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Publications of Benjamin Linard

Journal articles23 documents

  • Guillaume Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi. Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers. Bioinformatics, Oxford University Press (OUP), 2020, pp.#btaa1020. ⟨10.1093/bioinformatics/btaa1020⟩. ⟨hal-03094833⟩
  • Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals. PEWO: a collection of workflows to benchmark phylogenetic placement. Bioinformatics, Oxford University Press (OUP), In press, ⟨10.1093/bioinformatics/btaa657⟩. ⟨hal-02905244⟩
  • Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, et al.. OrthoInspector 3.0: open portal for comparative genomics. Nucleic Acids Research, Oxford University Press, 2019, 47 (D1), pp.D411-D418. ⟨10.1093/nar/gky1068⟩. ⟨hal-01984857⟩
  • Benjamin Linard, Krister Swenson, Fabio Pardi. Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics, Oxford University Press (OUP), 2019, 35 (18), pp.3303-3312. ⟨10.1093/bioinformatics/btz068⟩. ⟨lirmm-02410441⟩
  • Carmelo Andujar, Paula Arribas, Michal Motyka, Mathew Bocek, Ladislav Bocak, et al.. New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencing. Mitochondrial DNA Part B Resources, Taylor & Francis Online, 2019, 4 (2), pp.2447-2450. ⟨10.1080/23802359.2019.1637289⟩. ⟨hal-02922399⟩
  • Paula Arribas, Carmelo Andujar, Maria Lourdes Moraza, Benjamin Linard, Brent Emerson, et al.. Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari. Molecular Biology and Evolution, Oxford University Press (OUP), 2019, ⟨10.1093/molbev/msz255⟩. ⟨hal-02385328⟩
  • Benjamin Linard, Alex Crampton-Platt, Jerome Moriniere, Martijn Timmermans, Carmelo Andujar, et al.. The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Molecular Phylogenetics and Evolution, Elsevier, 2018, 128, pp.1-11. ⟨10.1016/j.ympev.2018.07.008⟩. ⟨hal-01984910⟩
  • Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian Altenhoff, et al.. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩. ⟨hal-01758841⟩
  • Carmelo Andujar, Paula Arribas, Benjamin Linard, Robin Kundrata, Ladislav Bocak, et al.. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles. Mitochondrial DNA Part A, Taylor and Francis, 2017, 28 (2), pp.156-158. ⟨10.3109/19401736.2015.1115488⟩. ⟨hal-01636908⟩
  • Benjamin Linard, P. Arribas, C. Andújar, A. Crampton-Platt, A. P. Vogler. Lessons from genome skimming of arthropod-preserving ethanol. Molecular Ecology Resources, Wiley/Blackwell, 2016, 16 (6), pp.1365-1377. ⟨10.1111/1755-0998.12539⟩. ⟨hal-01636888⟩
  • Benjamin Linard, P. Arribas, C. Andújar, A. Crampton-Platt, A. P. Vogler. The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera. Mitochondrial DNA Part A, Taylor and Francis, 2016, 28 (1), pp.71-72. ⟨10.3109/19401736.2015.1110803⟩. ⟨hal-01636904⟩
  • Adrian Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutiérrez, Daniel Dalquen, Todd Deluca, et al.. Standardized benchmarking in the quest for orthologs. Nature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩. ⟨hal-01636892⟩
  • Débora Paula, Benjamin Linard, Alex Crampton-Platt, Amrita Srivathsan, Martijn Timmermans, et al.. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents. PLoS ONE, Public Library of Science, 2016, 11 (9), pp.e0161841. ⟨10.1371/journal.pone.0161841⟩. ⟨hal-01636900⟩
