Publications

Machine learning detection of heteroresistance in Escherichia coli

Guliaev, Andrei; Hjort, Karin; Rossi, Michele; Jonsson, Sofia et al.

Part of EBioMedicine, 2025

• DOI for Machine learning detection of heteroresistance in Escherichia coli
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Host–bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts

Bontemps, Zélia; Paranjape, Kiran; Guy, Lionel

Part of FEMS Microbiology Reviews, 2024

• DOI for Host–bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts
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Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota

Odelgard, Anna; Hägglund, Emil; Guy, Lionel; Andersson, Siv G. E.

Part of Genome Biology and Evolution, 2024

• DOI for Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota
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Rapid adaptations of Legionella pneumophila to the human host

Leenheer, Daniël; Moreno, Anaísa B.; Paranjape, Kiran; Murray, Susan et al.

Part of Microbial Genomics, 2023

• DOI for Rapid adaptations of Legionella pneumophila to the human host
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TADA: Taxonomy-Aware Dataset Aggregator

Hägglund, Emil; Andersson, Siv; Guy, Lionel

Part of Bioinformatics, 2023

• DOI for TADA: Taxonomy-Aware Dataset Aggregator
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The evolution of intramitochondriality in Midichloria bacteria

Floriano, Anna Maria; Batisti Biffignandi, Gherard; Castelli, Michele; Olivieri, Emanuela et al.

Part of Environmental Microbiology, p. 2102-2117, 2023

• DOI for The evolution of intramitochondriality in Midichloria bacteria

Early divergence of translation initiation and elongation factors

Fer, Evrim; McGrath, Kaitlyn M.; Guy, Lionel; Hockenberry, Adam J. et al.

Part of Protein Science, 2022

• DOI for Early divergence of translation initiation and elongation factors
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Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis

Hugoson, Eric; Guliaev, Andrei; Ammunét, Tea; Guy, Lionel

Part of Molecular biology and evolution, 2022

• DOI for Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis
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Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact

Martijn, Joran; Vosseberg, Julian; Guy, Lionel; Offre, Pierre et al.

Part of Nature Ecology & Evolution, p. 1829-1831, 2022

• DOI for Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact

Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination in Salmonella

Garmendia, Eva; Brandis, Gerrit; Guy, Lionel; Cao, Sha et al.

Part of mBio, 2021

• DOI for Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination in Salmonella
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Expression of the qepA1 gene is induced under antibiotic exposure

Brandis, Gerrit; Gockel, Jonas; Garoff, Linnéa; Guy, Lionel et al.

Part of Journal of Antimicrobial Chemotherapy, p. 1433-1440, 2021

• DOI for Expression of the qepA1 gene is induced under antibiotic exposure
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Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding

Survery, Sabeen; Hurtig, Fredrik; Haq, Syed Razaul; Eriksson, Jens et al.

Part of Communications Biology, 2021

• DOI for Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding
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Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden

Karlsson, Philip A.; Tano, Eva; Jernberg, Cecilia; Hickman, Rachel A. et al.

Part of Frontiers in Microbiology, 2021

• DOI for Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden
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Chlamydia psittaci in Fulmars on The Faroe Islands: A Causative Link to South American Psittacines Eight Decades After a Severe Epidemic

Wang, Helen; Jensen, Jens-Kjeld; Olsson, Anna; Vorimore, Fabien et al.

Part of Microbes and infection, p. 356-359, 2020

• DOI for Chlamydia psittaci in Fulmars on The Faroe Islands: A Causative Link to South American Psittacines Eight Decades After a Severe Epidemic
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miComplete: weighted quality evaluation of assembled microbial genomes

Hugoson, Eric; Lam, Wai Tin; Guy, Lionel

Part of Bioinformatics, p. 936-937, 2020

• DOI for miComplete: weighted quality evaluation of assembled microbial genomes
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Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

Mahajan, Mayank; Yee, Benjamin; Hägglund, Emil; Guy, Lionel et al.

Part of Molecular biology and evolution, p. 1020-1040, 2020

• DOI for Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

Asgard archaea are the closest prokaryotic relatives of eukaryotes

Spang, Anja; Eme, Laura; Saw, Jimmy H.; Fernández Cáceres, Eva et al.

Part of PLOS Genetics, 2018

• DOI for Asgard archaea are the closest prokaryotic relatives of eukaryotes
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Deep mitochondrial origin outside the sampled alphaproteobacteria

Martijn, Joran; Vosseberg, Julian; Guy, Lionel; Offre, Pierre et al.

Part of Nature, p. 101-105, 2018

• DOI for Deep mitochondrial origin outside the sampled alphaproteobacteria

Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA

Lundin, Erik; Tang, Po-Cheng; Guy, Lionel; Näsvall, Joakim et al.

Part of Molecular biology and evolution, p. 704-718, 2018

• DOI for Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA
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Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle.

Lind, Anders E.; Lewis, William H; Spang, Anja; Guy, Lionel et al.

Part of The ISME Journal, p. 2655-2667, 2018

• DOI for Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle.

Legionella pneumophila recurrently isolated in a Spanish hospital: Two years of antimicrobial resistance surveillance

Graells, Tiscar; Hernández-García, Marta; Pérez-Jové, Josefa; Guy, Lionel et al.

