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Items: 13

1.

Disparities in spread and control of influenza in slums of Delhi: findings from an agent-based modelling study.

Adiga A, Chu S, Eubank S, Kuhlman CJ, Lewis B, Marathe A, Marathe M, Nordberg EK, Swarup S, Vullikanti A, Wilson ML.

BMJ Open. 2018 Jan 21;8(1):e017353. doi: 10.1136/bmjopen-2017-017353.

2.

Isolation and molecular characterization of group B Streptococcus from laboratory Long-Evans rats (Rattus norvegicus) with and without invasive group B streptococcal disease.

Bodi Winn C, Bakthavatchalu V, Esmail MY, Feng Y, Dzink-Fox J, Richey L, Perkins SE, Nordberg EK, Fox JG.

J Med Microbiol. 2017 Nov 21. doi: 10.1099/jmm.0.000627. [Epub ahead of print]

3.

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
4.

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.

5.

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

Tufariello JM, Kerantzas CA, Vilch├Ęze 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.

6.

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.

7.

Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.

Driscoll T, Gillespie JJ, Nordberg EK, Azad AF, Sobral BW.

Genome Biol Evol. 2013;5(4):621-45. doi: 10.1093/gbe/evt036.

8.

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.

9.

Phylogeny of gammaproteobacteria.

Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW.

J Bacteriol. 2010 May;192(9):2305-14. doi: 10.1128/JB.01480-09. Epub 2010 Mar 5.

10.

Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.

Gillespie JJ, Williams K, Shukla M, Snyder EE, Nordberg EK, Ceraul SM, Dharmanolla C, Rainey D, Soneja J, Shallom JM, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, Setubal JC, Azad AF, Sobral BS.

PLoS One. 2008;3(4):e2018. doi: 10.1371/journal.pone.0002018. Epub 2008 Apr 16.

11.

PATRIC: the VBI PathoSystems Resource Integration Center.

Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW.

Nucleic Acids Res. 2007 Jan;35(Database issue):D401-6. Epub 2006 Nov 16.

12.

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL.

Science. 2006 Sep 1;313(5791):1261-6.

13.

YODA: selecting signature oligonucleotides.

Nordberg EK.

Bioinformatics. 2005 Apr 15;21(8):1365-70. Epub 2004 Nov 30.

PMID:
15572465

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