Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 76

1.

Amazonian deforestation and soil biodiversity.

Franco ALC, Sobral BW, Silva ALC, Wall DH.

Conserv Biol. 2019 Jun;33(3):590-600. doi: 10.1111/cobi.13234. Epub 2019 Jan 4.

PMID:
30306643
2.

Curation, integration and visualization of bacterial virulence factors in PATRIC.

Mao C, Abraham D, Wattam AR, Wilson MJ, Shukla M, Yoo HS, Sobral BW.

Bioinformatics. 2015 Jan 15;31(2):252-8. doi: 10.1093/bioinformatics/btu631. Epub 2014 Sep 30.

3.

Comparative genomic analysis at the PATRIC, a bioinformatic resource center.

Wattam AR, Gabbard JL, Shukla M, Sobral BW.

Methods Mol Biol. 2014;1197:287-308. doi: 10.1007/978-1-4939-1261-2_17.

PMID:
25172288
4.

Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence.

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.

J Bacteriol. 2014 Mar;196(5):920-30. doi: 10.1128/JB.01091-13. Epub 2013 Dec 13.

5.

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.

6.

The condition-dependent transcriptional landscape of Burkholderia pseudomallei.

Ooi WF, Ong C, Nandi T, Kreisberg JF, Chua HH, Sun G, Chen Y, Mueller C, Conejero L, Eshaghi M, Ang RM, Liu J, Sobral BW, Korbsrisate S, Gan YH, Titball RW, Bancroft GJ, Valade E, Tan P.

PLoS Genet. 2013;9(9):e1003795. doi: 10.1371/journal.pgen.1003795. Epub 2013 Sep 12.

7.

Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.

Driscoll T, Gillespie JJ, Nordberg EK, Azad AF, Sobral BW.

Genome Biol Evol. 2013;5(4):621-45. doi: 10.1093/gbe/evt036.

8.

Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition.

Mao C, Shukla M, Larrouy-Maumus G, Dix FL, Kelley LA, Sternberg MJ, Sobral BW, de Carvalho LP.

Tuberculosis (Edinb). 2013 Jan;93(1):40-6. doi: 10.1016/j.tube.2012.11.008. Epub 2013 Jan 1. Review.

PMID:
23287603
9.

Helicobacter pylori colonization ameliorates glucose homeostasis in mice through a PPAR γ-dependent mechanism.

Bassaganya-Riera J, Dominguez-Bello MG, Kronsteiner B, Carbo A, Lu P, Viladomiu M, Pedragosa M, Zhang X, Sobral BW, Mane SP, Mohapatra SK, Horne WT, Guri AJ, Groeschl M, Lopez-Velasco G, Hontecillas R.

PLoS One. 2012;7(11):e50069. doi: 10.1371/journal.pone.0050069. Epub 2012 Nov 15.

10.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Nov 6;3(5):e00246-11. doi: 10.1128/mBio.00388-12.

11.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Aug 28;3(5):e00246-12. doi: 10.1128/mBio.00246-12. Print 2012. Erratum in: MBio. 2012 Nov-Dec;3(6):e00388-12.

12.

A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle.

Gillespie JJ, Joardar V, Williams KP, Driscoll T, Hostetler JB, Nordberg E, Shukla M, Walenz B, Hill CA, Nene VM, Azad AF, Sobral BW, Caler E.

J Bacteriol. 2012 Jan;194(2):376-94. doi: 10.1128/JB.06244-11. Epub 2011 Nov 4.

13.

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.

Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW.

Infect Immun. 2011 Nov;79(11):4286-98. doi: 10.1128/IAI.00207-11. Epub 2011 Sep 6. Review.

14.

Integration and visualization of host-pathogen data related to infectious diseases.

Driscoll T, Gabbard JL, Mao C, Dalay O, Shukla M, Freifeld CC, Hoen AG, Brownstein JS, Sobral BW.

Bioinformatics. 2011 Aug 15;27(16):2279-87. doi: 10.1093/bioinformatics/btr391. Epub 2011 Jun 27.

15.

Supervised learning and prediction of physical interactions between human and HIV proteins.

Dyer MD, Murali TM, Sobral BW.

Infect Genet Evol. 2011 Jul;11(5):917-23. doi: 10.1016/j.meegid.2011.02.022. Epub 2011 Mar 5.

16.

Abscisic acid regulates inflammation via ligand-binding domain-independent activation of peroxisome proliferator-activated receptor gamma.

