May 1;31(9):1496-8. doi: 10.1093/bioinformatics/btv002. Epub 2015 Jan 7.

24.

Enabling comparative modeling of closely related genomes: example genus Brucella.

Faria JP, Edirisinghe JN, Davis JJ, Disz T, Hausmann A, Henry CS, Olson R, Overbeek RA, Pusch GD, Shukla M, Vonstein V, Wattam AR.

3 Biotech. 2015 Feb;5(1):101-105. doi: 10.1007/s13205-014-0202-4. Epub 2014 Mar 8.

25.

Curation, integration and visualization of bacterial virulence factors in PATRIC.

Mao C, Abraham D, Wattam AR, Wilson MJ, Shukla M, Yoo HS, Sobral BW.

Bioinformatics. 2015 Jan 15;31(2):252-8. doi: 10.1093/bioinformatics/btu631. Epub 2014 Sep 30.

26.

Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids.

Panas MW, Jain P, Yang H, Mitra S, Biswas D, Wattam AR, Letvin NL, Jacobs WR Jr.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13264-71. doi: 10.1073/pnas.1414207111. Epub 2014 Sep 2.

27.

Comparative genomic analysis at the PATRIC, a bioinformatic resource center.

Wattam AR, Gabbard JL, Shukla M, Sobral BW.

Methods Mol Biol. 2014;1197:287-308. doi: 10.1007/978-1-4939-1261-2_17.

PMID:
25172288
28.

Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.

Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, Keim P, Pearson T, Shukla M, Ward DV, Williams KP, Sobral BW, Tsolis RM, Whatmore AM, O'Callaghan D.

J Bacteriol. 2014 Mar;196(5):920-30. doi: 10.1128/JB.01091-13. Epub 2013 Dec 13.

29.

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.

Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29.

30.

PATRIC, the bacterial bioinformatics database and analysis resource.

Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12.

31.

Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages.

Rajasekaran P, Alexander JC, Seleem MN, Jain N, Sriranganathan N, Wattam AR, Setubal JC, Boyle SM.

Int J Antimicrob Agents. 2013 Apr;41(4):358-62. doi: 10.1016/j.ijantimicag.2012.11.017. Epub 2013 Jan 8.

32.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Nov 6;3(5):e00246-11. doi: 10.1128/mBio.00388-12.

33.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Aug 28;3(5):e00246-12. doi: 10.1128/mBio.00246-12. Print 2012. Erratum in: MBio. 2012 Nov-Dec;3(6):e00388-12.

34.

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.

Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW.

Infect Immun. 2011 Nov;79(11):4286-98. doi: 10.1128/IAI.00207-11. Epub 2011 Sep 6. Review.

35.

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.

Wattam AR, Williams KP, Snyder EE, Almeida NF Jr, Shukla M, Dickerman AW, Crasta OR, Kenyon R, Lu J, Shallom JM, Yoo H, Ficht TA, Tsolis RM, Munk C, Tapia R, Han CS, Detter JC, Bruce D, Brettin TS, Sobral BW, Boyle SM, Setubal JC.

J Bacteriol. 2009 Jun;191(11):3569-79. doi: 10.1128/JB.01767-08. Epub 2009 Apr 3.

36.

PIML: the Pathogen Information Markup Language.

He Y, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BW.

Bioinformatics. 2005 Jan 1;21(1):116-21. Epub 2004 Aug 5.

PMID:
15297293
37.

An important step forward in the genetic manipulation of mosquito vectors of human disease.

Kidwell MG, Wattam AR.

Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3349-50. No abstract available.

38.
39.

Variation in Aedes aegypti mRNA populations related to strain, sex, and development.

Wattam AR, Christensen BM.

Am J Trop Med Hyg. 1992 Nov;47(5):702-7.

PMID:
1449211
40.

Induced polypeptides associated with filarial worm refractoriness in Aedes aegypti.

Wattam AR, Christensen BM.

Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6502-5.

41.

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