Part of Environmental Research, p. 638-646, 2018

• DOI for Legionella pneumophila recurrently isolated in a Spanish hospital: Two years of antimicrobial resistance surveillance

Origin and evolution of the Bartonella Gene Transfer Agent

Tamarit, Daniel; Neuvonen, Minna M.; Engel, Philipp; Guy, Lionel et al.

Part of Molecular biology and evolution, p. 451-464, 2018

• DOI for Origin and evolution of the Bartonella Gene Transfer Agent
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The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant.

Graells, Tiscar; Ishak, Helena; Larsson, Madeleine; Guy, Lionel

Part of FEMS Microbiology Ecology, 2018

• DOI for The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant.
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phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics

Guy, Lionel

Part of Bioinformatics, p. 1230-1232, 2017

• DOI for phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
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Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

Kacar, Betul; Guy, Lionel; Smith, Eric; Baross, John

Part of Philosophical Transactions. Series A, 2017

• DOI for Resurrecting ancestral genes in bacteria to interpret ancient biosignatures
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Proposal of Coetzeea brasiliensis gen. nov. sp. nov. isolated from larvae of Anopheles darlingi

Kämpfer, Peter; Glaeser, Stefanie P; Marinotti, Osvaldo; Guy, Lionel et al.

Part of International Journal of Systematic and Evolutionary Microbiology, p. 5211-5217, 2016

• DOI for Proposal of Coetzeea brasiliensis gen. nov. sp. nov. isolated from larvae of Anopheles darlingi

The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation

Neuvonen, Minna M.; Tamarit, Daniel; Näslund, Kristina; Liebig, Juergen et al.

Part of Scientific Reports, p. 1-11, 2016

• DOI for The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation
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Complex archaea that bridge the gap between prokaryotes and eukaryotes

Spang, Anja; Saw, Jimmy H.; Jorgensen, Steffen L.; Zaremba-Niedzwiedzka, Katarzyna et al.

Part of Nature, p. 173-179, 2015

• DOI for Complex archaea that bridge the gap between prokaryotes and eukaryotes

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

Saw, Jimmy H.; Spang, Anja; Zaremba-Niedzwiedzka, Katarzyna; Juzokaite, Lina et al.

Part of Philosophical Transactions of the Royal Society of London. Biological Sciences, 2015

• DOI for Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from the larvae of Anopheles arabiensis as members of the family Thorselliaceae fam. nov.

Kämpfer, Peter; Glaeser, Stefanie P.; Nilsson, Louise K. J.; Eberhard, Thomas et al.

Part of International Journal of Systematic and Evolutionary Microbiology, p. 444-451, 2015

• DOI for Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from the larvae of Anopheles arabiensis as members of the family Thorselliaceae fam. nov.

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution

Martijn, Joran; Schulz, Frederik; Zaremba-Niedzwiedzka, Katarzyna; Viklund, Johan et al.

Part of The ISME Journal, p. 2373-2385, 2015

• DOI for Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution

'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum

Guy, Lionel; Spang, Anja; Saw, Jimmy Hser Wah; Ettema, Thijs J. G.

Part of The ISME Journal, p. 1353-1357, 2014

• DOI for 'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum

The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective

Guy, Lionel; Saw, Jimmy Hser Wah; Ettema, Thijs J. G.

Part of Cold Spring Harbor Perspectives in Biology, 2014

• DOI for The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective

A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella

Guy, Lionel; Nystedt, Björn; Toft, Christina; Zaremba-Niedzwiedzka, Katarzyna et al.

Part of PLOS Genetics, 2013

• DOI for A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
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Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population

Guy, Lionel; Jernberg, Cecilia; Norling, Jenny Arven; Ivarsson, Sofie et al.

Part of PLOS ONE, 2013

• DOI for Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population
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Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

Spang, Anja; Martijn, Joran; Saw, Jimmy Hser Wah; Lind, Anders E. et al.

Part of Archaea, p. 202358, 2013

• DOI for Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

Community-wide plasmid gene mobilization and selection

Sentchilo, Vladimir; Mayer, Antonia P.; Guy, Lionel; Miyazaki, Ryo et al.

Part of The ISME Journal, p. 1173-1186, 2013

• DOI for Community-wide plasmid gene mobilization and selection
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A genome-wide study of recombination rate variation in Bartonella henselae

Guy, Lionel; Nystedt, Björn; Sun, Yu; Näslund, Kristina et al.

Part of BMC Evolutionary Biology, p. 65, 2012

• DOI for A genome-wide study of recombination rate variation in Bartonella henselae
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Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4

Guy, Lionel; Jernberg, Cecilia; Ivarsson, Sofie; Hedenstrom, Ingela et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2012

• DOI for Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

Guy, Lionel; Ettema, Thijs J. G.

Part of Trends in Microbiology, p. 580-587, 2011

• DOI for The archaeal ‘TACK’ superphylum and the origin of eukaryotes

genoPlotR: comparative gene and genome visualization in R

Guy, Lionel; Roat Kultima, Jens; Andersson, Siv G.E.

Part of Bioinformatics, p. 2334-2335, 2010

• DOI for genoPlotR: comparative gene and genome visualization in R
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M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island

Panchaud, Alexandre; Guy, Lionel; Collyn, François; Haenni, Marisa et al.

Part of BMC Genomics, 2009

• DOI for M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island
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Genomic insights into two independent events of archaeal endosymbiosis

Lind, Anders E; Lewis, William H; Spang, Anja; Guy, Lionel et al.