106
Oany AR, Mia M, Pervin T, Hasan MN, Hirashima A (2018) Identification of potential drug targets
and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic
approach. In Silico Pharmacol 6(1). https://doi.org/10.1007/s40203-018-0048-2
Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320. https://doi.org/10.1038/msb.2009.77
Odds FC, Brown AJP, Gow NAR (2003) Antifungal agents: mechanisms of action. Trends
Microbiol 11(6):272–279
Panjkovich A, Gibert I, Daura X (2014) antibacTR: dynamic antibacterial-drug-target ranking
integrating comparative genomics, structural analysis and experimental annotation. BMC
Genomics 15:36. https://doi.org/10.1186/1471-2164-15-36
Parise D, Parise MTD, Viana MVC, Munoz-Bucio AV, Cortes-Perez YA, Arellano-Reynoso B
et al (2018) First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. Stand Genomic Sci 13:21. https://doi.org/10.1186/
s40793-018-0325-z
Perlin DS, Rautemaa-Richardson R, Alastruey-Izquierdo A (2017) The global problem of antifungal resistance: prevalence, mechanisms, and management. Lancet Infect Dis 17(12):e383–
e392. https://doi.org/10.1016/S1473-3099(17)30316-X
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V et al (2012) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res 40(Database
issue):D593–D598. https://doi.org/10.1093/nar/gkr859
Podschun R, Ullmann U (1998) Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11(4):589–603
Pradeepkiran JA, P, R.b, Konidala K, Bhaskar (2015) Complete genome-wide screening and
subtractive genomic approach revealed new virulence factors, potential drug targets against
bio-war pathogen Brucella melitensis 16M. Drug Des Devel Ther. https://doi.org/10.2147/
dddt.S76948
Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL et al (2008)
Cataloguing the HIV type 1 human protein interaction network. AIDS Res Hum Retrovir
24(12):1497–1502. https://doi.org/10.1089/aid.2008.0113
Raghunathan A, Shin S, Daefler S (2010) Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella
tularensis. BMC Syst Biol 4:118. https://doi.org/10.1186/1752-0509-4-118
Rahman MA, Noore MS, Hasan MA, Ullah MR, Rahman MH, Hossain MA et al (2014)
Identification of potential drug targets by subtractive genome analysis of Bacillus anthracis A0248: an in silico approach. Comput Biol Chem 52:66–72. https://doi.org/10.1016/j.
compbiolchem.2014.09.005
Ramage G, Rajendran R, Sherry L, Williams C (2012) Fungal biofilm resistance. Int J Microbiol
2012:1–14. https://doi.org/10.1155/2012/528521
Raman K, Yeturu K, Chandra N (2008) targetTB: a target identification pipeline for Mycobacterium
tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC
Syst Biol 2:109. https://doi.org/10.1186/1752-0509-2-109
Ramos PIP, Fernandez Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM et al (2018)
An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug
targets. Sci Rep 8(1):10755. https://doi.org/10.1038/s41598-018-28916-7
Rasko DA, Altherr MR, Han CS, Ravel J (2005) Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 29(2):303–329. https://doi.org/10.1016/j.femsre.2004.12.005
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P et al (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and
pathogenic isolates. J Bacteriol 190(20):6881–6893. https://doi.org/10.1128/JB.00619-08
Remmele CW, Luther CH, Balkenhol J, Dandekar T, Muller T, Dittrich MT (2015) Integrated
inference and evaluation of host-fungi interaction networks. Front Microbiol 6:764. https://doi.
org/10.3389/fmicb.2015.00764
M. Santana et al.
Oany AR, Mia M, Pervin T, Hasan MN, Hirashima A (2018) Identification of potential drug targets
and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic
approach. In Silico Pharmacol 6(1). https://doi.org/10.1007/s40203-018-0048-2
Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320. https://doi.org/10.1038/msb.2009.77
Odds FC, Brown AJP, Gow NAR (2003) Antifungal agents: mechanisms of action. Trends
Microbiol 11(6):272–279
Panjkovich A, Gibert I, Daura X (2014) antibacTR: dynamic antibacterial-drug-target ranking
integrating comparative genomics, structural analysis and experimental annotation. BMC
Genomics 15:36. https://doi.org/10.1186/1471-2164-15-36
Parise D, Parise MTD, Viana MVC, Munoz-Bucio AV, Cortes-Perez YA, Arellano-Reynoso B
et al (2018) First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. Stand Genomic Sci 13:21. https://doi.org/10.1186/
s40793-018-0325-z
Perlin DS, Rautemaa-Richardson R, Alastruey-Izquierdo A (2017) The global problem of antifungal resistance: prevalence, mechanisms, and management. Lancet Infect Dis 17(12):e383–
e392. https://doi.org/10.1016/S1473-3099(17)30316-X
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V et al (2012) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res 40(Database
issue):D593–D598. https://doi.org/10.1093/nar/gkr859
Podschun R, Ullmann U (1998) Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11(4):589–603
Pradeepkiran JA, P, R.b, Konidala K, Bhaskar (2015) Complete genome-wide screening and
subtractive genomic approach revealed new virulence factors, potential drug targets against
bio-war pathogen Brucella melitensis 16M. Drug Des Devel Ther. https://doi.org/10.2147/
dddt.S76948
Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, Robertson DL et al (2008)
Cataloguing the HIV type 1 human protein interaction network. AIDS Res Hum Retrovir
24(12):1497–1502. https://doi.org/10.1089/aid.2008.0113
Raghunathan A, Shin S, Daefler S (2010) Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella
tularensis. BMC Syst Biol 4:118. https://doi.org/10.1186/1752-0509-4-118
Rahman MA, Noore MS, Hasan MA, Ullah MR, Rahman MH, Hossain MA et al (2014)
Identification of potential drug targets by subtractive genome analysis of Bacillus anthracis A0248: an in silico approach. Comput Biol Chem 52:66–72. https://doi.org/10.1016/j.
compbiolchem.2014.09.005
Ramage G, Rajendran R, Sherry L, Williams C (2012) Fungal biofilm resistance. Int J Microbiol
2012:1–14. https://doi.org/10.1155/2012/528521
Raman K, Yeturu K, Chandra N (2008) targetTB: a target identification pipeline for Mycobacterium
tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC
Syst Biol 2:109. https://doi.org/10.1186/1752-0509-2-109
Ramos PIP, Fernandez Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM et al (2018)
An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug
targets. Sci Rep 8(1):10755. https://doi.org/10.1038/s41598-018-28916-7
Rasko DA, Altherr MR, Han CS, Ravel J (2005) Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 29(2):303–329. https://doi.org/10.1016/j.femsre.2004.12.005
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P et al (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and
pathogenic isolates. J Bacteriol 190(20):6881–6893. https://doi.org/10.1128/JB.00619-08
Remmele CW, Luther CH, Balkenhol J, Dandekar T, Muller T, Dittrich MT (2015) Integrated
inference and evaluation of host-fungi interaction networks. Front Microbiol 6:764. https://doi.
org/10.3389/fmicb.2015.00764
M. Santana et al.