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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

PLoS biology, 2019-07, Vol.17 (7), p.e3000390-e3000390

2019

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MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems

PloS one, 2014-10, Vol.9 (10), p.e110726-e110726

2014

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The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems

PLoS genetics, 2012-09, Vol.8 (9), p.e1002983-e1002983

2012

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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments

mBio, 2020-10, Vol.11 (5)

2020

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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Proceedings of the National Academy of Sciences - PNAS, 2012-10, Vol.109 (43), p.17513-17518

2012

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Lateral gene transfer as a support for the tree of life

Proceedings of the National Academy of Sciences - PNAS, 2012-03, Vol.109 (13), p.4962-4967

2012

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Geochemical transition zone powering microbial growth in subsurface sediments

Proceedings of the National Academy of Sciences - PNAS, 2020-12, Vol.117 (51), p.32617-32626

2020

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Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

Frontiers in microbiology, 2018-01, Vol.9, p.28-28

2018

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Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

International journal of molecular sciences, 2023-09, Vol.24 (17), p.13280

2023

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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

International journal of molecular sciences, 2022-09, Vol.23 (18), p.10323

2022

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Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

Frontiers in microbiology, 2019-07, Vol.10 (JULY), p.1571-1571

2019

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Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Systematic and applied microbiology, 2018-07, Vol.41 (4), p.311-323

2018

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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

BMC bioinformatics, 2010-06, Vol.11 (1), p.324-324, Article 324

2010

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Identification of protein secretion systems in bacterial genomes

Scientific reports, 2016-03, Vol.6 (1), p.23080-23080, Article 23080

2016

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Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Proceedings of the National Academy of Sciences - PNAS, 2016-12, Vol.113 (49), p.E7937-E7946

2016

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Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens

PLoS pathogens, 2012-02, Vol.8 (2), p.e1002503-e1002503

2012

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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries

Trends in microbiology (Regular ed.), 2020-05, Vol.28 (5), p.372-386

2020

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Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework

Journal of chemical information and modeling, 2024-07, Vol.64 (13), p.5175-5193

2024

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A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin

Journal of Bacteriology, 2012-09, Vol.194 (18), p.4951-4958

2012

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Investment in rapid growth shapes the evolutionary rates of essential proteins

Proceedings of the National Academy of Sciences - PNAS, 2011-12, Vol.108 (50), p.20030-20035

2011

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Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Nucleic acids research, 2014-05, Vol.42 (9), p.5715-5727

2014

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Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

The ISME Journal, 2020-11, Vol.14 (11), p.2659-2674

2020

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Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution

Molecular biology and evolution, 2023-10, Vol.40 (10)

2023

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Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

The ISME Journal, 2021-09, Vol.15 (9), p.2792-2808

2021

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Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

Methods in molecular biology (Clifton, N.J.), 2017, Vol.1615, p.1

2017

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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems

The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems

Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Lateral gene transfer as a support for the tree of life

Geochemical transition zone powering microbial growth in subsurface sediments

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Identification of protein secretion systems in bacterial genomes

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens

The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries

Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework

A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin

Investment in rapid growth shapes the evolutionary rates of essential proteins

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

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