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authFullName_s : Thomas Cokelaer
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JC Polyomavirus whole genome sequencing at the single molecule level reveals emerging neurotropic populations in Progressive Multifocal Leucoencephalopathy

Anne-Sophie L’honneur , Juliana Pipoli da Fonseca , Thomas Cokelaer , Flore Rozenberg
Journal of Infectious Diseases, In press, ⟨10.1093/infdis/jiab639⟩
Journal articles pasteur-03509651v1
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Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models

Dimitri Desvillechabrol , Christiane Bouchier , Sean Kennedy , Thomas Cokelaer
GigaScience, 2018, 7 (12), pp.giy110. ⟨10.1093/gigascience/giy110⟩
Journal articles pasteur-02552049v1

SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

Sarah Temmam , Xavier Montagutelli , Cécile Herate , Flora Donati , Béatrice Regnault , et al.
EMBO Reports, 2023, 24 (4), pp.e56055. ⟨10.15252/embr.202256055⟩
Journal articles pasteur-04072738v1
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Complete Genome Sequences of Bioluminescent Staphylococcus aureus Strains Xen31 and Xen36, Derived from Two Clinical Isolates

Océane Blaise , Clarisse Leseigneur , Thomas Cokelaer , Elena Capuzzo , Nadira Frescaline , et al.
Microbiology Resource Announcements, 2023, 12 (3), pp.e0002423. ⟨10.1128/mra.00024-23⟩
Journal articles pasteur-04120590v1
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Spectrum': Spectral Analysis in Python

Thomas Cokelaer , Juergen Hasch
Journal of Open Source Software, 2017, 2 (18), pp.348. ⟨10.21105/joss.00348⟩
Journal articles pasteur-03111917v1
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Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis

Juliana Pipoli da Fonseca , Etienne Kornobis , Elodie Turc , Vincent Enouf , Laure Lemée , et al.
Scientific Reports, 2022, 12 (1), pp.19274. ⟨10.1038/s41598-022-23422-3⟩
Journal articles pasteur-03884256v1
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Autotransporters drive biofilm formation and auto-aggregation in the diderm Firmicute Veillonella parvula

Nathalie Bechon , Alicia Jiménez-Fernández , Jerzy Witwinowski , Emilie Bierque , Najwa Taïb , et al.
Journal of Bacteriology, 2020, ⟨10.1128/JB.00461-20⟩
Journal articles pasteur-02924221v1
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Sequana': a Set of Snakemake NGS pipelines

Thomas Cokelaer , Dimitri Desvillechabrol , Rachel Legendre , Mélissa Cardon
Journal of Open Source Software, 2017, 2 (16), pp.352. ⟨10.21105/joss.00352⟩
Journal articles pasteur-03111935v1
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Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad

Laurence Armand-Lefèvre , Emilie Rondinaud , Dimitri Desvillechabrol , Jimmy Mullaert , Olivier Clermont , et al.
Microbial Genomics, 2021, 7 (7), pp.000576. ⟨10.1099/mgen.0.000576⟩
Journal articles pasteur-03509051v1
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Broad spectrum compounds targeting early stages of rabies virus (RABV) infection

Sabrina Kali , Corinne Jallet , Saliha Azebi , Thomas Cokelaer , Juliana Pipoli da Fonseca , et al.
Antiviral Research, 2021, 188, pp.105016. ⟨10.1016/j.antiviral.2021.105016⟩
Journal articles pasteur-03281530v1
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High acquisition rate of extended-spectrum β-lactamase-producing Enterobacteriaceae among French military personnel on mission abroad, without evidence of inter-individual transmission

Naouale Maataoui , Aurélie Mayet , Sandrine Duron , Hervé Delacour , France Mentré , et al.
Clinical Microbiology and Infection, 2018, 25 (5), pp.631.e1-631.e9. ⟨10.1016/j.cmi.2018.07.030⟩
Journal articles inserm-02093954v1
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Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

Linda Grillova , Thomas Cokelaer , Jean-François Mariet , Juliana Pipoli da Fonseca , Mathieu Picardeau
BMC Infectious Diseases, 2023, 23 (1), pp.157. ⟨10.1186/s12879-023-08126-x⟩
Journal articles pasteur-04120601v1
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SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination

