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Samuel Blanquart

27
Documents

Presentation

Main research topics - **Phylogenetics**. Phylogenetic modelling (PhD thesis 2007), phylogenetic inferences and ancestral sequence reconstruction (*e.g.* see Blanquart *et al.* 2021). Phylogenetic and functional nalysis of a complex multi-paralog and multidomaine gene familly, the ADAM TS/TSL (PhD student: Olivier Dennler). - **Metagenomics**. Reconstruction of phylogenetic markers from metagenomic data (PhD student, Pierre Pericard). - **Transcriptomics**. Modelling of the gene orthologous splicing structures and prediction of orthologous isoforms (PhD student: Nicolas Guillaudeux. Postdoctoral fellow: Antoine Aymeric-Lorquin, 2018). Evolution of the TRPM8 isoforms in Amniota (Blanquart et al 2019). - **System biology.** Estimating ecosystem metabolisms from sequenced 16S RNA environmental samples (PhD student Arnaud Belcour). PhD Students - **Pierre Pericard**. PhD defense December 2017. BONSAI team, Inria / Lille University. - **Nicolas Guillaudeux**. 2018-2021. PhD defense December 2021. DYLISS team, Inria Rennes University. - **Arnaud Belcour**. Since 2019. DYLISS team, Inria / Rennes University. - **Olivier Dennler**. Since 2019. DYLISS team, Inria / Rennes University. Positions - **Since 2018**. Junior researcher at Inria Rennes - Bretagne Atlantique, DYLISS team (Rennes, France). - **2010 to 2018**. Junior researcher at Inria Lille - Nord Europe, BONSAI team (Lille France). - **2010**. Posdoctoral fellow at ISEM, Molecular evolution team (Montpellier, France). - **2009**. Postdoctoral fellow at EBI, Goldman group (Cambridge, UK). - **2007 to 2009**. Postdoctoral fellow at LIRMM, MAB team (Montepellier, France). - **2004 to 2007**. PhD student at LIRMM, MAB team (Montpellier, France).

Publications

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Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén
Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩
Journal articles hal-04192851v3
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Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

Nicolas Guillaudeux , Catherine Belleannée , Samuel Blanquart
BMC Genomics, 2022, 23 (1), pp.1-14. ⟨10.1186/s12864-022-08429-4⟩
Journal articles hal-03616626v1
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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Samuel Blanquart , Mathieu Groussin , Aline Le Roy , Gergely J Szöllosi , Eric Girard
Molecular Biology and Evolution, 2021, 38 (9), pp.3754-3774. ⟨10.1093/molbev/msab146⟩
Journal articles hal-03231689v1
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Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

Kristina Straub , Mona Linde , Cosimo Kropp , Samuel Blanquart , Patrick Babinger
Biological Chemistry, 2019, 400 (3), pp.367-381. ⟨10.1515/hsz-2018-0344⟩
Journal articles hal-02284913v1
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Evolution of the human cold/menthol receptor, TRPM8

Samuel Blanquart , Anne-Sophie Borowiec , Philippe Delcourt , Martin Figeac , Christopher A Emerling
Molecular Phylogenetics and Evolution, 2019, 136, pp.104-118. ⟨10.1016/j.ympev.2019.04.011⟩
Journal articles hal-02284919v1
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MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

Pierre Pericard , Yoann Dufresne , Loïc Couderc , Samuel Blanquart , Hélène Touzet
Bioinformatics, 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩
Journal articles hal-01646297v2
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Assisted transcriptome reconstruction and splicing orthology

Samuel Blanquart , Jean-Stéphane Varré , Paul Guertin , Amandine Perrin , Anne Bergeron
BMC Genomics, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. ⟨10.1186/s12864-016-3103-6⟩
Journal articles hal-01396410v1
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders

Amandine Perrin , Jean-Stéphane Varré , Samuel Blanquart , Aïda Ouangraoua
BMC Genomics, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩
Journal articles hal-01217311v1
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Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era

Bernd Reisinger , Josef Sperl , Alexandra Holinski , Veronika Schmid , Chitra Rajendran
Journal of the American Chemical Society, 2014, pp.122-9. ⟨10.1021/ja4115677⟩
Journal articles hal-00924047v1
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The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin , Bastien Boussau , Sandrine Charles , Samuel Blanquart , Manolo Gouy
Biology Letters, 2013, 9 (5), pp.20130608. ⟨10.1098/rsbl.2013.0608⟩
Journal articles hal-00918283v1
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Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes

Samuel Blanquart , Olivier Gascuel
BMC Evolutionary Biology, 2011, 11 (1), pp.70. ⟨10.1186/1471-2148-11-70⟩
Journal articles hal-00784426v1

Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds.

