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Items: 1 to 20 of 101

1.

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM, Gabbard JL, Gerdes S, Guard A, Kenyon RW, Machi D, Mao C, Murphy-Olson D, Nguyen M, Nordberg EK, Olsen GJ, Olson RD, Overbeek JC, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomas C, VanOeffelen M, Vonstein V, Warren AS, Xia F, Xie D, Yoo H, Stevens R.

Nucleic Acids Res. 2019 Oct 31. pii: gkz943. doi: 10.1093/nar/gkz943. [Epub ahead of print]

PMID:
31667520
2.

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.

3.

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.

4.

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.

5.

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.

6.

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. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083.

7.

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
8.

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.

9.

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
10.

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.

11.

Public health and evidence-informed policy-making: The case of a commonly used herbicide.

Vainio H.

Scand J Work Environ Health. 2019 Sep 5. pii: 3851. doi: 10.5271/sjweh.3851. [Epub ahead of print]

12.

Database resources for the tuberculosis community.

Lew JM, Mao C, Shukla M, Warren A, Will R, Kuznetsov D, Xenarios I, Robertson BD, Gordon SV, Schnappinger D, Cole ST, Sobral B.

Tuberculosis (Edinb). 2013 Jan;93(1):12-7. doi: 10.1016/j.tube.2012.11.003. Epub 2013 Jan 17. Review.

13.

The BioExtract Server: a web-based bioinformatic workflow platform.

Lushbough CM, Jennewein DM, Brendel VP.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W528-32. doi: 10.1093/nar/gkr286. Epub 2011 May 5.

14.

The Pathogen-annotated Tracking Resource Network (PATRN) system: a web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease.

Gopinath G, Hari K, Jain R, Mammel MK, Kothary MH, Franco AA, Grim CJ, Jarvis KG, Sathyamoorthy V, Hu L, Datta AR, Patel IR, Jackson SA, Gangiredla J, Kotewicz ML, LeClerc JE, Wekell M, McCardell BA, Solomotis MD, Tall BD.

Food Microbiol. 2013 Jun;34(2):303-18. doi: 10.1016/j.fm.2013.01.001. Epub 2013 Jan 23.

PMID:
23541197
15.

Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.

Lefkowitz EJ, Upton C, Changayil SS, Buck C, Traktman P, Buller RM.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D311-6.

16.

Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.

Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH.

Viruses. 2012 Nov 19;4(11):3209-26. doi: 10.3390/v4113209.

17.

A Comparison of Microbial Genome Web Portals.

Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R.

Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019. Review.

18.

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S; VectorBase Consortium, Madey G, Collins FH, Lawson D.

Nucleic Acids Res. 2015 Jan;43(Database issue):D707-13. doi: 10.1093/nar/gku1117. Epub 2014 Dec 15.

19.

Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned.

Sullivan DE, Gabbard JL Jr, Shukla M, Sobral B.

Chem Biodivers. 2010 May;7(5):1124-41. doi: 10.1002/cbdv.200900317. Review.

20.

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. Epub 2006 Dec 1.

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