Skip to Main content

Co-authors

Number of documents

22

Samuel Blanquart, Inria researcher in bioinformatics and molecular biology


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).


Journal articles15 documents

  • Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, et al.. Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties. Molecular Biology and Evolution, Oxford University Press (OUP), 2021, pp.1-44. ⟨10.1093/molbev/msab146⟩. ⟨hal-03231689⟩
  • Kristina Straub, Mona Linde, Cosimo Kropp, Samuel Blanquart, Patrick Babinger, et al.. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biological Chemistry, De Gruyter, 2019, 400 (3), pp.367-381. ⟨10.1515/hsz-2018-0344⟩. ⟨hal-02284913⟩
  • Samuel Blanquart, Anne-Sophie Borowiec, Philippe Delcourt, Martin Figeac, Christopher A Emerling, et al.. Evolution of the human cold/menthol receptor, TRPM8. Molecular Phylogenetics and Evolution, Elsevier, 2019, 136, pp.104-118. ⟨10.1016/j.ympev.2019.04.011⟩. ⟨hal-02284919⟩
  • Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. Bioinformatics, Oxford University Press (OUP), 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩. ⟨hal-01646297v2⟩
  • Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron, et al.. Assisted transcriptome reconstruction and splicing orthology. BMC Genomics, BioMed Central, 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⟩. ⟨hal-01396410⟩
  • Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics, BioMed Central, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩. ⟨hal-01217311⟩
  • Bernd Reisinger, Josef Sperl, Alexandra Holinski, Veronika Schmid, Chitra Rajendran, et al.. Evidence for the Existence of Elaborate Enzyme Complexes in the Paleoarchean Era. Journal of the American Chemical Society, American Chemical Society, 2014, pp.122-9. ⟨10.1021/ja4115677⟩. ⟨hal-00924047⟩
  • Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy. The molecular signal for the adaptation to cold temperature during early life on Earth. Biology Letters, Royal Society, The, 2013, 9 (5), pp.20130608. ⟨10.1098/rsbl.2013.0608⟩. ⟨hal-00918283⟩
  • Samuel Blanquart, Olivier Gascuel. Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes. BMC Evolutionary Biology, BioMed Central, 2011, 11 (1), pp.70. ⟨10.1186/1471-2148-11-70⟩. ⟨hal-00784426⟩
  • Markus Richter, Manal Bosnali, Linn Carstensen, Tobias Seitz, Helmut Durchschlag, et al.. Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds.. Journal of Molecular Biology, Elsevier, 2010, 398 (5), pp.763-73. ⟨10.1016/j.jmb.2010.03.057⟩. ⟨hal-00755666⟩
  • Tiratha Raj Singh, Georgia Tsagkogeorga, Frédéric Delsuc, Samuel Blanquart, Noa Shenkar, et al.. Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.. BMC Genomics, BioMed Central, 2009, 10, pp.534. ⟨10.1186/1471-2164-10-534⟩. ⟨halsde-00438100⟩
  • Samuel Blanquart, Nicolas Lartillot. A Site- and Time-Heterogeneous Model of Amino Acid Replacement. Molecular Biology and Evolution, Oxford University Press (OUP), 2008, 25 (5), pp.842-858. ⟨10.1093/molbev/msn018⟩. ⟨lirmm-00324422⟩
  • Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy. Parallel Adaptations to High Temperatures in the Archean Eon. Nature, Nature Publishing Group, 2008, 456 (7224), pp.942-945. ⟨10.1038/nature07393⟩. ⟨lirmm-00324159⟩
  • Roxane M. Barthelemy, Anne Chenuil, Samuel Blanquart, Jean-Paul Casanova, Eric Faure. Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression. BMC Evolutionary Biology, BioMed Central, 2007, 7 (1), ⟨10.1186/1471-2148-7-146⟩. ⟨hal-01631361⟩
  • Samuel Blanquart, Nicolas Lartillot. A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution. Molecular Biology and Evolution, Oxford University Press (OUP), 2006, 23 (11), pp.2058-2071. ⟨10.1093/molbev/msl091⟩. ⟨lirmm-00135037⟩

Conference papers2 documents

  • Pierre Pericard, Yoann Dufresne, Samuel Blanquart, Hélène Touzet. Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574629⟩
  • Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. ISCB-Latin America, Oct 2014, Belo Horizonte, Brazil. ⟨hal-01083841⟩

Poster communications3 documents

  • Olivier Dennler, Samuel Blanquart, François Coste, Catherine Belleannée, Nathalie Theret. Phylogenetic Functional Module Characterization of the ADAMTS / ADAMTS like Protein Family. WABI 2021 - Workshop on Algorithms in Bioinformatics, Aug 2021, Chicago (Online), United States. ⟨hal-03543214⟩
  • Olivier Dennler, Samuel Blanquart, François Coste, Catherine Belleannée, Nathalie Theret. Phylogenetic Functional Module Characterization of the ADAMTS / ADAMTS like Protein Family. JOBIM : Journées Ouvertes en Biologie, Informatique & Mathématiques, Jul 2021, Paris, France. ⟨hal-03543182v2⟩
  • Nicolas Guillaudeux, Catherine Belleannée, Samuel Blanquart, Jean-Stéphane Varré. Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 8, pp.1, 2019, ⟨10.7490/f1000research.1117311.1⟩. ⟨hal-02267357⟩

Preprints, Working Papers, ...2 documents

  • Arnaud Belcour, Jeanne Got, Méziane Aite, Ludovic Delage, Jonas Collen, et al.. AuCoMe: inferring and comparing metabolisms across heterogeneous sets of annotated genomes. 2022. ⟨hal-03778267⟩
  • Arnaud Belcour, Baptiste Ruiz, Clémence Frioux, Samuel Blanquart, Anne Siegel. EsMeCaTa: Estimating metabolic capabilities from taxonomic affiliations. 2022. ⟨hal-03697249⟩