Publications by PATRIC¶
The publications listed below were developed, at least in part, by members of the PATRIC team and supported by the PATRIC contract. For a list of publications that cite PATRIC, visit the PATRIC Google Scholar page.
2021¶
Long SW, Olsen RJ, Christensen PA, Subedi S, Olson R, Davis JJ, Saavedra MO, Yerramilli P, Pruitt L, Reppond K, Shyer MN, Cambric J, Finkelstein IJ, Gollihar J, Musser JM. Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. Am J Pathol. 2021 Mar 16:S0002-9440(21)00108-5. doi: 10.1016/j.ajpath.2021.03.004. Epub ahead of print. PMID: 33741335. PMCID: PMC7962948.
Musser JM, Olsen RJ, Christensen PA, Long SW, Subedi S, Davis JJ, Gollihar J. Rapid, widespread, and preferential increase of SARS-CoV-2 B. 1.1. 7 variant in Houston, TX, revealed by 8,857 genome sequences. medRxiv. 2021 Jan 1. doi: 2021.03.16.21253753.
2020¶
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. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020 Jan 8;48(D1):D606-D612. doi: 10.1093/nar/gkz943. PMID: 31667520. PMCID: PMC7145515.
Gagetti P, Errecalde L, Wattam AR, De Belder D, Ojeda Saavedra M, Corso A, Rosato AE. Characterization of the First mecA-Positive Multidrug-Resistant Staphylococcus pseudintermedius Isolated from an Argentinian Patient. 2020. Microb Drug Resist. doi: 10.1089/mdr.2019.0308. PMID: 32031908. PMCID: PMC7368382 (available on 2021-07-01).
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio. 2020 Oct 30;11(6):e02707-20. doi: 10.1128/mBio.02707-20. PMID: 33127862. PMCID: PMC7642679.
Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA, Westoby M.Sci Data. 2020. A synthesis of bacterial and archaeal phenotypic trait data. Jun 5;7(1):170. doi: 10.1038/s41597-020-0497-4. PMID: 32503990. PMCID: PMC7275036.
McDermott PF, Davis JJ. Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. Journal of Veterinary Pharmacology and Therapeutics. doi: 10.1111/jvp.12913. PMID: 33010049.
Nguyen M, Olson R, Shukla M, VanOeffelen M, Davis JJ. Predicting antimicrobial resistance using conserved genes. PLoS Comput Biol. 2020 Oct 19;16(10):e1008319. doi: 10.1371/journal.pcbi.1008319. eCollection 2020 Oct. PMID: 33075053. PMCID: PMC7595632.
Pincus NB, Ozer EA, Allen JP, Nguyen M, Davis JJ, Winter DR, Chuang CH, Chiu CH, Zamorano L, Oliver A, Hauser AR. A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates. mBio. 2020 Aug 25;11(4):e01527-20. doi: 10.1128/mBio.01527-20. PMID: 32843552. PMCID: PMC7448275.
Saranathan R, Levi MH, Wattam AR, Malek A, Asare E, Behin DS, Pan DH, Jacobs WR Jr, Szymczak WA. J Clin Microbiol. Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing. 2020 Feb 24;58(3). pii: e01591-19. doi: 10.1128/JCM.01591-19. Print 2020 Feb 24. PMID: 31801839 PMCID: PMC7041580.
Varela MC, Roch M, Taglialegna A, W Long SW, Saavedra MO, Rose WE, Wattam AR, Davis JJ, Hoffman LR, Hernandez RE, Rosato RR and Rosato AE. Carbapenems as a key driver of collateral ceftaroline resistance in cystic fibrosis patients with MRSA. Nature Communications Biology 2020. doi: 10.1038/s42003-020-01313-5. PMID: 33093601. PMCID: PMC7582194.
Viana MVC, Profeta R, da Silva AL, Hurtado R, Cerqueira JC, Ribeiro BFS, Almeida MO, Morais-Rodrigues F, Soares SC, Oliveira M, Tavares L, Figueiredo H, Wattam AR, Barh D, Ghosh P, Silva A, Azevedo V. Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum. PLoS One. 2020 Dec 21;15(12):e0244210. doi: 10.1371/journal.pone.0244210. eCollection 2020. PMID: 33347470. PMCID: PMC7751848.
2019¶
Gagetti P, Wattam AR, Giacoboni G, De Paulis A, Bertona E, Corso A, Rosato AE. Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina. BMC Vet Res. 2019 Jul 27;15(1):264. doi: 10.1186/s12917-019-1990-x.PMID: 31351494. PMCID: PMC6660709.