Bassaganya-Riera J, Guri AJ, Lu P, Climent M, Carbo A, Sobral BW, Horne WT, Lewis SN, Bevan DR, Hontecillas R.

J Biol Chem. 2011 Jan 28;286(4):2504-16. doi: 10.1074/jbc.M110.160077. Epub 2010 Nov 18.

17.

Immunoregulatory mechanisms of macrophage PPAR-γ in mice with experimental inflammatory bowel disease.

Hontecillas R, Horne WT, Climent M, Guri AJ, Evans C, Zhang Y, Sobral BW, Bassaganya-Riera J.

Mucosal Immunol. 2011 May;4(3):304-13. doi: 10.1038/mi.2010.75. Epub 2010 Nov 10.

18.

Analysis of high-throughput sequencing data.

Mane SP, Modise T, Sobral BW.

Methods Mol Biol. 2011;678:1-11. doi: 10.1007/978-1-60761-682-5_1.

PMID:
20931368
19.

The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, Bassaganya-Riera J, Murali TM, Sobral BW.

PLoS One. 2010 Aug 9;5(8):e12089. doi: 10.1371/journal.pone.0012089.

20.

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types.

Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z.

BMC Genomics. 2010 Jun 17;11:384. doi: 10.1186/1471-2164-11-384.

21.

Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses.

Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J.

J Bacteriol. 2010 Jun;192(12):3078-92. doi: 10.1128/JB.00063-10. Epub 2010 Apr 16.

22.

Phylogeny of gammaproteobacteria.

Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW.

J Bacteriol. 2010 May;192(9):2305-14. doi: 10.1128/JB.01480-09. Epub 2010 Mar 5.

23.

Phylogenomics reveals a diverse Rickettsiales type IV secretion system.

Gillespie JJ, Brayton KA, Williams KP, Diaz MA, Brown WC, Azad AF, Sobral BW.

Infect Immun. 2010 May;78(5):1809-23. doi: 10.1128/IAI.01384-09. Epub 2010 Feb 22. Review.

24.

Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis.

Buss SN, Hamano S, Vidrich A, Evans C, Zhang Y, Crasta OR, Sobral BW, Gilchrist CA, Petri WA Jr.

Int J Parasitol. 2010 Jun;40(7):833-43. doi: 10.1016/j.ijpara.2009.12.007. Epub 2010 Jan 18.

25.

Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection.

Mohapatra SK, Cole LE, Evans C, Sobral BW, Bassaganya-Riera J, Hontecillas R, Vogel SN, Crasta OR.

BMC Infect Dis. 2010 Jan 18;10:10. doi: 10.1186/1471-2334-10-10.

26.

Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvI and its phenotypic characteristics.

Wang C, Kemp J, Da Fonseca IO, Equi RC, Sheng X, Charles TC, Sobral BW.

Mol Plant Microbe Interact. 2010 Feb;23(2):153-60. doi: 10.1094/MPMI-23-2-0153.

27.

A typhus group-specific protease defies reductive evolution in rickettsiae.

Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF.

J Bacteriol. 2009 Dec;191(24):7609-13. doi: 10.1128/JB.01077-09. Epub 2009 Oct 9.

28.

Variations on the tmRNA gene.

Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C, Sobral BW, Williams KP.

RNA Biol. 2009 Sep-Oct;6(4):355-61. Epub 2009 Sep 4.

PMID:
19617710
29.

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.

Wattam AR, Williams KP, Snyder EE, Almeida NF Jr, Shukla M, Dickerman AW, Crasta OR, Kenyon R, Lu J, Shallom JM, Yoo H, Ficht TA, Tsolis RM, Munk C, Tapia R, Han CS, Detter JC, Bruce D, Brettin TS, Sobral BW, Boyle SM, Setubal JC.

J Bacteriol. 2009 Jun;191(11):3569-79. doi: 10.1128/JB.01767-08. Epub 2009 Apr 3.

30.

Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella.

Beare PA, Unsworth N, Andoh M, Voth DE, Omsland A, Gilk SD, Williams KP, Sobral BW, Kupko JJ 3rd, Porcella SF, Samuel JE, Heinzen RA.

Infect Immun. 2009 Feb;77(2):642-56. doi: 10.1128/IAI.01141-08. Epub 2008 Dec 1.

31.

PIG--the pathogen interaction gateway.

Driscoll T, Dyer MD, Murali TM, Sobral BW.

Nucleic Acids Res. 2009 Jan;37(Database issue):D647-50. doi: 10.1093/nar/gkn799. Epub 2008 Nov 4.

32.

Targets of the Entamoeba histolytica transcription factor URE3-BP.

