© 2000 - 2012 Virginia Bioinformatics Institute
Wednesday, 16 May 2012
Sobral, Bruno , Ph.D.
Faculty - Publications - Sobral, Bruno

Professor, Virginia Bioinformatics Institute
Director, Cyberinfrastructure Division, Virginia Bioinformatics Institute
Professor, Department of Plant Pathology, Physiology and Weed Science, College of Agriculture and Life Sciences

Phone: (540) 231-2317
Email:sobral@vt.edu
Fax: 540-231-6191

Administrative Specialist: Kimberly Clifton
Phone: (540) 231-9882
Email: kimvt05@vbi.vt.edu
Fax:540-231-2606

Personal_Page | Computational Biology and Bioinformatics | Cyberinfrastructure Division | Cyberinfrastructure Division



Publications:

2011


Althammer S, Gonzalez-Vallinas J, Ballare C, Beato M, Eyras E. Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21994224

Gillespie JJ, Wattam AR, Cammer SA, et al. PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species. Infect Immun. 2011;79:4286–4298.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21896772

Hoffmann S. Computational analysis of high throughput sequencing data. Methods Mol Biol. 2011;719:199–217.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21370085

Mane SP, Modise T, Sobral BW. Analysis of high-throughput sequencing data. Methods Mol Biol. 2011;678:1–11.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20931368

Pyysalo STO Rafal Rak Dan Sullivan Chunhong Mao Chunxia Wang Bruno Sobral Jun. Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. Portland, Oregon, USA; 2011:26–35. Proceedings of Association for Computational Linguistics: Human Language Technologies.  

Shulaev V, Sargent DJ, Crowhurst RN, et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 2011;43:109–151.  

Sobral B and AW. Comparative genomics and phylogenomics of the Brucella. In: O, ed. Brucella: Molecular microbiology and Genetics. Horizon Scientific Press; 2011.  

2010


Buss SN, Hamano S, Vidrich A, et al. Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis. Int J Parasitol. 2010;40:833–843.  http://www.ncbi.nlm.nih.gov/pubmed/20083116

Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20383131

Demir E, Cary MP, Paley S, et al. The BioPAX community standard for pathway data sharing. Nat Biotech. 2010;28:935–942.  http://dx.doi.org/10.1038%2Fnbt.1666

Demir E, Cary MP, Paley S, et al. The BioPAX community standard for pathway data sharing (vol 28, pg 935, 2010). Nature Biotechnology. 2010;28:1308.  

Dyer MD, Neff C, Dufford M, et al. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One. 2010;5:e12089.  http://www.ncbi.nlm.nih.gov/pubmed/20711500

Gillespie JJ, Brayton KA, Williams KP, et al. Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect Immun. 2010;78:1809–1823.  http://www.ncbi.nlm.nih.gov/pubmed/20176788

Guo S, Zheng Y, Joung JG, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics. 2010;11:384.  http://www.ncbi.nlm.nih.gov/pubmed/20565788

Huss M. Introduction into the analysis of high-throughput-sequencing based epigenome data. Brief Bioinform. 2010;11:512–523.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20457755

Mane SP, Dominguez-Bello MG, Blaser MJ, et al. Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. J Bacteriol. 2010;192:3078–3092.  http://www.ncbi.nlm.nih.gov/pubmed/20400544

Mohapatra SK, Cole LE, Evans C, et al. Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection. BMC Infect Dis. 2010;10:10.  http://www.ncbi.nlm.nih.gov/pubmed/20082697

Pushalkar S Mane S.P. Ji X. Li Y. Evans C. Crasta O.R. Morse D. Meagher R. Singh A. and Saxena D. Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunology and Medical Microbiology. 2010.  http://onlinelibrary.wiley.com/doi/10.1111/j.1574-695X.2010.00773.x/abstract;jsessionid=E80992F4416DB8E36615296479E37026.d03t03

Sullivan DE, Gabbard JL Jr., Shukla M, Sobral B. Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned. Chem Biodivers. 2010;7:1124–1141.  http://www.ncbi.nlm.nih.gov/pubmed/20491070

Wang C, Kemp J, Da Fonseca IO, et al. Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvI and its phenotypic characteristics. Mol Plant Microbe Interact. 2010;23:153–160.  http://www.ncbi.nlm.nih.gov/pubmed/20064059

Williams KP, Gillespie JJ, Sobral BW, et al. Phylogeny of gammaproteobacteria. J Bacteriol. 2010;192:2305–2314.  http://www.ncbi.nlm.nih.gov/pubmed/20207755

2009


Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF. A typhus group-specific protease defies reductive evolution in rickettsiae. J Bacteriol. 2009;191:7609–7613.  http://www.ncbi.nlm.nih.gov/pubmed/19820087