Nguyen M, Long SW, McDermott PF, Olsen RJ, Olson R, Stevens RL, Tyson GH, Zhao S, Davis JJ. Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella. Journal of clinical microbiology. 2019 Feb 1;57(2):e01260-18. PMID: 30333126. DOI: 10.1128/JCM.01260-18.
Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch GD, Vonstein V, Overbeek R. A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinformatics. 2019; 20, Article number: 486. Open Access.
2018¶
Banerjee K, Sekar P, Krishnan P, Wattam AR, Roy S, Hays JP, Menezes GA. Whole genome sequence analysis of NDM-1, CMY-4, and sHV-12 coproducing Salmonella enterica serovar typhimurium isolated from a case of fatal burn wound infection. Infection and Drug Resistance. 2018;11:2491. PMID: 30555248. PMCID: PMC6278884.
Folador EL, Gomide AC, Goes-Neto AR, Azevedo VA, Wattam AR. Cell Division in genus Corynebacterium: protein-protein interaction and molecular docking of SepF and FtsZ in the understanding of cytokinesis in pathogenic species. Anais da Academia Brasileira de Ciências. 2018 Aug. 90(2 suppl 1):2179-2188. doi: 10.1590/0001-3765201820170385. Epub 2018 Feb 15. PMID: 29451601. DOI: 10.1590/0001-3765201820170385.
Nguyen M, Brettin T, Long SW, Musser JM, Olsen RJ, Olson R, Shukla M, Stevens RL, Xia F, Yoo H, Davis JJ. Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Sci Rep. 2018 Jan 11;8(1):421. doi: 10.1038/s41598-017-18972-w. PMID: 29323230. PMCID:PMC5765115.
Viana MV, Sahm A, Neto AG, Figueiredo HC, Wattam AR, Azevedo V. Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis. PloS one. 2018 Nov 12;13(11):e0207304. PMID: 30419061. PMCID: PMC6231662.
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. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. Methods Mol Biol. 2018;1704:79-101. PMID:29277864. DOI: 10.1007/978-1-4939-7463-4_4
2017¶
Al Dahouk S, Köhler S, Occhialini A, Jiménez de Bagüés MP, Hammerl JA, Eisenberg T, Vergnaud G, Cloeckaert A, Zygmunt MS, Whatmore AM, Melzer F, Drees KP, Foster JT, Wattam AR, Scholz HC. "Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts." Sci Rep. 2017 Mar 16;7:44420. PMID:28300153. PMCID:PMC5353553.
Kumar P, Kaushik A, Bell DT, Chauhan V, Xia F, Stevens RL, Lamichhane G. "Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis." Antimicrob Agents Chemother. 2017 Feb 23;61(3). pii: e02234-16. Print 2017 Mar. PMID:28069655. PMCID:PMC5328524.
Long, S. W., S. E. Linson, M. Ojeda Saavedra, C. Cantu, J. J. Davis, T. Brettin and R. J. Olsen (2017). "Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae." mSphere 2(4). PMID:28776045. PMCID:PMC5541162.
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. PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. PMID:28968762.
Long, S. W., R. J. Olsen, T. N. Eagar, S. B. Beres, P. Zhao, J. J. Davis, T. Brettin, F. Xia and J. M. Musser (2017). "Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307." mBio 8(3): e00489-00417. PMID:28512093. PMCID:PMC5433097.
Roch M, Gagetti P, Davis J, Ceriana P, Errecalde L, Corso A, Rosato AE. Daptomycin Resistance in Clinical MRSA Strains Is Associated with a High Biological Fitness Cost. Front Microbiol. 2017 Dec 5;8:2303. doi: 10.3389/fmicb.2017.02303. PMID:29259579. PMCID:PMC5723333.
Vélez JR, Cameron M, Rodríguez-Lecompte JC, Xia F, Heider LC, Saab M, McClure JT, Sánchez J (2017). Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds." Front Vet Sci. 4:63. PMID:28589129. PMCID:PMC5438997.
Viana MVC, Figueiredo H, Ramos R, Guimarães LC, Pereira FL, Dorella FA, Selim SAK, Salaheldean M, Silva A, Wattam AR, Azevedo V (2017). Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo." PLoS One. 12(4): e0176347. PMID:28445543. PMCID:PMC5406005.
Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR. "Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart." Genome Announc. 2017 Mar 2;5(9). pii: e01687-16. PMID:28254974. PMCID:PMC5334581.
Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR. "Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog." Genome Announc. 2017 Feb 23;5(8). pii: e01688-16. PMID:28232424. PMCID:PMC5323635.
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. "Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center." Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. Epub 2016 Nov 29. PMID:27899627. PMCID:PMC5210524.
2016¶
Davis, J. J., Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R. "Antimicrobial Resistance Prediction in PATRIC and RAST." Sci Rep (2016) 6:27930. PMID:27297683. PMCID:PMC4906388.
Davis, J. J., S. Gerdes, G. J. Olsen, R. Olson, G. D. Pusch, M. Shukla, V. Vonstein, A. R. Wattam, and H. Yoo. "PATtyFams: Protein families for the microbial genomes in the PATRIC database." Frontiers in Microbiology 7 (2016): 118. PMID:26903996. PMCID:PMC4744870.
Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT. "Network for Salmonella enterica Serovar Typhimurium Invasion." MBio. 2016 Sep 6;7(5). pii: e01024-16. PMID:27601571. PMCID:PMC5013294.
2015¶
Brettin, T., J. J. Davis, T. Disz, R. A. Edwards, S. Gerdes, G. J. Olsen, R. Olson, R. Overbeek, B. Parrello, G. D. Pusch, M. Shukla, J. A. Thomason, 3rd, R. Stevens, V. Vonstein, A. R. Wattam and F. Xia (2015). "RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes." Sci Rep 5: 8365. PMID: 25666585. PMCID: PMC4322359.
Cheng, Y., A. A. Pedroso, S. Porwollik, M. McClelland, M. D. Lee, T. Kwan, K. Zamperini, V. Soni, H. S. Sellers, S. M. Russell and J. J. Maurer (2015). "rpoS-Regulated Core Genes Involved in the Competitive Fitness of Salmonella enterica Serovar Kentucky in the Intestines of Chickens." Appl Environ Microbiol 81(2): 502-514. PMID: 25362062. PMCID: PMC4277580.
Warren, A. S., C. Aurrecoechea, B. Brunk, P. Desai, S. Emrich, G. I. Giraldo-Calderon, O. Harb, D. Hix, D. Lawson, D. Machi, C. Mao, M. McClelland, E. Nordberg, M. Shukla, L. B. Vosshall, A. R. Wattam, R. Will, H. S. Yoo and B. Sobral (2015). "RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research." Bioinformatics 31:1496-8 PMID: 25573919.
2014¶
Bonner, C. A., G. I. Byrne and R. A. Jensen (2014). "Chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence." Frontiers in Cellular and Infection Microbiology 4: 17. PMID: 24616884. PMCID: PMC3937554.
Davis, J., G. Olsen, R. Overbeek, V. Vonstein and F. Xia (2014). "In search of genome annotation consistency: solid gene clusters and how to use them." 3 Biotech 4(3): 331-335. PMCID: PMC4026451.
Deng, X., P. T. Desai, H. C. den Bakker, M. Mikoleit, B. Tolar, E. Trees, R. S. Hendriksen, J. G. Frye, S. Porwollik, B. C. Weimer, M. Wiedmann, G. M. Weinstock, P. I. Fields and M. McClelland (2014). "Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages." Emerg Infect Dis 20(9): 1481-1489. PMID: 25147968. PMCID: PMC4178404.
Dugan V.G., S.J. Emrich, G.I. Giraldo-Calderón, O.S. Harb, R.M. Newman, B.E. Pickett, L.M. Schriml, T.B. Stockwell, C. J. Stoeckert Jr, D. E. Sullivan, I. Singh, D.V. Ward, A. Yao, J. Zheng, T. Barrett, B. Birren, L. Brinkac,V.M. Bruno, E. Caler, S. Chapman, F.H. Collins, C.A. Cuomo, V. Di Francesco, S. Durkin, M. Eppinger, M. Feldgarden, C. Fraser, W.F. Fricke, M. Giovanni, M.R. Henn, E. Hine, J.D. Hotopp, I. Karsch-Mizrachi, J.C. Kissinger, E.M. Lee, P. Mathur, E.F. Mongodin, C.I. Murphy, G. Myers, D.E. Neafsey, K.E. Nelson, W.C. Nierman, J. Puzak, D. Rasko, D.S. Roos, L. Sadzewicz, J.C. Silva, B. Sobral, R.B. Squires, R.L. Stevens, L. Tallon, H. Tettelin, D. Wentworth, O. White, R. Will, J. Wortman, Y. Zhang, R.H. Scheuermann. (2014). "Standardized metadata for human pathogen/vector genomic sequences." PLoS ONE 9(6): e99979. doi: 10.1371/journal.pone.0099979. PMID: 24936976.
