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1. Overbeek, R., Devine, D., and Vonstein, V. Curation Is Forever: Comparative Genomics Approaches to Functional Annotation. TARGETS 2003 2:138-146

2. Farahi K, Pusch GD, Overbeek R, Whitman WB.  Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method.  J Mol Evol. 2004 May;58(5):615-31.

3. Overbeek R., Disz T. and Stevens R. The SEED: A Peer-to-Peer Environment for Genome Annotation. Communications of the ACM, November 2004 Volume 47(11):46-50.

4. Ye Y, Osterman A, Overbeek R, Godzik A. (2005) Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics. 21 Suppl 1:i478-i486.

5. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-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, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33(17):5691-702.

6. Weinstock, G. M., Robinson, G. E., Gibbs, R. A., Worley, K. C., Evans, J. D., Maleszka, R., Robertson, H. M., Weaver, D. B., Beye, M., Bork, P., Elsik, C. G., Hartfelder, K., Hunt, G. J., Zdobnov, E. M., Amdam, G. V., Bitondi, M. M. G., Collins, A. M., Cristino, A. S., Lattorff, H. M. G., Lobo, C. H., Moritz, R. F. A., Nunes, F. M. F., Page Jr., R. E., Simes, Z. L. P., Wheeler, Diana, Carninci, P., Fukuda, S., Hayashizaki, Y., Kai, C., Kawai, J., Sakazume, Sasaki, D., Tagami, M., Albert, S., Baggerman, G., Beggs, K. T., Bloch, G., Cazzamali, G., Cohen, M., Drapeau, M. D., Eisenhardt, D., Emore, C., Ewing, M. A., Fahrbach, S. E., Fort, S., Grimmelikhuijzen, C. J. P., Hauser, F., Hummon, A. B., Huybrechts, J., Jones, A. K., Kadowaki, T., Kaplan, N., Kucharski, R., Leboulle, G., Linial, M., Littleton, J. T., Mercer, A. R., Richmond, T. A., Rodriguez-Zas, S. L., Rubin, E. B., Sattelle, D. B., Schlipalius, D., Schoofs, L., Shemesh, Y., Sweedler, J. V., Velarde, R., Verleyen, P., Vierstraete, E., Williamson, M. R., Ament, S. A., Brown, S. J., Corona, M., Dearden, P. K., Dunn, W. A., Elekonich, M. M., Fujiyuki, T., Gattermeier, I., Gempe, T., Hasselmann, M., Kage, E., Kamikouchi, A., Kubo, T., Kunieda, T., Lorenzen, M., Milshina, N. V., Morioka, M., Ohashi, K., Overbeek, R., Ross, C. A., Schioett, M., Shippy, T., Takeuchi, H., Toth, A. L., Willis, J. H., Wilson, M. J., Gordon, K. H. J., Let
unic, I., Hackett, K., Peterson, J., Felsenfeld, A., Guyer, M., Solignac, M., Agarwala, R., Cornuet, J. M., Monnerot, M., Mougel, F., Reese, J. T., Vautrin, D., Gillespie, J. J., Cannone, J. J., Gutell, R. R., Johnston, J. S., Eisen, M. B., Iyer, V. N., Iyer, V., Kosarev, P., Mackey, A. J., Solovyev, V., Souvorov, A., Aronstein, K. A., Bilikova, K., Chen, Y. P., Clark, A. G., Decanini, L. I., Gelbart, W. M., Hetru, C., Hultmark, D., Imler, J.-L., Jiang, H., Kanost, M., Kimura, K., Lazzaro, B. P., Lopez, D. L., Simuth, J., Thompson, G. J., Zou, Z., de Jong, P., Sodergren, E., Csrs, M., Milosavljevic, A., Osoegawa, K., Richards, S., Shu, C.-L., Duret, L., Elhaik, E., Graur, D., Anzola, J. M., Campbell, K. S., Childs, K. L., Collinge, D., Crosby, M. A., Dickens, C. M., Grametes, L. S., Grozinger, C. M., Jones, P. L., Jorda, M., Ling, X., Matthews, B. B., Miller, J., Mizzen, C., Peinado, M. A., Reid, J. G., Russo, S. M., Schroeder, A. J., St Pierre, S. E., Wang, Y. Zhou, P., Kitts, P., Ruef, B., Venkatraman, A., Zhang, L., Aquino-Perez, G., Whitfield, C. W., Behura, S. K., Berlocher, S. H., Sheppard, W. S., Smith, D. R., Suarez, A. V., Tsutsui, N. D., Wei, X., Wheeler, David, Havlak, P., Li, B., Liu, Y., Jolivet, A., Lee, S., Nazareth, L. V., Pu, L.-L., Thorn, R., Stolc, V., Newman, T., Samanta, M., Tongprasit, W. A., Claudianos, C., Berenbaum, M. R., Biswas, S., de Graaf, D. C., Feyereisen, R., Johnson, R. M., Oakeshott, J. G., Ranson, H., Schuler, M. A., Muzny, D., Chacko, J., Davis, C., Dinh, H., Gill, R., Hernandez, J., Hines, S., Hume, J., Jackson, L., Kovar, C., Lewis, L., Miner, G., Morgan, M., Nguyen, N., Okwuonu, G., Paul, H., Santibanez, J., Savery, G., Svatek, A., Villasana, D., and Wright, R. 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443: 931-949.

7. Roberts C, Anderson KL, Murphy E, Projan SJ, Mounts W, Hurlburt B, Smeltzer M, Overbeek R, Disz T, Dunman PM. (2006) Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives. J. Bacteriol. 188(7):2593-603.

8. Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL. (2006) Comparative genomics of NAD biosynthesis in cyanobacteria. J. Bacteriol. 188(8):3012-23.

9. Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM. (2006) Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J. Bacteriol. 188(19):6739-56.

10. 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. (2007) The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35(Database issue):D347-53. Epub 2006 Dec 1.

11. Overbeek R (2007) Moving to a higher level of abstraction. Environ Microbiol 9(1):7-8.

12. Overbeek R, Bartels D, Vonstein V, Meyer F. (2007) Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev. Aug;107(8):3431-47. Epub 2007 Jul 21.

13. 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. (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 9(1):75.

14. Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA. (2008) Cohesion Group Approach for Evolutionary Analysis of TyrA, a Protein Family with Wide-Ranging Substrate Specificities. Microbiol Mol Biol Rev. 72(1):13-53.

15. Meyer F, Overbeek R, Rodriguez A. (2009) FIGfams: yet another set of protein families. Nucleic Acids Res. 2009 Nov;37(20):6643-54. Epub 2009 Sep 17 PMID: 19762480

16. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA. (2010) Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics. 2010 Jun 14; 11:319.PMID: 20546611

17. Henry C, Overbeek R, Stevens RL. (2010) Building the blueprint of life. Biotechnol J. 2010 Jul;5(7):695-704. Review.PMID: 20665643

18. 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. (2010) Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics. 2010 Sep 13; 11:494.PMID: 20836887

19. 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. (2011) Connecting genotype to phenotype in the era of high-throughput sequencing. Biochim Biophys Acta. 1810(10):967-77. Epub 2011 Mar 21. PMID:21421023

20. Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Nez A, Pribat A, Waller JC, Wilke A, Overbeek R, Hanson AD, de Crcy-Lagard V. (2011) Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics. 2011 Jun 15;12 Suppl 1:S2. PMID:21810204

21. 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. (2011) Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. PMID: 21810205

22. Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R. (2012) Real time metagenomics: using k-mers to annotate metagenomes. Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9. PMID: 23047562

23. 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. (2012) SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24. PMID: 23110173

24. Devoid S, Overbeek R, DeJongh M, Vonstein V, Best AA, Henry C. (2013) Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED. Methods Mol Biol. 2013;985:17-45. doi: 10.1007/978-1-62703-299-5_2. PMID: 23417797

25. Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS. (2013) Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Brief Bioinform. 2013 Feb 18. [Epub ahead of print] PMID: 23422247

26. Davis JJ, Xia F, Overbeek RA, Olsen GJ. (2013) Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes. Int J Syst Evol Microbiol. 2013 Jul;63(Pt 7):2727-41. doi: 10.1099/ijs.0.048983-0. Epub 2013 Apr 19. PMID: 23606477

27. 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. (2013) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91. doi: 10.1093/nar/gkt1099. Epub 2013 Nov 12. PMID: 24225323

28. 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. (2013) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29. PMID: 24293654

29  Davis JJ, Olsen GJ, Overbeek R, Vonstein V, Xia F. (2014) In search of genome annotation consistency: solid gene clusters and how to use them. 3 Biotech. 2014 Jun;4(3):331-335. doi: 10.1007/s13205-013-0152-2. Epub 2013 Jul 6. PMID: 28324432

30. 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 Crecy-Lagard V, Ware D, Hanson AD, Henry CS. (2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9645-50. doi: 10.1073/pnas.1401329111. Epub 2014 Jun 9. PMID: 24927599

31.  Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS. (2014) Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Brief Bioinform. 2014 Jul;15(4):592-611. PMID: 23422247

32.  Faria JP, Edirisinghe JN, Davis JJ, Disz T, Hausmann A, Henry CS, Olson R, Overbeek RA, Pusch GD, Shukla M, Vonstein V, Wattam AR. (2015) Enabling comparative modeling of closely related genomes: example genus Brucella. 3 Biotech. 2015 Feb;5(1):101-105. doi: 10.1007/s13205-014-0202-4. Epub 2014 Mar 8. PMID: 28324362

33.  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. (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365. PMID: 25666585

34.  Faria JP, Overbeek R, Taylor RC, Conrad N, Vonstein V, Goelzer A, Fromion V, Rocha M, Rocha I, Henry CS. (2016) Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. Front Microbiol. 2016 Mar 18;7:275. doi: 10.3389/fmicb.2016.00275. eCollection 2016. PMID: 27047450

35.  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. (2016) Antimicrobial Resistance Prediction in PATRIC and RAST. Sci Rep. 2016 Jun 14;6:27930. doi: 10.1038/srep27930. PMID: 27297683

36. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H. (2016) PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. Front Microbiol. 2016 Feb 8;7:118. doi:10.3389/fmicb.2016.00118. eCollection 2016. PMID: 26903996

37  Cuevas DA, Edirisinghe J, Henry CS, Overbeek R, O'Connell TG, Edwards RA. (2016) From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. Front Microbiol. 2016 Jun 17;7:907. doi: 10.3389/fmicb.2016.00907. eCollection 2016. PMID: 27379044

38.  Edirisinghe JN, Weisenhorn P, Conrad N, Xia F, Overbeek R, Stevens RL, Henry CS. (2016) Modeling central metabolism and energy biosynthesis across microbial life. BMC Genomics. 2016 Aug 8;17:568. doi: 10.1186/s12864-016-2887-8. PMID: 27502787

39.  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. (2016) Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. Front Microbiol. 2016 Nov 24;7:1819. eCollection 2016. PMID: 27933038

40.  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. (2017) Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29. PMID: 27899627