Baliji S, Cammer SA, Sobral B, Baker SC. Detection of nonstructural protein 6 in murine coronavirus-infected cells and analysis of the transmembrane topology by using bioinformatics and molecular approaches. J Virol. 2009;83:6957–6962.  http://www.ncbi.nlm.nih.gov/pubmed/19386712

Beare PA, Unsworth N, Andoh M, et al. Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. Infect Immun. 2009;77:642–656.  http://www.ncbi.nlm.nih.gov/pubmed/19047403

Djavani M, Crasta OR, Zhang Y, et al. Gene expression in primate liver during viral hemorrhagic fever. Virol J. 2009;6:20.  http://www.ncbi.nlm.nih.gov/pubmed/19216742

Driscoll T, Dyer MD, Murali TM, Sobral BW. PIG--the pathogen interaction gateway. Nucleic Acids Res. 2009;37:D647–50.  http://www.ncbi.nlm.nih.gov/pubmed/18984614

Gillespie JJ, Ammerman NC, Beier-Sexton M, Sobral BS, Azad AF. Louse- and flea-borne rickettsioses: biological and genomic analyses. Vet Res. 2009;40:12.  http://www.ncbi.nlm.nih.gov/pubmed/19036234

Gillespie JJ, Ammerman NC, Dreher-Lesnick SM, et al. An anomalous type IV secretion system in Rickettsia is evolutionarily conserved. PLoS One. 2009;4:e4833.  http://www.ncbi.nlm.nih.gov/pubmed/19279686

Li S, Brazhnik P, Sobral B, Tyson JJ. Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus. PLoS Comput Biol. 2009;5:e1000463.  http://www.ncbi.nlm.nih.gov/pubmed/19680425

Mao C, Bhardwaj K, Sharkady SM, et al. Variations on the tmRNA gene. RNA Biol. 2009;6:355–361.  http://www.ncbi.nlm.nih.gov/pubmed/19617710

McGarvey PB, Huang H, Mazumder R, et al. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PLoS One. 2009;4:e7162.  http://www.ncbi.nlm.nih.gov/pubmed/19779614

Wattam AR, Williams KP, Snyder EE, et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191:3569–3579.  http://www.ncbi.nlm.nih.gov/pubmed/19346311

2008


Abhyankar MM, Hochreiter AE, Hershey J, et al. Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection. Eukaryot Cell. 2008;7:1565–1572.  http://www.ncbi.nlm.nih.gov/pubmed/18658254

Crasta OR, Folkerts O, Fei Z, et al. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS One. 2008;3:e2193.  http://www.ncbi.nlm.nih.gov/pubmed/18478107

Dyer MD, Murali TM, Sobral BW. The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog. 2008;4:e32.  http://www.ncbi.nlm.nih.gov/pubmed/18282095

Gilchrist CA, Baba DJ, Zhang Y, et al. Targets of the Entamoeba histolytica transcription factor URE3-BP. PLoS Negl Trop Dis. 2008;2:e282.  http://www.ncbi.nlm.nih.gov/pubmed/18846235

Gillespie JJ, Williams K, Shukla M, et al. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One. 2008;3:e2018.  http://www.ncbi.nlm.nih.gov/pubmed/19194535

Li S, Brazhnik P, Sobral B, Tyson JJ. A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput Biol. 2008;4:e9.  http://www.ncbi.nlm.nih.gov/pubmed/18225942

Mao C, Evans C, Jensen RV, Sobral BW. Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system. BMC Microbiol. 2008;8:72.  http://www.ncbi.nlm.nih.gov/pubmed/18454850

Zhang C, Crasta O, Cammer S, et al. An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. 2008;36:D884–91.  http://www.ncbi.nlm.nih.gov/pubmed/17984082

2007


Djavani MM, Crasta OR, Zapata JC, et al. Early blood profiles of virus infection in a monkey model for Lassa fever. J Virol. 2007;81:7960–7973.  http://www.ncbi.nlm.nih.gov/pubmed/17522210

Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen protein-protein interactions. Bioinformatics. 2007;23:i159–66.  http://www.ncbi.nlm.nih.gov/pubmed/17646292

Gillespie JJ, Beier MS, Rahman MS, et al. Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS One. 2007;2:e266.  http://www.ncbi.nlm.nih.gov/pubmed/17342200

Greene JM, Collins F, Lefkowitz EJ, et al. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007;75:3212–3219.  http://www.ncbi.nlm.nih.gov/pubmed/17420237