Elhadad, D., M. McClelland, G. Rahav and O. Gal-Mor (2014). "Feverlike Temperature is a Virulence Regulatory Cue Controlling the Motility and Host Cell Entry of Typhoidal Salmonella." Journal of Infectious Diseases. PMID: 25492917. doi: 10.1093/infdis/jiu663
Faria, J.P., Edirisinghe J.N., J.J. Davis, T. Disz, A. Hausmann, C.S. Henry, R. Olson, R.A. Overbeek, G.D. Pusch, M. Shukla, V. Vonstein, A.R. Wattam (2014). "Enabling comparative modeling of closely related genomes: example genus Brucella." 3 Biotech 2190-572X: 1-5. doi: 10.1007/s13205-014-0202-4.
Flynn, T. M., E. J. O’Loughlin, B. Mishra, T. J. DiChristina and K. M. Kemner (2014). "Sulfur-mediated electron shuttling during bacterial iron reduction." Science 344(6187): 1039-1042. PMID: 24789972.
Gillespie, J. J., T. P. Driscoll, V. I. Verhoeve, T. Utsuki, C. Husseneder, V. N. Chouljenko, A. F. Azad and K. R. Macaluso (2014). "Genomic diversification in strains of Rickettsia felis isolated from different arthropods." Genome Biol Evol. PMID: 25477419. doi: 10.1093/gbe/evu262.
Mao, C., D. Abraham, A. R. Wattam, M. J. Wilson, M. Shukla, H. S. Yoo and B. W. Sobral (2014). "Curation, integration and visualization of bacterial virulence factors in PATRIC." Bioinformatics. Epub ahead of print. doi: 10.1093/bioinformatics/btu631. PMID: 25273106.
Meng, H., Zhang, Y., L. Zhao, W. Zhao, C. He, C.F. Honaker, Z. Zhai, Z. Sun, P.B. Siegel (2014). "Body Weight Selection Affects Quantitative Genetic Correlated Responses in Gut Microbiota." PLoS ONE 9(3): e89862. doi: 10.1371/journal.pone.0089862. PMID: 24608294. PMCID: PMC3946484
Overbeek, R., R. Olson, P.D. G. D. Pusch, G.J. Olsen, J.J. Davis, T. Disz, R.A. Edwards, S. Gerdes, B. Parrello, M. Shukla, V. Vonstein, A.R. Wattam, F. Xia, R. Stevens (2014). "The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)." Nucl Acids Res 42 (D1): D206-D214. doi: 10.1093/nar/gkt1226. PMID: 24293654.
Panas, M. W., P. Jain, H. Yang, S. Mitra, D. Biswas, A. R. Wattam, N. L. Letvin and W. R. Jacobs, Jr. (2014). "Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids." Proc Natl Acad Sci USA 111(37): 13264-13271. PMID: 25197070. PMCID: PMC4169951.
Park, J., Gabbard, J.L. (2014). "User Experiences with Open Access Knowledge Sharing Platforms: Preliminary User-Centered Design Implications for Complex Data-intensive Domains." Proceedings of the Human Factors and Ergonomics Society Annual Meeting 58(1): 1496-1500.
Pontel, L. B., N. L. Scampoli, S. Porwollik, S. K. Checa, M. McClelland and F. C. Soncini (2014). "Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess." Microbiology 160(Pt 8): 1659-1669. PMID: 24858080. PMCID: PMC4117220.
Porwollik, S., C. A. Santiviago, P. Cheng, F. Long, P. Desai, J. Fredlund, S. Srikumar, C. A. Silva, W. Chu, X. Chen, R. Canals, M. M. Reynolds, L. Bogomolnaya, C. Shields, P. Cui, J. Guo, Y. Zheng, T. Endicott-Yazdani, H. J. Yang, A. Maple, Y. Ragoza, C. J. Blondel, C. Valenzuela, H. Andrews-Polymenis and M. McClelland (2014). "Defined single-gene and multi-gene deletion mutant collections in Salmonella enterica sv Typhimurium." PLoS One 9(7): e99820. PMID: 25007190. PMCID: PMC4089911.