Markus Richter , Manal Bosnali , Linn Carstensen , Tobias Seitz , Helmut Durchschlag
Journal of Molecular Biology, 2010, 398 (5), pp.763-73. ⟨10.1016/j.jmb.2010.03.057⟩
Journal articles hal-00755666v1
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Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.

Tiratha Raj Singh , Georgia Tsagkogeorga , Frédéric Delsuc , Samuel Blanquart , Noa Shenkar
BMC Genomics, 2009, 10, pp.534. ⟨10.1186/1471-2164-10-534⟩
Journal articles halsde-00438100v1
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A Site- and Time-Heterogeneous Model of Amino Acid Replacement

Samuel Blanquart , Nicolas Lartillot
Molecular Biology and Evolution, 2008, 25 (5), pp.842-858. ⟨10.1093/molbev/msn018⟩
Journal articles lirmm-00324422v1
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Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau , Samuel Blanquart , Anamaria Necsulea , Nicolas Lartillot , Manolo Gouy
Nature, 2008, 456 (7224), pp.942-945. ⟨10.1038/nature07393⟩
Journal articles lirmm-00324159v1
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Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Roxane M. Barthelemy , Anne Chenuil , Samuel Blanquart , Jean-Paul Casanova , Eric Faure
BMC Evolutionary Biology, 2007, 7 (1), ⟨10.1186/1471-2148-7-146⟩
Journal articles hal-01631361v1
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A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution

Samuel Blanquart , Nicolas Lartillot
Molecular Biology and Evolution, 2006, 23 (11), pp.2058-2071. ⟨10.1093/molbev/msl091⟩
Journal articles lirmm-00135037v1
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Functional Motif Prediction in ADAMTS-TSL proteins Based on Module(s) and Phenotype(s) Co-appearance

Olivier Dennler , Samuel Blanquart , François Coste , Catherine Belleannée , Nathalie Théret
ALPHY/AIEM 2022 - Rencontres Génomique évolutive, Bioinformatique, Alignement et Phylogénie, Mar 2022, Rennes, France
Conference poster hal-03870590v1

Machine Learning classification performance on mechanistic representations of the gut microbiota built from abundance profiles

Baptiste Ruiz , Arnaud Belcour , Samuel Blanquart , Isabelle Luron Le Huërou-Luron , Sylvie Buffet-Bataillon
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2022, Rennes, France. , pp.181, 2022, Proceedings
Conference poster hal-04155624v1
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Phylogenetic Functional Module Characterization of the ADAMTS / ADAMTS like Protein Family

Olivier Dennler , Samuel Blanquart , François Coste , Catherine Belleannée , Nathalie Theret
WABI 2021 - Workshop on Algorithms in Bioinformatics, Aug 2021, Chicago (Online), United States
Conference poster hal-03543214v1
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Phylogenetic Functional Module Characterization of the ADAMTS / ADAMTS like Protein Family

Olivier Dennler , Samuel Blanquart , François Coste , Catherine Belleannée , Nathalie Theret
JOBIM : Journées Ouvertes en Biologie, Informatique & Mathématiques, Jul 2021, Paris, France
Conference poster hal-03543182v2
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Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?

Nicolas Guillaudeux , Catherine Belleannée , Samuel Blanquart , Jean-Stéphane Varré
JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 8, pp.1, 2019, ⟨10.7490/f1000research.1117311.1⟩
Conference poster hal-02267357v1

Phylogénie moléculaire

Samuel Blanquart , Alexis Criscuolo , Christophe J Douady , Emmanuel Douzery , Nicolas Lartillot
Thierry Lefèvre; Michel Raymond; Frédéric Thomas. Biologie évolutive, De Boeck, 2010, 9782804101619
Book sections hal-04001134v1