Koterski J, Twenhafel N, Porter A, et al. Gene expression profiling of nonhuman primates exposed to aerosolized Venezuelan equine encephalitis virus. FEMS Immunol Med Microbiol. 2007;51:462–472.  http://www.ncbi.nlm.nih.gov/pubmed/17894805

Snyder EE, Kampanya N, Lu J, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007;35:D401–6.  http://www.ncbi.nlm.nih.gov/pubmed/17142235

Torto-Alalibo TA, Tripathy S, Smith BM, et al. Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection. Mol Plant Microbe Interact. 2007;20:781–793.  http://www.ncbi.nlm.nih.gov/pubmed/17601166

Wang C, Saldanha M, Sheng X, et al. Roles of poly-3-hydroxybutyrate (PHB) and glycogen in symbiosis of Sinorhizobium meliloti with Medicago sp. Microbiology. 2007;153:388–398.  http://www.ncbi.nlm.nih.gov/pubmed/17259610

Wang C, Sheng X, Equi RC, Trainer MA, Charles TC, Sobral BW. Influence of the poly-3-hydroxybutyrate (PHB) granule-associated proteins (PhaP1 and PhaP2) on PHB accumulation and symbiotic nitrogen fixation in Sinorhizobium meliloti Rm1021. J Bacteriol. 2007;189:9050–9056.  http://www.ncbi.nlm.nih.gov/pubmed/17921298

Wang C, Sobral BW, Williams KP. Loss of a universal tRNA feature. J Bacteriol. 2007;189:1954–1962.  http://www.ncbi.nlm.nih.gov/pubmed/17172343

Williams KP, Sobral BW, Dickerman AW. A robust species tree for the alphaproteobacteria. J Bacteriol. 2007;189:4578–4586.  http://www.ncbi.nlm.nih.gov/pubmed/17483224

Yu GX, Snyder EE, Boyle SM, et al. A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Res. 2007;35:3953–3962.  http://www.ncbi.nlm.nih.gov/pubmed/17553834

2006


Baker SC, Jukneliene D, Purkayastha A, et al. Developing bioinformatic resources for coronaviruses. Adv Exp Med Biol. 2006;581:395–398.  http://www.ncbi.nlm.nih.gov/pubmed/17037566

Fletcher J, Bender C, Budowle B, et al. Plant pathogen forensics: capabilities, needs, and recommendations. Microbiol Mol Biol Rev. 2006;70:450–471.  http://www.ncbi.nlm.nih.gov/pubmed/16760310

He Y, Reichow S, Ramamoorthy S, et al. Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophages. Infect Immun. 2006;74:5035–5046.  http://www.ncbi.nlm.nih.gov/pubmed/16926395

Tyler BM, Tripathy S, Zhang X, et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. 2006;313:1261–1266.  http://www.ncbi.nlm.nih.gov/pubmed/16946064

2005


Hance ME, Czar MJ, Azad A, et al. The pathogen resource integration center: implications for Rickettsial research. Ann N Y Acad Sci. 2005;1063:459–465.  http://www.ncbi.nlm.nih.gov/pubmed/16481560

He Y, Vines RR, Wattam AR, et al. PIML: the Pathogen Information Markup Language. Bioinformatics. 2005;21:116–121.  http://www.ncbi.nlm.nih.gov/pubmed/15297293

Mao C, Qiu J, Wang C, Charles TC, Sobral BW. NodMutDB: a database for genes and mutants involved in symbiosis. Bioinformatics. 2005;21:2927–2929.  http://www.ncbi.nlm.nih.gov/pubmed/15817696

2004


Olden K, Call N, Sobral B, Oakes R. Toxicogenomics through the eyes of informatics: conference overview and recommendations. Environ Health Perspect. 2004;112:805–807.  http://www.ncbi.nlm.nih.gov/pubmed/15159210

2003


Eckart JD, Sobral BW. A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework. Omics. 2003;7:79–88.  http://www.ncbi.nlm.nih.gov/pubmed/12831562

2001


Huala E, Dickerman AW, Garcia-Hernandez M, et al. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001;29:102–105.  http://www.ncbi.nlm.nih.gov/pubmed/11125061

Siepel A, Farmer A, Tolopko A, et al. ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics. 2001;17:83–94.  http://www.ncbi.nlm.nih.gov/pubmed/11222265

Sobral BW, Mangalam H, Siepel A, Mendes P, Pecherer R, McLaren G. Bioinformatics for rice resources. Novartis Found Symp. 2001;236:59–81; discussion 81–4.  http://www.ncbi.nlm.nih.gov/pubmed/11387987

2000


Qutob D, Hraber PT, Sobral BW, Gijzen M. Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol. 2000;123:243–254.  http://www.ncbi.nlm.nih.gov/pubmed/10806241