Scaria, J., J. W. Chen, N. Useh, H. He, S. P. McDonough, C. Mao, B. Sobral and Y. F. Chang (2014). "Comparative nutritional and chemical phenome of Clostridium difficile isolates determined using phenotype microarrays." Int J Infect Dis 27: 20-25. PMID: 25130165. PMCID: PMC4197074.
Wattam, A., J. Gabbard, M. Shukla, and B. Sobral. (2014). Comparative Genomics Analysis at the PATRIC, A Bioinformatic Resource Center. In A. Vergunst and D. O’Callaghan (Eds.), Host Bacterial Infections, Methods in Molecular Microbiology (v. 1197, pp. 287-308). Springer New York. doi: 10.1007/978-1-4939-1261-2_17. PMID: 25172288.
Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, Keim P, Pearson T, Shukla M, Ward DV, Williams KP, Sobral BW, Tsolis RM, Whatmore AM, O’Callaghan D (2014). "Comparative phylogenomics and evolution of the brucellae: A path to virulence." Journal of Bacteriology, 196(5): 920-30. doi: 10.1128/JB.01091-13. PMID: 24336939. PMCID: PMC3957692.
Wattam, A.R., D. Abraham, O. Dalay, T.L. Disz, T. Driscoll, J.L. Gabbard, J.J. Gillespie, R. Gough, D. Hix, R. Kenyon, D. Machi, C. Mao, E.K. Nordberg, R. Olson, R. Overbeek, G.D. Pusch, M. Shukla, J. Schulman, R.L. Stevens, D.E. Sullivan, V. Vonstein, A. Warren, R. Will, M.J.C. Wilson, H. Seung Yoo, C. Zhang, Y. Zhang, B.W. Sobral (2014). "PATRIC, the bacterial bioinformatics database and analysis resource." Nucl Acids Res 42 (D1): D581-D591. doi:10.1093/nar/gkt1099. PMID: 24225323.
2013¶
Brennan P.J., R. Brosch, B. Birren and B. Sobral (2013). "TBCAP; tuberculosis annotation project." Tuberculosis. 16 January 2013. [Epub ahead of print] doi: 10.1016/j.tube.2012.11.013 PMID: 23332402.
Chen J.W., J. Scaria, C. Mao, B. Sobral, S. Zhang, T. Lawley and Y.F Chang (2013). "Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains." J Proteome Res. 2013 Jan 8. [Epub ahead of print] doi: 10.1021/pr3007528 PMID: 23298230.
Driscoll, T., J.J. Gillespie, E.K. Nordberg, A.F Azad, and B.W. Sobral (2013). Bacterial DNA sifted from the Trichoplax adhaerens (Animalia:Placozoa) genome project reveals a putative rickettsial endosymbiont. Genome Biol Evol 5(4): 621-645. doi: 10.1093/gbe/evt036. PMID: 23475938
Lew, J.M., M. C. Mao, M. Shukla, A. Warren, R. Will, D. Kuznetsov, I. Xenarios, B.D. Robertson, S.V. Gordon, D. Schnappinger, S.T. Cole and B. Sobral (2013). "Database resources for the tuberculosis community." Tuberculosis. 17 January 2013. [Epub ahead of print] doi: 10.1016/j.tube.2012.11.003 PMID: 23332401.
Mao C., M. Shukla, G. Larrouy-Maumus, F.L. Dix, L.A. Kelley, M.J. Sternberg, B.W. Sobral, L.P. de Carvalho (2013). "Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition." Tuberculosis. 31 December 2012. [Epub ahead of print] doi: 10.1016/j.tube.2012.11.008 PMID: 23287603.
Ooi, W.F., Ong C., T. Nandi, J.F. Kreisberg, H.H. Chua, G. Sun, Y. Chen, C. Mueller, L. Conejero, M. Eshaghi, R.M.L. Ang, J. Liu, B.W. Sobral, S. Korbsrisate, Y.H. Gan, R.W. Titball, G.J. Bancroft, E. Valade, P. Tan (2013). "The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei." PLoS Genet 9(9): e1003795. doi:10.1371/journal.pgen.1003795. PMID: 24068961.
