In silico prediction of human pathogenicity in the γ-proteobacteria.
PLoS One. 2010.
PMID: 21048922
Free PMC article.
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Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.
BMC Genomics. 2018 Nov 6;19(1):801. doi: 10.1186/s12864-018-5137-4.
BMC Genomics. 2018.
PMID: 30400810
Free PMC article.
RESULTS: WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically cl …
RESULTS: WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm enviro …
In silico prediction of human pathogenicity in the γ-proteobacteria.
PLoS One. 2010 Oct 27;5(10):e13680. doi: 10.1371/journal.pone.0013680.
PLoS One. 2010.
PMID: 21048922
Free PMC article.
METHODOLOGY/PRINCIPAL FINDINGS: We describe a new in silico method for the prediction of bacterial pathogenicity, based on the identification in microbial genomes of features that appear to correlate with virulence. ...Whether a new bacterium carries p …
METHODOLOGY/PRINCIPAL FINDINGS: We describe a new in silico method for the prediction of bacterial pathogenicity, based …
Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa.
Ann N Y Acad Sci. 2019 Jan;1435(1):5-17. doi: 10.1111/nyas.13358. Epub 2017 Jun 2.
Ann N Y Acad Sci. 2019.
PMID: 28574575
Free PMC article.
Review.
There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation. ...Coupled with bac …
There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silic …
hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.
J Clin Microbiol. 2019 May 24;57(6):e00190-19. doi: 10.1128/JCM.00190-19. Print 2019 Jun.
J Clin Microbiol. 2019.
PMID: 30944197
Free PMC article.
Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. ...Given the increasing incidence of encapsulated strains and the high frequency of Hib in co …
Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invas …
Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance.
Sci Rep. 2022 Aug 23;12(1):14372. doi: 10.1038/s41598-022-16760-9.
Sci Rep. 2022.
PMID: 35999234
Free PMC article.
As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as go …
As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where …
In silico prediction of escherichia coli proteins targeting the host cell nucleus, with special reference to their role in colon cancer etiology.
J Comput Biol. 2014 Jun;21(6):466-75. doi: 10.1089/cmb.2014.0001. Epub 2014 Mar 10.
J Comput Biol. 2014.
PMID: 24611522
This situation provides an opportunity for competitive interaction of host and pathogen proteins with similar cellular substrates, thereby increasing the chances of development of colon cancer. Moreover, the results indicated that proteins localized in the membrane of E. c …
This situation provides an opportunity for competitive interaction of host and pathogen proteins with similar cellular substrates, th …
In silico prediction of silver nitrate nanoparticles and Nitrate Reductase A (NAR A) interaction in the treatment of infectious disease causing clinical strains of E. coli.
J Infect Public Health. 2020 Oct;13(10):1580-1585. doi: 10.1016/j.jiph.2020.08.004. Epub 2020 Aug 25.
J Infect Public Health. 2020.
PMID: 32855089
Free article.
The enzyme is composed of three different chains alpha, beta and gamma, all having properties of metal binding regions and domains. ...The 3D structure of the NAR A protein was predicted with the Phyre2 protein modeling software. The generated structures from Phyre2 …
The enzyme is composed of three different chains alpha, beta and gamma, all having properties of metal binding regions and domains. . …
In-silico design of a multivalent epitope-based vaccine against Candida auris.
Microb Pathog. 2021 Jun;155:104879. doi: 10.1016/j.micpath.2021.104879. Epub 2021 Apr 18.
Microb Pathog. 2021.
PMID: 33848597
Candida auris is a rapidly emerging human pathogenic fungus with a high mortality rate. Recent report suggests that the new clinical isolates are showing resistance to the major classes of antifungal drugs. ...We have selected the agglutinin-like sequence-3 (Als3) a …
Candida auris is a rapidly emerging human pathogenic fungus with a high mortality rate. Recent report suggests that the new cl …
An integrative in silico approach to the structure of Omp33-36 in Acinetobacter baumannii.
Comput Biol Chem. 2018 Feb;72:77-86. doi: 10.1016/j.compbiolchem.2018.01.003. Epub 2018 Jan 12.
Comput Biol Chem. 2018.
PMID: 29414099
Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen metabolic fitness as well as its adherence and invasion to human epithelial cells. ...The signal peptide within the sequence was de …
Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen …
Combination of in vivo phage therapy data with in silico model highlights key parameters for pneumonia treatment efficacy.
Cell Rep. 2022 May 17;39(7):110825. doi: 10.1016/j.celrep.2022.110825.
Cell Rep. 2022.
PMID: 35584666
Free article.
Here, we develop a general strategy coupling in vitro and in vivo experiments with a mathematical model to characterize the interplay between phage and bacteria during pneumonia induced by a pathogenic strain of Escherichia coli. The model allows the estimation of several …
Here, we develop a general strategy coupling in vitro and in vivo experiments with a mathematical model to characterize the interplay betwee …
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