Estelle Vincendeau , Wenming Wei , Xuefei Zhang , Cyril Planchais , Wei Yu , et al.
Nature Communications, 2022, 13 (1), pp.3707. ⟨10.1038/s41467-022-31287-3⟩
Journal articles pasteur-04120567v1
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BioConvert: a comprehensive format converter for life sciences

Hugo Caro , Sulyvan Dollin , Anne Biton , Bryan Brancotte , Dimitri Desvillechabrol , et al.
Preprints, Working Papers, ... pasteur-04126319v1
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Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis

Cecilia Patitucci , Juan Diego Hernández-Camacho , Elodie Vimont , Thomas Cokelaer , Thibault Chaze , et al.
Preprints, Working Papers, ... pasteur-04093359v1
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Experimental evolution links post-transcriptional regulation to Leishmania fitness gain

Laura Piel , K. Shanmugha Rajan , Giovanni Bussotti , Hugo Varet , Rachel Legendre , et al.
PLoS Pathogens, 2022, 18 (3), pp.e1010375. ⟨10.1371/journal.ppat.1010375⟩
Journal articles pasteur-03615912v1
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Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity

Alexis Proutière , Laurence Du Merle , Marta Garcia-Lopez , Corentin Léger , Alexis Voegele , et al.
Microbiology Spectrum, 2023, 11 (2), pp.e0508522. ⟨10.1128/spectrum.05085-22⟩
Journal articles pasteur-04098925v1
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Investigating the role of the carbon storage regulator A (CsrA) in Leptospira spp.

Theerapat Phoka , Lenka Fule , Juliana Pipoli da Fonseca , Thomas Cokelaer , Mathieu Picardeau , et al.
PLoS ONE, 2021, 16 (12), pp.e0260981. ⟨10.1371/journal.pone.0260981⟩
Journal articles pasteur-03509058v1
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Compatibility of 5-ethynyl-2′F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers

Fabienne Levi-Acobas , Adam Katolik , Pascal Röthlisberger , Thomas Cokelaer , Ivo Sarac , et al.
Organic & Biomolecular Chemistry, 2019, 17 (35), pp.8083-8087. ⟨10.1039/C9OB01515A⟩
Journal articles pasteur-02860714v1
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Attenuation of clinical and immunological outcomes during SARS‐CoV‐2 infection by ivermectin

Guilherme Dias de Melo , Françoise Lazarini , Florence Larrous , Lena Feige , Etienne Kornobis , et al.
EMBO Molecular Medicine, 2021, 13 (8), pp.e14122. ⟨10.15252/emmm.202114122⟩
Journal articles pasteur-03279176v1
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Sequanix: a dynamic graphical interface for Snakemake workflows

Dimitri Desvillechabrol , Rachel Legendre , Claire Rioualen , Christiane Bouchier , Jacques van Helden , et al.
Bioinformatics, 2018, 34 (11), pp.1934 - 1936. ⟨10.1093/bioinformatics/bty034⟩
Journal articles hal-01874933v1
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Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry

Mathieu Claireaux , Rémy Robinot , Jérôme Kervevan , Mandar Patgaonkar , Isabelle Staropoli , et al.
Nature Communications, 2022, 13 (1), pp.521. ⟨10.1038/s41467-022-28130-0⟩
Journal articles pasteur-03654265v1
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Efficient randomization of biological networks while preserving functional characterization of individual nodes

Francesco Iorio , Marti Bernardo-Faura , Andrea Gobbi , Thomas Cokelaer , Giuseppe Jurman , et al.
BMC Bioinformatics, 2016, 17 (1), pp.542. ⟨10.1186/s12859-016-1402-1⟩
Journal articles pasteur-03112917v1
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COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters

Guilherme Dias de Melo , Françoise Lazarini , Sylvain Levallois , Charlotte Hautefort , Vincent Michel , et al.
Science Translational Medicine, 2021, pp.eabf8396. ⟨10.1126/scitranslmed.abf8396⟩
Journal articles pasteur-03242618v1
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GDSCTools for mining pharmacogenomic interactions in cancer

Thomas Cokelaer , Elisabeth Chen , Francesco Iorio , Michael Menden , Howard Lightfoot , et al.
Bioinformatics, 2018, 34 (7), pp.1226-1228. ⟨10.1093/bioinformatics/btx744⟩
Journal articles pasteur-03111932v1