Rajasekaran, P., J. C. Alexander, M. N. Seleem, N. Jain, N. Sriranganathan, A. R. Wattam, J. C. Setubal and S. M. Boyle (2013). "Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages." Int J Antimicrob Ag (2013). Article in Press doi: 10.1016/j.ijantimicag.2012.11.017
Scaria, J., C. Mao, J. W. Chen, S.P. McDonough, B. Sobral, Y.F. Chang (2013). "Differential Stress Transcriptome Landscape of Historic and Recently Emerged Hypervirulent Strains of Clostridium difficile Strains Determined Using RNA-seq." PLoS One 8(11): e78489. doi: 10.1371/journal.pone.0078489. PMID: 24244315. PMCID: PMC3820578.
Sobral, B., C. Mao, M. Shukla, D. Sullivan, C. Zhang (2013). "Informatics-Driven Infectious Disease Research." In: Fred A., J. Filipe, H. Gamboa, eds. Biomedical Engineering Systems and Technologies. Springer Berlin Heidelberg; 2013, pp 3–11. Communications in Computer and Information Science Volume 273.
2012¶
Aziz RK, D. S., Disz T, Edwards RA, Henry CS, et al. (2012). "SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models." PloS ONE 7(10): e48053. doi: 10.1371/journal.pone.0048053.
Canals, R., X. Q. Xia, C. Fronick, S. W. Clifton, B. M. Ahmer, H. L. Andrews-Polymenis, S. Porwollik and M. McClelland (2012). "High-throughput comparison of gene fitness among related bacteria." BMC Genomics 13(1): 212. doi: 10.1186/1471-2164-13-212. PMID: 22646920.
Gillespie, J. J., V. Joardar, K. P. Williams, T. Driscoll, J. B. Hostetler, E. Nordberg, M. Shukla, B. Walenz, C. A. Hill, V. M. Nene, A. F. Azad, B. W. Sobral and E. Caler (2012). "A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle." J Bacteriol 194(2): 376-394. doi: 10.1128/ JB.06244-11. PMID: 22056929. PMCID: PMC3256634.
Gillespie, J. J., Nordberg, E., Azad, A.F., Sobral, B.W. (2012). Phylogeny and Comparative Genomics: The Shifting Landscape in the Genomics Era. Intracellular Pathogens II: Rickettsiales. A. F. Azad, Palmer, G. H., American Society of Microbiology. NLMID: 101571352.
Kaur, S. J., M. S. Rahman, N. C. Ammerman, M. Beier-Sexton, S. M. Ceraul, J. J. Gillespie and A. F. Azad (2012). "TolC-Dependent Secretion of an Ankyrin Repeat-Containing Protein of Rickettsia typhi." J Bacteriol 194(18): 4920-4932. doi: 10.1128/JB.00793-12. PMID: 22773786. PMCID: PMC3430354.
Pyysalo, S., T. Ohta, R. Rak, D. Sullivan, C. Mao, C. Wang, B. Sobral, J. Tsujii and S. Ananiadou (2012). "Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011." BMC Bioinformatics. doi: 10.1186/1471-2105-13-S11-S2. PMID: 22759456. PMCID: PMC3384257.
Rak, R., A. Rowley, W. Black and S. Ananiadou (2012). "Argo: an integrative, interactive, text mining-based workbench supporting curation." Database (Oxford) 2012: bas010. doi:10.1093/database/bas010. PMID: 22434844. PMCID: PMC 3308166.
Sears, K. T., S. M. Ceraul, J. J. Gillespie, E. D. Allen, Jr., V. L. Popov, N. C. Ammerman, M. S. Rahman and A. F. Azad (2012). "Surface proteome analysis and characterization of surface cell antigen (Sca) or autotransporter family of Rickettsia typhi." PLoS Pathog 8(8): e1002856. doi: 10.1371/journal.ppat.1002856. PMID: 22912578. PMCID: PMC3415449.
Wattam, A. R., T. J. Inzana, K. P. Williams, S. P. Mane, M. Shukla, N. F. Almeida, A. W. Dickerman, S. Mason, I. Moriyon, D. O’Callaghan, A. M. Whatmore, B. W. Sobral, R. V. Tiller, A. R. Hoffmaster, M. A. Frace, C. De Castro, A. Molinaro, S. M. Boyle, B. K. De and J. C. Setubal (2012). "Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway." MBio 3(5). doi: 10.1128/mBio.00246-12. PMID: 22930339. PMCID: PMC3445970.