Waugh M, Hraber P, Weller J, et al. The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research. Nucleic Acids Res. 2000;28:87–90.  http://www.ncbi.nlm.nih.gov/pubmed/10592189

1999


de Oliveira VM, Coutinho HL, Sobral BW, Guimaraes CT, van Elsas JD, Manfio GP. Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S-23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE). Lett Appl Microbiol. 1999;28:137–141.  http://www.ncbi.nlm.nih.gov/pubmed/10063643

Kamoun S, Hraber P, Sobral B, Nuss D, Govers F. Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences. Fungal Genet Biol. 1999;28:94–106.  http://www.ncbi.nlm.nih.gov/pubmed/10587472

Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 1999;20:317–332.  http://www.ncbi.nlm.nih.gov/pubmed/10571892

1997


Gershon D, Sobral BW, Horton B, Wickware P, Gavaghan H, Strobl M. Bioinformatics in a post-genomics age. Nature. 1997;389:417–422.  http://www.ncbi.nlm.nih.gov/pubmed/9324648

Guimaraes CT, Sills GR, Sobral BW. Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc Natl Acad Sci U S A. 1997;94:14261–14266.  http://www.ncbi.nlm.nih.gov/pubmed/9405600

Honeycutt R, Sobral BW, McClelland M. Polymerase chain reaction (PCR) detection and quantification using a short PCR product and a synthetic internal positive control. Anal Biochem. 1997;248:303–306.  http://www.ncbi.nlm.nih.gov/pubmed/9177760

1995


Honeycutt RJ, Sobral BW, McClelland M. tRNA intergenic spacers reveal polymorphisms diagnostic for Xanthomonas albilineans. Microbiology. 1995;141 ( Pt 12):3229–3239.  http://www.ncbi.nlm.nih.gov/pubmed/8574414

Tigano-Milani MS, Honeycutt RJ, Lacey LA, Assis R, McClelland M, Sobral BW. Genetic variability of Paecilomyces fumosoroseus isolates revealed by molecular markers. J Invertebr Pathol. 1995;65:274–282.  http://www.ncbi.nlm.nih.gov/pubmed/7745282

Tigano-Milani MS, Samson RA, Martins I, Sobral BW. DNA markers for differentiating isolates of Paecilomyces lilacinus. Microbiology. 1995;141 ( Pt 1):239–245.  http://www.ncbi.nlm.nih.gov/pubmed/7894717

1993


al-Janabi SM, Honeycutt RJ, McClelland M, Sobral BW. A genetic linkage map of Saccharum spontaneum L. 'SES 208'. Genetics. 1993;134:1249–1260.  http://www.ncbi.nlm.nih.gov/pubmed/8375659

Honeycutt RJ, McClelland M, Sobral BW. Physical map of the genome of Rhizobium meliloti 1021. J Bacteriol. 1993;175:6945–6952.  http://www.ncbi.nlm.nih.gov/pubmed/8226638

1992


Honeycutt RJ, Sobral BW, McClelland M, Atherly AG. Analysis of large DNA from soybean (Glycine max L. Merr.) by pulsed-field gel electrophoresis. Plant J. 1992;2:133–135.  http://www.ncbi.nlm.nih.gov/pubmed/1303793

1991


Sobral BW, Honeycutt RJ, Atherly AG. The genomes of the family Rhizobiaceae: size, stability, and rarely cutting restriction endonucleases. J Bacteriol. 1991;173:704–709.  http://www.ncbi.nlm.nih.gov/pubmed/1846148

Sobral BW, Honeycutt RJ, Atherly AG, McClelland M. Electrophoretic separation of the three Rhizobium meliloti replicons. J Bacteriol. 1991;173:5173–5180.  http://www.ncbi.nlm.nih.gov/pubmed/1860826

1990


Sobral BW, Sadowsky MJ, Atherly AG. Genome analysis of Bradyrhizobium japonicum serocluster 123 field isolates by using field inversion gel electrophoresis. Appl Environ Microbiol. 1990;56:1949–1953.  http://www.ncbi.nlm.nih.gov/pubmed/2383015

1989


Sobral BW, Atherly AG. A rapid and cost-effective method for preparing genomic DNA from gram-negative bacteria in agarose plugs for pulsed-field gel electrophoresis. Biotechniques. 1989;7:938.  http://www.ncbi.nlm.nih.gov/pubmed/2517213

Sobral BW, Atherly AG. Pulse time and agarose concentration affect the electrophoretic mobility of cccDNA during PFGE and FIGE [corrected]. Nucleic Acids Res. 1989;17:7359–7369.  http://www.ncbi.nlm.nih.gov/pubmed/2798097