Gilchrist CA, Baba DJ, Zhang Y, Crasta O, Evans C, Caler E, Sobral BW, Bousquet CB, Leo M, Hochreiter A, Connell SK, Mann BJ, Petri WA.

PLoS Negl Trop Dis. 2008;2(8):e282. doi: 10.1371/journal.pntd.0000282. Epub 2008 Aug 27.

33.

Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection.

Abhyankar MM, Hochreiter AE, Hershey J, Evans C, Zhang Y, Crasta O, Sobral BW, Mann BJ, Petri WA Jr, Gilchrist CA.

Eukaryot Cell. 2008 Sep;7(9):1565-72. doi: 10.1128/EC.00123-08. Epub 2008 Jul 25.

34.

Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.

Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW.

PLoS One. 2008 May 14;3(5):e2193. doi: 10.1371/journal.pone.0002193.

35.

Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.

Mao C, Evans C, Jensen RV, Sobral BW.

BMC Microbiol. 2008 May 2;8:72. doi: 10.1186/1471-2180-8-72.

36.

The landscape of human proteins interacting with viruses and other pathogens.

Dyer MD, Murali TM, Sobral BW.

PLoS Pathog. 2008 Feb 8;4(2):e32. doi: 10.1371/journal.ppat.0040032.

37.
38.

Computational prediction of host-pathogen protein-protein interactions.

Dyer MD, Murali TM, Sobral BW.

Bioinformatics. 2007 Jul 1;23(13):i159-66.

PMID:
17646292
39.

Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection.

Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C, Sobral BW, Waugh ME, Mitchell TK, Dean RA, Tyler BM.

Mol Plant Microbe Interact. 2007 Jul;20(7):781-93.

40.

A robust species tree for the alphaproteobacteria.

Williams KP, Sobral BW, Dickerman AW.

J Bacteriol. 2007 Jul;189(13):4578-86. Epub 2007 May 4.

41.

Roles of poly-3-hydroxybutyrate (PHB) and glycogen in symbiosis of Sinorhizobium meliloti with Medicago sp.

Wang C, Saldanha M, Sheng X, Shelswell KJ, Walsh KT, Sobral BW, Charles TC.

Microbiology. 2007 Feb;153(Pt 2):388-98.

PMID:
17259610
42.

Loss of a universal tRNA feature.

Wang C, Sobral BW, Williams KP.

J Bacteriol. 2007 Mar;189(5):1954-62. Epub 2006 Dec 15.

43.

PATRIC: the VBI PathoSystems Resource Integration Center.

Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW.

Nucleic Acids Res. 2007 Jan;35(Database issue):D401-6. Epub 2006 Nov 16.

44.

Developing bioinformatic resources for coronaviruses.

Baker SC, Jukneliene D, Purkayastha A, Snyder EE, Crasta OR, Czar MJ, Setubal JC, Sobral BW.

Adv Exp Med Biol. 2006;581:395-8. Review. No abstract available.

PMID:
17037566
45.

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL.

Science. 2006 Sep 1;313(5791):1261-6.

46.

Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophages.

He Y, Reichow S, Ramamoorthy S, Ding X, Lathigra R, Craig JC, Sobral BW, Schurig GG, Sriranganathan N, Boyle SM.

Infect Immun. 2006 Sep;74(9):5035-46.

47.

Plant pathogen forensics: capabilities, needs, and recommendations.

Fletcher J, Bender C, Budowle B, Cobb WT, Gold SE, Ishimaru CA, Luster D, Melcher U, Murch R, Scherm H, Seem RC, Sherwood JL, Sobral BW, Tolin SA.

Microbiol Mol Biol Rev. 2006 Jun;70(2):450-71. Review.

48.

The pathogen resource integration center: implications for Rickettsial research.

Hance ME, Czar MJ, Azad A, Purkayastha A, Snyder EE, Crasta OR, Setubal JC, Sobral BW.

Ann N Y Acad Sci. 2005 Dec;1063:459-65. No abstract available.

PMID:
16481560
49.

NodMutDB: a database for genes and mutants involved in symbiosis.

Mao C, Qiu J, Wang C, Charles TC, Sobral BW.

Bioinformatics. 2005 Jun 15;21(12):2927-9. Epub 2005 Apr 7.

PMID:
15817696
50.

PIML: the Pathogen Information Markup Language.

He Y, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BW.

Bioinformatics. 2005 Jan 1;21(1):116-21. Epub 2004 Aug 5.

PMID:
15297293

Supplemental Content

Loading ...
Support Center