2011¶
Ananiadou, S., D. Sullivan, W. Black, G. A. Levow, J. J. Gillespie, C. Mao, S. Pyysalo, B. Kolluru, J. Tsujii and B. Sobral (2011). "Named Entity Recognition for Bacterial Type IV Secretion Systems." PLoS One 6(3): e14780. doi: 10.1371/journal.pone.0014780. PMID: 21468321. PMCID: PMC3066171.
Driscoll, T., J. L. Gabbard, C. Mao, O. Dalay, M. Shukla, C. C. Freifeld, A. G. Hoen, J. S. Brownstein and B. W. Sobral (2011). "Integration and visualization of host-pathogen data related to infectious diseases." Bioinformatics 27(16): 2279-2287. doi: 10.1093/bioinformatics/btr391. PMID: 21712250. PMCID: PMC3150046.
Gillespie, J. J., A. R. Wattam, S. A. Cammer, J. L. Gabbard, M. P. Shukla, O. Dalay, T. Driscoll, D. Hix, S. P. Mane, C. Mao, E. K. Nordberg, M. Scott, J. R. Schulman, E. E. Snyder, D. E. Sullivan, C. Wang, A. Warren, K. P. Williams, T. Xue, H. S. Yoo, C. Zhang, Y. Zhang, R. Will, R. W. Kenyon and B. W. Sobral (2011). "PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species." Infect Immun 79(11): 4286-4298. doi:10.1128/IAI.00207-11. PMID: 21896772. PMCID: PMC 3257917.
Sobral, B. and A. Wattam (2011). Comparative genomics and phylogenomics of the Brucella. Brucella: Molecular microbiology and Genetics. I. L.-G. D. O’Callaghan, Horizon Scientific Press.
2010¶
Dyer, M. D., C. Neff, M. Dufford, C. G. Rivera, D. Shattuck, J. Bassaganya-Riera, T. M. Murali and B. W. Sobral (2010). "The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis." PLoS One 5(8): e12089. doi:10.1371/journal.pone.0012089. PMID: 20711500. PMCID: PMC2918508.
Gillespie, J. J., K. A. Brayton, K. P. Williams, M. A. Diaz, W. C. Brown, A. F. Azad and B. W. Sobral (2010). "Phylogenomics reveals a diverse Rickettsiales type IV secretion system." Infect Immun 78(5): 1809-1823. doi: 10.1128/IAI.01384-09. PMID: 20176788. PMCID: PMC2863512.
Pyysalo, S. O., T., Cho, H., Sullivan, D. Mao, C. (2010). Towards event extraction from full texts on infectious diseases. 2010 Workshop on Biomedical Natural Language Processing, Stroudsburg, PA, USA. (View Full Paper at the Association of Computational Linguistics Website).
Sullivan, D. E., J. L. Gabbard, Jr., M. Shukla and B. Sobral (2010). "Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned." Chem Biodivers 7(5): 1124-1141. doi: 10.1002/cbdv.200900317. PMID: 20491070. PMCID: PMC2894471.
Sutten, E. L., J. Norimine, P. A. Beare, R. A. Heinzen, J. E. Lopez, K. Morse, K. A. Brayton, J. J. Gillespie and W. C. Brown (2010). "Anaplasma marginale type IV secretion system proteins VirB2, VirB7, VirB11, and VirD4 are immunogenic components of a protective bacterial membrane vaccine." Infect Immun 78(3): 1314-1325. doi: 10.1128/IAI.01207-09. PMID: 20065028. PMCID: PMC2825951.
Williams, K. P., J. J. Gillespie, B. W. Sobral, E. K. Nordberg, E. E. Snyder, J. M. Shallom and A. W.
Dickerman (2010). "Phylogeny of gammaproteobacteria." J Bacteriol 192(9): 2305-2314. doi: 10.1128/JB.01480-09. PMID:
2009¶
Ammerman, N. C., J. J. Gillespie, A. F. Neuwald, B. W. Sobral and A. F. Azad (2009). "A typhus group-specific protease defies reductive evolution in rickettsiae." J Bacteriol 191(24): 7609-7613. doi: 10.1128/JB.01077-09. PMID: 19820087. PMCID: PMC2786609.
Dreher-Lesnick, S. M., S. M. Ceraul, S. C. Lesnick, J. J. Gillespie, J. M. Anderson, R. C. Jochim, J. G. Valenzuela and A. F. Azad (2009). "Analysis of Rickettsia typhi-infected and uninfected cat flea (Ctenocephalides felis) midgut cDNA libraries: deciphering molecular pathways involved in host response to R. typhi infection." Insect Mol Biol. doi: 10.1111/j.1365-2583.2009.00978.x. PMID: 20017753. PMCID: PMC3179627.
