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pyseer: a comprehensive tool for microbial pangenome-wide association studies

Bioinformatics, 2018-12, Vol.34 (24), p.4310-4312

2018

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Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

PLoS genetics, 2020-10, Vol.16 (10), p.e1009065-e1009065

2020

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Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome

PLoS genetics, 2022-03, Vol.18 (3), p.e1010112-e1010112

2022

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A resource of variant effect predictions of single nucleotide variants in model organisms

Molecular systems biology, 2018-12, Vol.14 (12), p.e8430-n/a

2018

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Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence

Nature communications, 2023-06, Vol.14 (1), p.3667-3667, Article 3667

2023

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The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae

Molecular systems biology, 2019-12, Vol.15 (12), p.e8831-n/a

2019

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The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

Scientific reports, 2023-04, Vol.13 (1), p.7038-7038, Article 7038

2023

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Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Cell systems, 2017-03, Vol.4 (3), p.291-305.e7

2017

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Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

Nature communications, 2016-07, Vol.7 (1), p.12219-12219, Article 12219

2016

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Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

mBio, 2020-07, Vol.11 (4)

2020

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CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Source code for biology and medicine, 2011-06, Vol.6 (1), p.11-11, Article 11

2011

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Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages

Nature communications, 2024-02, Vol.15 (1), p.952-952, Article 952

2024

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High-throughput functional characterization of protein phosphorylation sites in yeast

Nature biotechnology, 2022-03, Vol.40 (3), p.382-390

2022

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The success of acinetobacter species; genetic, metabolic and virulence attributes

PloS one, 2012-10, Vol.7 (10), p.e46984-e46984

2012

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Phenotype inference in an Escherichia coli strain panel

eLife, 2017-12, Vol.6

2017

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Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species

Frontiers in microbiology, 2018-08, Vol.9, p.1940-1940

2018

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Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Genome biology and evolution, 2013-03, Vol.5 (3), p.542-558

2013

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Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

PLoS computational biology, 2015-09, Vol.11 (9), p.e1004478-e1004478

2015

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Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Genes, 2011-11, Vol.2 (4), p.1017-1032

2011

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Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

BMC genomics, 2011-05, Vol.12 (1), p.235-235, Article 235

2011

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MeDuSa: a multi-draft based scaffolder

Bioinformatics, 2015-08, Vol.31 (15), p.2443-2451

2015

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ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling

Bioinformatics (Oxford, England), 2023-04, Vol.39 (4)

2023

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Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis

Methods in molecular biology (Clifton, N.J.), 2021-01, Vol.2189, p.199

2021

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Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k -mers

Microbial genomics, 2023-11, Vol.9 (11)

2023

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Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems

Nature (London), 2022-09, Vol.609 (7925), p.144-150

2022

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pyseer: a comprehensive tool for microbial pangenome-wide association studies

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome

A resource of variant effect predictions of single nucleotide variants in model organisms

Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages

High-throughput functional characterization of protein phosphorylation sites in yeast

The success of acinetobacter species; genetic, metabolic and virulence attributes

Phenotype inference in an Escherichia coli strain panel

Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

MeDuSa: a multi-draft based scaffolder

ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling

Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis

Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k -mers

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems

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