Additional file 1: Table S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Bacteria responsible for fluoroquinolone resistance genes in 16 metagenomes.

Lisa M. Durso (122485)
Daniel N. Miller (122491)
Brian J. Wienhold (122499)

November 2012

<p>Percent of fluoroquinolone resistance genes within each metagenome that are assigned to the liste...

Additional file 2: Table S2. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Brittan Scales (3401519)
John Erb-Downward (3401513)
Ian Huffnagle (3401525)
John LiPuma (3401522)
Gary Huffnagle (3401516)

December 2015

The nucleotide sequence of the 16S rRNA sequences was used to query the NCBI nucleotide collection (...

Additional file 1: Table S1. of Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Alexander Greninger (3568193)
Samia Naccache (727339)
Scot Federman (829734)
Guixia Yu (123189)
Placide Mbala (3568181)
Vanessa Bres (3568184)
Doug Stryke (14115)
Jerome Bouquet (3568199)
Sneha Somasekar (727338)
Jeffrey Linnen (3568202)
Roger Dodd (3568187)
Prime Mulembakani (131494)
Bradley Schneider (3568196)
Jean-Jacques Muyembe-Tamfum (122740)
Susan Stramer (3568190)
Charles Chiu (269887)

September 2015

Optimization of word count for MegaBLAST alignment to the NT reference database. (XLSX 12 kb

Additional file 5: Table S3. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund (4411366)
Fanny Berglund (4411363)
Carl-Fredrik Flach (769245)
Johan Bengtsson-Palme (3455993)
Nachiket Marathe (1778848)
DG Larsson (4411333)
Erik Kristiansson (75825)

September 2017

MIC measurements. Raw data for Fig. 1. MIC measurements of assembled, putatively novel, qnr gene seq...

Additional file 3: Figure S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund (4411366)
Fanny Berglund (4411363)
Carl-Fredrik Flach (769245)
Johan Bengtsson-Palme (3455993)
Nachiket Marathe (1778848)
DG Larsson (4411333)
Erik Kristiansson (75825)

September 2017

Complete gene tree. Description: A gene tree containing all assembled putative qnr gene sequences id...

Additional file 6: of Identification and reconstruction of novel antibiotic resistance genes from metagenomes

Fanny Berglund (4411363)
Tobias Ăsterlund (3467861)
Fredrik Boulund (4411366)
Nachiket Marathe (1778848)
D. Larsson (3455996)
Erik Kristiansson (75825)

April 2019

Table S2. A list of all reconstructed and predicted genes together with their amino acid sequences. ...

Additional file 2: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S1. Significant predictive power of different subsets of resistance genes on known mobile anti...

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Boulund, Fredrik
Berglund, Fanny
Flach, Carl-Fredrik
Bengtsson-Palme, Johan
Marathe, Nachiket
Larsson, D. G. Joakim
Kristiansson, Erik

January 2017

Background: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range o...

Additional file 3: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S2. Commonly used target genes for qPCR-based studies of resistance genes in the environments ...

Additional file 4: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S3. Significant predictive power of different subsets of resistance genes on antibiotic resist...

Additional file 1: of Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

Chandan Pal (3455990)
Johan Bengtsson-Palme (3455993)
Erik Kristiansson (75825)
D. Larsson (3455996)

November 2015

Additional data file 1 contains additional tables and figures. Table S1. Metadata of 2522 completely...

Additional file 4 of Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Alexandre Drouin (2239411)
Sébastien Giguère (718094)
Maxime Déraspe (3480068)
Mario Marchand (718096)
Michael Tyers (1575610)
Vivian Loo (3480065)
Anne-Marie Bourgault (729915)
François Laviolette (718095)
Jacques Corbeil (51262)

September 2016

Supplemental Figures. Figure S1. An illustration of the resistance models generated for each antibio...

Additional file 3: of Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

Tra-My Ngo (6318062)
Yik-Ying Teo (159446)

February 2019

Characteristics of the four bioinformatics software for predicting drug resistance from Mtb genome s...

Additional file 1: of Evaluation of co-transfer of plasmid-mediated fluoroquinolone resistance genes and blaNDM gene in Enterobacteriaceae causing neonatal septicaemia

Shravani Mitra (6409403)
Suchandra Mukherjee (6409406)
Sharmi Naha (6409409)
Pinaki Chattopadhyay (6409412)
Shanta Dutta (185742)
Sulagna Basu (663199)

March 2019

Detailed information of allÂ studied EnterobacteriaceaeÂ :Â MIC values of meropenem and cirpfloxacin...

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund
Fanny Berglund
Carl-Fredrik Flach
Johan Bengtsson-Palme
Nachiket P. Marathe
DG Joakim Larsson
Erik Kristiansson

September 2017

Abstract Background Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide...

Bacteria responsible for fluoroquinolone resistance genes in 16 metagenomes.

Lisa M. Durso (122485)
Daniel N. Miller (122491)
Brian J. Wienhold (122499)

November 2012

<p>Percent of fluoroquinolone resistance genes within each metagenome that are assigned to the liste...

Additional file 2: Table S2. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Brittan Scales (3401519)
John Erb-Downward (3401513)
Ian Huffnagle (3401525)
John LiPuma (3401522)
Gary Huffnagle (3401516)

December 2015

The nucleotide sequence of the 16S rRNA sequences was used to query the NCBI nucleotide collection (...

