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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.


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.


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.


Phage Genome Annotation Using the RAST Pipeline.

McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R.

Methods Mol Biol. 2018;1681:231-238. doi: 10.1007/978-1-4939-7343-9_17.


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.


Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

Faria JP, Davis JJ, Edirisinghe JN, Taylor RC, Weisenhorn P, Olson RD, Stevens RL, Rocha M, Rocha I, Best AA, DeJongh M, Tintle NL, Parrello B, Overbeek R, Henry CS.

Front Microbiol. 2016 Nov 24;7:1819. eCollection 2016.


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.


Modeling central metabolism and energy biosynthesis across microbial life.

Edirisinghe JN, Weisenhorn P, Conrad N, Xia F, Overbeek R, Stevens RL, Henry CS.

BMC Genomics. 2016 Aug 8;17:568. doi: 10.1186/s12864-016-2887-8.


From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model.

Cuevas DA, Edirisinghe J, Henry CS, Overbeek R, O'Connell TG, Edwards RA.

Front Microbiol. 2016 Jun 17;7:907. doi: 10.3389/fmicb.2016.00907. eCollection 2016.


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.


A relationship between temperature and aggression in NFL football penalties.

Craig C, Overbeek RW, Condon MV, Rinaldo SB.

J Sport Health Sci. 2016 Jun;5(2):205-210. doi: 10.1016/j.jshs.2015.01.001. Epub 2015 Jan 9.


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.


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.


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.


High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS.

Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9645-50. doi: 10.1073/pnas.1401329111. Epub 2014 Jun 9.


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.


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.


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.


Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes.

Davis JJ, Xia F, Overbeek RA, Olsen GJ.

Int J Syst Evol Microbiol. 2013 Jul;63(Pt 7):2727-41. doi: 10.1099/ijs.0.048983-0. Epub 2013 Apr 19.


Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS.

Brief Bioinform. 2014 Jul;15(4):592-611.


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.


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.


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.


Assessment of appropriateness of screening community-dwelling older people to prevent functional decline.

Drewes YM, Gussekloo J, van der Meer V, Rigter H, Dekker JH, Goumans MJ, Metsemakers JF, van Overbeek R, de Rooij SE, Schers HJ, Schuurmans MJ, Sturmans F, de Vries K, Westendorp RG, Wind AW, Assendelft WJ.

J Am Geriatr Soc. 2012 Jan;60(1):42-50. doi: 10.1111/j.1532-5415.2011.03775.x. Epub 2011 Dec 16.


Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. doi: 10.1186/1471-2164-12-S1-S3.


Synergistic use of plant-prokaryote comparative genomics for functional annotations.

Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Núñez A, Pribat A, Waller JC, Wilke A, Overbeek R, Hanson AD, de Crécy-Lagard V.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S2. doi: 10.1186/1471-2164-12-S1-S2.


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.


Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.

Rodionov DA, Yang C, Li X, Rodionova IA, Wang Y, Obraztsova AY, Zagnitko OP, Overbeek R, Romine MF, Reed S, Fredrickson JK, Nealson KH, Osterman AL.

BMC Genomics. 2010 Sep 13;11:494. doi: 10.1186/1471-2164-11-494.


Building the blueprint of life.

Henry C, Overbeek R, Stevens RL.

Biotechnol J. 2010 Jul;5(7):695-704. doi: 10.1002/biot.201000076. Review.


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.


FIGfams: yet another set of protein families.

Meyer F, Overbeek R, Rodriguez A.

Nucleic Acids Res. 2009 Nov;37(20):6643-54. doi: 10.1093/nar/gkp698. Epub 2009 Sep 17.


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.


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.


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.


Moving to a higher level of abstraction.

Overbeek R.

Environ Microbiol. 2007 Jan;9(1):7-8. No abstract available.


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.


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.


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.


Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives.

Roberts C, Anderson KL, Murphy E, Projan SJ, Mounts W, Hurlburt B, Smeltzer M, Overbeek R, Disz T, Dunman PM.

J Bacteriol. 2006 Apr;188(7):2593-603.


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.


Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.

Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, Markd'Souza, Larsen N, Pusch G, Liolios K, Grechkin Y, Lapidus A, Goltsman E, Chu L, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N, Ivanova N.

FEMS Microbiol Lett. 2005 Sep 15;250(2):175-84.


Automatic detection of subsystem/pathway variants in genome analysis.

Ye Y, Osterman A, Overbeek R, Godzik A.

Bioinformatics. 2005 Jun;21 Suppl 1:i478-86.


Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.

Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P.

Nat Biotechnol. 2004 Dec;22(12):1554-8. Epub 2004 Nov 14.


Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL.

J Bacteriol. 2003 Oct;185(19):5673-84.


Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.

Kapatral V, Ivanova N, Anderson I, Reznik G, Bhattacharyya A, Gardner WL, Mikhailova N, Lapidus A, Larsen N, D'Souza M, Walunas T, Haselkorn R, Overbeek R, Kyrpides N.

Genome Res. 2003 Jun;13(6A):1180-9.


Bioinformatics classification and functional analysis of PhoH homologs.

Kazakov AE, Vassieva O, Gelfand MS, Osterman A, Overbeek R.

In Silico Biol. 2003;3(1-2):3-15. Epub 2002 Dec 30.


Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.

Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N.

Nature. 2003 May 1;423(6935):87-91.


Missing genes in metabolic pathways: a comparative genomics approach.

Osterman A, Overbeek R.

Curr Opin Chem Biol. 2003 Apr;7(2):238-51. Review.


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.

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