  • Benjamin Linard, Alexis Allot, Raphaël Schneider, Can Morel, Raymond Ripp, et al.. OrthoInspector 2.0: Software and database updates. Bioinformatics, Oxford University Press (OUP), 2015, 31 (3), pp.447-448. ⟨10.1093/bioinformatics/btu642⟩. ⟨hal-01636893⟩
  • Benjamin Linard, Alex Crampton-Platt, Conrad Gillett, Martijn Timmermans, Alfried Vogler. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (6), pp.1474-1489. ⟨10.1093/gbe/evv086⟩. ⟨hal-01636899⟩
  • Débora P. Paula, Benjamin Linard, David Andow, Edison Sujii, Carmen Pires, et al.. Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. Molecular Ecology Resources, Wiley/Blackwell, 2015, 15 (4), pp.880-892. ⟨10.1111/1755-0998.12364⟩. ⟨hal-01636897⟩
  • Florence Bedez, Benjamin Linard, Xavier Brochet, Raymond Ripp, Julie Thompson, et al.. Functional insights into the core-TFIIH from a comparative survey. Genomics, Elsevier, 2013, 101 (3), pp.178-186. ⟨10.1016/j.ygeno.2012.11.003⟩. ⟨hal-01636894⟩
  • Benjamin Linard, Ngoc Hoan Nguyen, Francisco Prosdocimi, Olivier Poch, Julie Thompson. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evolutionary Bioinformatics, Libertas Academica (New Zealand), 2012, 8, pp.61-77. ⟨10.4137/EBO.S8814⟩. ⟨hal-01636866⟩
  • Christophe Dessimoz, Toni Gabaldon, David Roos, Erik Sonnhammer, Javier Herrero, et al.. Toward community standards in the quest for orthologs. Bioinformatics, Oxford University Press (OUP), 2012, 28 (6), pp.900-904. ⟨10.1093/bioinformatics/bts050⟩. ⟨hal-01636872⟩
  • Tien-Dao Luu, Alin Rusu, Vincent Walter, Benjamin Linard, Laetitia Poidevin, et al.. KD4v: comprehensible knowledge discovery system for missense variant. Nucleic Acids Research, Oxford University Press, 2012, 40 (W1), pp.W71-W75. ⟨10.1093/nar/gks474⟩. ⟨hal-01636871⟩
  • Francisco Prosdocimi, Benjamin Linard, Pierre Pontarotti, Olivier Poch, Julie Thompson. Controversies in modern evolutionary biology: the imperative for error detection and quality control.. BMC Genomics, BioMed Central, 2012, 13 (1), pp.5. ⟨10.1186/1471-2164-13-5⟩. ⟨inserm-00682055⟩
  • Benjamin Linard, Julie Thompson, Olivier Poch, Odile Lecompte. OrthoInspector: comprehensive orthology analysis and visual exploration.. BMC Bioinformatics, BioMed Central, 2011, 12 (1), pp.11. ⟨10.1186/1471-2105-12-11⟩. ⟨inserm-00663697⟩
  • Julie Thompson, Benjamin Linard, Odile Lecompte, Olivier Poch. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives. PLoS ONE, Public Library of Science, 2011, 6 (3), pp.18093 - 18093. ⟨10.1371/journal.pone.0018093⟩. ⟨hal-01636867⟩

Conference papers1 document

  • Benjamin Linard, Krister Swenson, Fabio Pardi. Rapid alignment-free phylogenec placement via ancestral k-mers. MCEB: Mathematical and Computational Evolutionary Biology, Jun 2018, St Martin de Londres, France. ⟨lirmm-01964481⟩

Preprints, Working Papers, ...2 documents

  • Benjamin Linard, Krister Swenson, Fabio Pardi. Rapid alignment-free phylogenetic identification of metagenomic sequences. 2019. ⟨lirmm-01964474v2⟩
  • Benjamin Linard, Ngoc Nguyen, Odile Lecompte, Olivier Poch, Julie Thompson. EvoKEN: evolutionary knowledge extraction in networks. 2017. ⟨hal-01636898⟩

Theses1 document

  • Benjamin Linard. Development of evolutionary knowledge extraction methods and their application in biological complex systems. Biochemistry, Molecular Biology. Université de Strasbourg, 2012. English. ⟨NNT : 2012STRAJ044⟩. ⟨tel-00766182⟩