reference s pneumoniae strain atcc 49619 Search Results


standard quality control reference strains  (ATCC)
99
ATCC standard quality control reference strains
Standard Quality Control Reference Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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s pneumoniae reference genomes  (ATCC)
99
ATCC s pneumoniae reference genomes
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
S Pneumoniae Reference Genomes, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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clsi recommended quality control reference strains  (ATCC)
99
ATCC clsi recommended quality control reference strains
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
Clsi Recommended Quality Control Reference Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference strains  (ATCC)
94
ATCC reference strains
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
Reference Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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wild campylohacterjejuni atcc 33560  (ATCC)
96
ATCC wild campylohacterjejuni atcc 33560
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
Wild Campylohacterjejuni Atcc 33560, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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qc reference strains  (ATCC)
99
ATCC qc reference strains
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
Qc Reference Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference microbial strains  (ATCC)
99
ATCC reference microbial strains
Two-stage GWAS analysis process used to detect infection-associated Streptococcus <t>pneumoniae</t> k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.
Reference Microbial Strains, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Two-stage GWAS analysis process used to detect infection-associated Streptococcus pneumoniae k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Two-stage GWAS analysis process used to detect infection-associated Streptococcus pneumoniae k-mers in study of disease-associated Streptococcus pneumoniae genetic variation. GWAS, genome-wide association studies; LASSO, least absolute shrinkage and selection operator; LMM, linear mixed model; VSURF, variable selection using random forests; WGS, whole-genome sequencing.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection, GWAS, Selection, Sequencing

Whole-genome phylogenetic tree showing genetic similarity of 783 Streptococcus pneumoniae isolates in a study of disease-associated Streptococcus pneumoniae genetic variation. The colored strips at the tips of the tree (from inner to outer) represent isolate metadata (source, STs, serotypes, and GPSCs) and infection-associated k-mers found in the final model. GPSC, global pneumococcal sequencing cluster; ST, sequence type.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Whole-genome phylogenetic tree showing genetic similarity of 783 Streptococcus pneumoniae isolates in a study of disease-associated Streptococcus pneumoniae genetic variation. The colored strips at the tips of the tree (from inner to outer) represent isolate metadata (source, STs, serotypes, and GPSCs) and infection-associated k-mers found in the final model. GPSC, global pneumococcal sequencing cluster; ST, sequence type.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection, Sequencing

Association analysis between dominant genotypes and disease status from study of disease-associated Streptococcus pneumoniae genetic variation*

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Association analysis between dominant genotypes and disease status from study of disease-associated Streptococcus pneumoniae genetic variation*

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection

Preliminary screening for infection-associated k-mers by linear mixed model in study of disease-associated Streptococcus pneumoniae genetic variation. A) Manhattan plot showing statistical significance and chromosomal location of k-mers mapped to a complete reference genome (TIGR4; GenBank accession no. NC_003028.3). B) Importance of the top 100 k-mer predictors in a simpler model with 886 k-mers. C) Gene ontology annotations of the top 100 k-mer predictors. OR, odds ratio.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Preliminary screening for infection-associated k-mers by linear mixed model in study of disease-associated Streptococcus pneumoniae genetic variation. A) Manhattan plot showing statistical significance and chromosomal location of k-mers mapped to a complete reference genome (TIGR4; GenBank accession no. NC_003028.3). B) Importance of the top 100 k-mer predictors in a simpler model with 886 k-mers. C) Gene ontology annotations of the top 100 k-mer predictors. OR, odds ratio.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection

Resubstitution estimate and cross-validation results based on random forest models used in study of disease-associated Streptococcus pneumoniae genetic variation*

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Resubstitution estimate and cross-validation results based on random forest models used in study of disease-associated Streptococcus pneumoniae genetic variation*

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques:

Further validation of infection-associated k-mers by multiple GWAS analyses in study of disease-associated Streptococcus pneumoniae genetic variation. A) Venn diagram visualization of the k-mers identified by 3 methods. B) UpSet plot visualization of the k-mers identified by 3 methods. LASSO, least absolute shrinkage and selection operator; VSURF, variable selection using random forests.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Further validation of infection-associated k-mers by multiple GWAS analyses in study of disease-associated Streptococcus pneumoniae genetic variation. A) Venn diagram visualization of the k-mers identified by 3 methods. B) UpSet plot visualization of the k-mers identified by 3 methods. LASSO, least absolute shrinkage and selection operator; VSURF, variable selection using random forests.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Biomarker Discovery, Infection, Selection

Prediction effect of the 8 k-mers identified in the final model used in study of disease-associated Streptococcus pneumoniae genetic variation. A) Receiver operating characteristic curve of the final model. B) Predictor importance of the 8 k-mers in the final model. C) Proportion of k-mer predictors between infection and carriage isolates. D) Change in risk score for a specific k-mer profile when the k-mer is present (y-axis) compared to absent (x-axis). AUC, area under the curve.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Prediction effect of the 8 k-mers identified in the final model used in study of disease-associated Streptococcus pneumoniae genetic variation. A) Receiver operating characteristic curve of the final model. B) Predictor importance of the 8 k-mers in the final model. C) Proportion of k-mer predictors between infection and carriage isolates. D) Change in risk score for a specific k-mer profile when the k-mer is present (y-axis) compared to absent (x-axis). AUC, area under the curve.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection

Association analysis between k-mers and disease status used in study of disease-associated Streptococcus pneumoniae genetic variation*

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Association analysis between k-mers and disease status used in study of disease-associated Streptococcus pneumoniae genetic variation*

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: Infection

Pathogenicity models for genetically related disease-causing isolates used in study of disease-associated Streptococcus pneumoniae genetic variation. A) Pathogenic clone hypothesis; B) opportunistic pathogenicity hypothesis; C) pathogenic-determinant hypothesis.

Journal: Emerging Infectious Diseases

Article Title: Disease-Associated Streptococcus pneumoniae Genetic Variation

doi: 10.3201/eid3001.221927

Figure Lengend Snippet: Pathogenicity models for genetically related disease-causing isolates used in study of disease-associated Streptococcus pneumoniae genetic variation. A) Pathogenic clone hypothesis; B) opportunistic pathogenicity hypothesis; C) pathogenic-determinant hypothesis.

Article Snippet: To identify the relevant genes by using BWA-MEM (the Burrows-Wheeler Aligner with maximal exact matches alignment tool, https://github.com/lh3/bwa ), we mapped all k-mers to 10 S. pneumoniae reference genomes (CGSP14, D39, Hungary 19A -6, R6, Taiwan 19F -14, TIGR4, Spain 23F -ST81, ATCC 49619, EF3030, and MDRSPN001) obtained from the Virulence Factor Database ( http://www.mgc.ac.cn/VFs ) and previous studies.

Techniques: