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Items: 30

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. 2020 Jan 8;48(D1):D606-D612. doi: 10.1093/nar/gkz943.

PMID:
31667520
2.

A machine learning-based service for estimating quality of genomes using PATRIC.

Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch GD, Vonstein V, Overbeek R.

BMC Bioinformatics. 2019 Oct 3;20(1):486. doi: 10.1186/s12859-019-3068-y.

3.

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
4.

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.

5.

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.

6.

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data.

Faria JP, Overbeek R, Taylor RC, Conrad N, Vonstein V, Goelzer A, Fromion V, Rocha M, Rocha I, Henry CS.

Front Microbiol. 2016 Mar 18;7:275. doi: 10.3389/fmicb.2016.00275. eCollection 2016.

7.

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.

8.

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.

9.

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.

10.

In search of genome annotation consistency: solid gene clusters and how to use them.

Davis JJ, Olsen GJ, Overbeek R, Vonstein V, Xia F.

3 Biotech. 2014 Jun;4(3):331-335. doi: 10.1007/s13205-013-0152-2. Epub 2013 Jul 6.

11.

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.

12.

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.

13.

Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.

Devoid S, Overbeek R, DeJongh M, Vonstein V, Best AA, Henry C.

Methods Mol Biol. 2013;985:17-45. doi: 10.1007/978-1-62703-299-5_2.

PMID:
23417797
14.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

15.

Real time metagenomics: using k-mers to annotate metagenomes.

Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R.

Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9.

16.

Connecting genotype to phenotype in the era of high-throughput sequencing.

Henry CS, Overbeek R, Xia F, Best AA, Glass E, Gilbert J, Larsen P, Edwards R, Disz T, Meyer F, Vonstein V, Dejongh M, Bartels D, Desai N, D'Souza M, Devoid S, Keegan KP, Olson R, Wilke A, Wilkening J, Stevens RL.

Biochim Biophys Acta. 2011 Oct;1810(10):967-77. doi: 10.1016/j.bbagen.2011.03.010. Epub 2011 Mar 21. Review.

PMID:
21421023
17.

Accessing the SEED genome databases via Web services API: tools for programmers.

Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA.

BMC Bioinformatics. 2010 Jun 14;11:319. doi: 10.1186/1471-2105-11-319.

18.

Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities.

Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA.

Microbiol Mol Biol Rev. 2008 Mar;72(1):13-53, table of contents. doi: 10.1128/MMBR.00026-07. Review.

19.

The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.

BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.

20.

Annotation of bacterial and archaeal genomes: improving accuracy and consistency.

Overbeek R, Bartels D, Vonstein V, Meyer F.

Chem Rev. 2007 Aug;107(8):3431-47. Epub 2007 Jul 21. Review. No abstract available.

PMID:
17658903
21.

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.

22.

Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover.

Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM.

J Bacteriol. 2006 Oct;188(19):6739-56.

23.

Comparative genomics of NAD biosynthesis in cyanobacteria.

Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL.

J Bacteriol. 2006 Apr;188(8):3012-23.

24.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005.

25.

The ERGO genome analysis and discovery system.

Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N.

Nucleic Acids Res. 2003 Jan 1;31(1):164-71.

26.

Archaeal shikimate kinase, a new member of the GHMP-kinase family.

Daugherty M, Vonstein V, Overbeek R, Osterman A.

J Bacteriol. 2001 Jan;183(1):292-300.

27.

Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools.

Kyrpides NC, Ouzounis CA, Iliopoulos I, Vonstein V, Overbeek R.

Nucleic Acids Res. 2000 Nov 15;28(22):4573-6.

28.

Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans.

Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M.

Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3509-14.

29.

Molecular cloning of the pyrE gene from the extreme thermophile Thermus flavus.

Vonstein V, Johnson SP, Yu H, Casadaban MJ, Pagratis NC, Weber JM, Demirjian DC.

J Bacteriol. 1995 Aug;177(15):4540-3.

30.

A chromosome integration system for stable gene transfer into Thermus flavus.

Weber JM, Johnson SP, Vonstein V, Casadaban MJ, Demirjian DC.

Biotechnology (N Y). 1995 Mar;13(3):271-5.

PMID:
9634770

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