Additional file 1: Table S1. of Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Alexander Greninger (3568193)
Samia Naccache (727339)
Scot Federman (829734)
Guixia Yu (123189)
Placide Mbala (3568181)
Vanessa Bres (3568184)
Doug Stryke (14115)
Jerome Bouquet (3568199)
Sneha Somasekar (727338)
Jeffrey Linnen (3568202)
Roger Dodd (3568187)
Prime Mulembakani (131494)
Bradley Schneider (3568196)
Jean-Jacques Muyembe-Tamfum (122740)
Susan Stramer (3568190)
Charles Chiu (269887)

September 2015

Optimization of word count for MegaBLAST alignment to the NT reference database. (XLSX 12 kb

Additional file 5: Table S3. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund (4411366)
Fanny Berglund (4411363)
Carl-Fredrik Flach (769245)
Johan Bengtsson-Palme (3455993)
Nachiket Marathe (1778848)
DG Larsson (4411333)
Erik Kristiansson (75825)

September 2017

MIC measurements. Raw data for Fig. 1. MIC measurements of assembled, putatively novel, qnr gene seq...

Additional file 3: Figure S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund (4411366)
Fanny Berglund (4411363)
Carl-Fredrik Flach (769245)
Johan Bengtsson-Palme (3455993)
Nachiket Marathe (1778848)
DG Larsson (4411333)
Erik Kristiansson (75825)

September 2017

Complete gene tree. Description: A gene tree containing all assembled putative qnr gene sequences id...

Additional file 6: of Identification and reconstruction of novel antibiotic resistance genes from metagenomes

Fanny Berglund (4411363)
Tobias Ăsterlund (3467861)
Fredrik Boulund (4411366)
Nachiket Marathe (1778848)
D. Larsson (3455996)
Erik Kristiansson (75825)

April 2019

Table S2. A list of all reconstructed and predicted genes together with their amino acid sequences. ...

Additional file 2: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S1. Significant predictive power of different subsets of resistance genes on known mobile anti...

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Boulund, Fredrik
Berglund, Fanny
Flach, Carl-Fredrik
Bengtsson-Palme, Johan
Marathe, Nachiket
Larsson, D. G. Joakim
Kristiansson, Erik

January 2017

Background: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range o...

Additional file 3: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S2. Commonly used target genes for qPCR-based studies of resistance genes in the environments ...

Additional file 4: of The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variantsâbut not always

Johan Bengtsson-Palme (3455993)

July 2018

Table S3. Significant predictive power of different subsets of resistance genes on antibiotic resist...

Additional file 1: of Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

Chandan Pal (3455990)
Johan Bengtsson-Palme (3455993)
Erik Kristiansson (75825)
D. Larsson (3455996)

November 2015

Additional data file 1 contains additional tables and figures. Table S1. Metadata of 2522 completely...

Additional file 4 of Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Alexandre Drouin (2239411)
Sébastien Giguère (718094)
Maxime Déraspe (3480068)
Mario Marchand (718096)
Michael Tyers (1575610)
Vivian Loo (3480065)
Anne-Marie Bourgault (729915)
François Laviolette (718095)
Jacques Corbeil (51262)

September 2016

Supplemental Figures. Figure S1. An illustration of the resistance models generated for each antibio...

Additional file 3: of Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

Tra-My Ngo (6318062)
Yik-Ying Teo (159446)

February 2019

Characteristics of the four bioinformatics software for predicting drug resistance from Mtb genome s...

Additional file 1: of Evaluation of co-transfer of plasmid-mediated fluoroquinolone resistance genes and blaNDM gene in Enterobacteriaceae causing neonatal septicaemia

Shravani Mitra (6409403)
Suchandra Mukherjee (6409406)
Sharmi Naha (6409409)
Pinaki Chattopadhyay (6409412)
Shanta Dutta (185742)
Sulagna Basu (663199)

March 2019

Detailed information of allÂ studied EnterobacteriaceaeÂ :Â MIC values of meropenem and cirpfloxacin...

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Fredrik Boulund
Fanny Berglund
Carl-Fredrik Flach
Johan Bengtsson-Palme
Nachiket P. Marathe
DG Joakim Larsson
Erik Kristiansson

September 2017

Abstract Background Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide...

Bacteria responsible for fluoroquinolone resistance genes in 16 metagenomes.

Lisa M. Durso (122485)
Daniel N. Miller (122491)
Brian J. Wienhold (122499)

November 2012

<p>Percent of fluoroquinolone resistance genes within each metagenome that are assigned to the liste...

Additional file 2: Table S2. of Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Brittan Scales (3401519)
John Erb-Downward (3401513)
Ian Huffnagle (3401525)
John LiPuma (3401522)
Gary Huffnagle (3401516)

December 2015

The nucleotide sequence of the 16S rRNA sequences was used to query the NCBI nucleotide collection (...

Additional file 1: Table S1. of Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Alexander Greninger (3568193)
Samia Naccache (727339)
Scot Federman (829734)
Guixia Yu (123189)
Placide Mbala (3568181)
Vanessa Bres (3568184)
Doug Stryke (14115)
Jerome Bouquet (3568199)
Sneha Somasekar (727338)
Jeffrey Linnen (3568202)
Roger Dodd (3568187)
Prime Mulembakani (131494)
Bradley Schneider (3568196)
Jean-Jacques Muyembe-Tamfum (122740)
Susan Stramer (3568190)
Charles Chiu (269887)

September 2015

Optimization of word count for MegaBLAST alignment to the NT reference database. (XLSX 12 kb

Additional file 1: Table S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Abstract

Extracted data

Additional file 1: Table S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

Abstract

Extracted data

Related items

Related items