Driscoll, T., M.D. Dyer, T.M. Murali and B.W. Sobral (2009). "PIG–the pathogen interaction gateway." Nucleic Acids Res 37(Database issue): p. D647-50. doi: 10.1093/nar/gkn799 PMID: 18984614 PMCID: PMC2686532
Gillespie, J.J, N.C. Ammerman, S.M. Dreher-Lesnick, M.S. Rahman, M.J. Worley, J.C. Setubal, B.S. Sobral and A.F. Azad (2009). "An anomalous type IV secretion system in Rickettsia is evolutionarily conserved." PLoS ONE 4(3): p. e4833. doi: 10.1371/journal.pone.0004833 PMID: 19279686 PMCID: PMC2653234
Gillespie, J.J., N.C. Ammerman, M. Beier-Sexton, B.S. Sobral and A.F. Azad (2009). "Louse- and flea-borne rickettsioses: biological and genomic analyses." Vet Res 40(2): p. 12. doi: 10.1051/vetres:2008050 PMID: 19036234 PMCID: PMC2695025
Wattam, A.R., K.P. Williams, E.E. Snyder, N.F. Almeida, M. Shukla, A.W. Dickerman, O.R. Crasta, R. Kenyon, J. Lu, J.M. Shallom, H. Yoo, T.A. Ficht, R.M. Tsolis, C. Munk, R. Tapia, C.S. Han, J.C. Detter, D. Bruce, T.S. Brettin, B.W. Sobral, S.M. Boyle and J.C. Setubal (2009). "Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle." J Bacteriol 191(11): p. 3569-79. doi: 10.1128/JB.01767-08 PMID: 19346311 PMCID: PMC2681906
2008¶
Dyer, M.D., T.M. Murali and B.W. Sobral (2008). "The landscape of human proteins interacting with viruses and other pathogens." PLoS Pathog 4(2): p. e32. doi: 10.1371/journal.ppat.0040032 PMID: 18282095 PMCID: PMC2242834
Gillespie, J.J., K. Williams, M. Shukla, E.E. Snyder, E.K. Nordberg, S.M. Ceraul, C. Dharmanolla, D. Rainey, J. Soneja, J.M. Shallom, N.D. Vishnubhat, R. Wattam, A. Purkayastha, M. Czar, O. Crasta, J.C. Setubal, A.F. Azad and B.S. Sobral (2008). "Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life." PLoS One 3(4): p. e2018. doi: 10.1371/journal.pone.0002018 PMID: 19194535 PMCID: PMC2635572
2007¶
Dyer, M.D., T.M. Murali and B.W. Sobral (2007). "Computational prediction of host-pathogen protein-protein interactions." Bioinformatics 23(13): p. i159-66. doi: 10.1093/bioinformatics/btm208 PMID: 17646292
Gillespie, J.J., M.S. Beier, M.S. Rahman, N.C. Ammerman, J.M. Shallom, A. Purkayastha, B.S. Sobral and A.F. Azad (2007). "Plasmids and rickettsial evolution: insight from Rickettsia felis." PLoS One 2(3): p. e266. doi: 10.1371/journal.pone.0000266 PMID: 17342200 PMCID: PMC1800911
Snyder E.E., N. Kampanya, J. Lu, E.K. Nordberg, H.R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, F. Zhang, C. Dharmanolla, N.V. Dongre, J.J. Gillespie, J. Hamelius, M. Hance, K.I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S.P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A.F. Azad, S.C. Baker, S.M. Boyle, Y. Khudyakov, X.J. Meng, C. Rupprecht, J. Vinje, O.R. Crasta, M.J. Czar, A. Dickerman, J.D. Eckart, R. Kenyon, R. Will, J.C. Setubal and B.W. Sobral (2007). "PATRIC: the VBI PathoSystems Resource Integration Center." Nucleic Acids Res 35(1). doi: 10.1093/nar/gkl858. PMID: 17142235. PMCID: PMC1669763.
Yu, G.X., E.E. Snyder, S.M. Boyle, O.R. Crasta, M. Czar, S.P. Mane, A. Purkayastha, B. Sobral and J.C. Setubal (2007). "A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case." Nucleic Acids Res 35(12): p. 3953-62. doi: 10.1093/nar/gkm377 PMID: 17553834 PMCID: PMC1919506