PATRIC Publications

2014

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.

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.

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. [Epub ahead of print]

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.

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: 20207755. PMCID: PMC2863478.

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