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Computing Phylo-k-mers

Nikolai Romashchenko , Benjamin Linard , Eric Rivals , Fabio Pardi
IEEE/ACM Transactions on Computational Biology and Bioinformatics, In press, ⟨10.1109/TCBB.2023.3278049⟩
Journal articles lirmm-03778953v2
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Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities

Zongxu Li , Benjamin Linard , Alfried P. Vogler , Douglas W. Yu , Zhengyang Wang
Molecular Ecology, In press, ⟨10.1111/mec.16747⟩
Journal articles hal-04102313v1
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Ten years of collaborative progress in the Quest for Orthologs

Benjamin Linard , Ingo Ebersberger , Shawn Mcglynn , Natasha Glover , Tomohiro Mochizuki
Molecular Biology and Evolution, 2021, pp.msab098. ⟨10.1093/molbev/msab098⟩
Journal articles hal-03217851v1
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Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers

Guillaume E. Scholz , Benjamin Linard , Nikolai Romashchenko , Eric Rivals , Fabio Pardi
Bioinformatics, 2020, pp.#btaa1020. ⟨10.1093/bioinformatics/btaa1020⟩
Journal articles hal-03094833v1
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PEWO: a collection of workflows to benchmark phylogenetic placement

Benjamin Linard , Nikolai Romashchenko , Fabio Pardi , Eric Rivals
Bioinformatics, 2020, 36 (21), pp.5264-5266. ⟨10.1093/bioinformatics/btaa657⟩
Journal articles hal-02905244v1
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Rapid alignment-free phylogenetic identification of metagenomic sequences

Benjamin Linard , Krister M. Swenson , Fabio Pardi
Bioinformatics, 2019, 35 (18), pp.3303-3312. ⟨10.1093/bioinformatics/btz068⟩
Journal articles lirmm-02410441v1
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New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencing

Carmelo Andujar , Paula Arribas , Michal Motyka , Mathew Bocek , Ladislav Bocak
Mitochondrial DNA Part B Resources, 2019, 4 (2), pp.2447-2450. ⟨10.1080/23802359.2019.1637289⟩
Journal articles hal-02922399v1
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OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers , Arnaud Kress , Audrey Defosset , Raymond Ripp , Benjamin Linard
Nucleic Acids Research, 2019, 47 (D1), pp.D411-D418. ⟨10.1093/nar/gky1068⟩
Journal articles hal-01984857v1
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Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari

Paula Arribas , Carmelo Andujar , Maria Lourdes Moraza , Benjamin Linard , Brent C. Emerson
Molecular Biology and Evolution, 2019, ⟨10.1093/molbev/msz255⟩
Journal articles hal-02385328v1
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Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund , Cécile Pereira , Salvador Capella-Gutiérrez , Alan Sousa da Silva , Adrian M Altenhoff
Bioinformatics, 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩
Journal articles hal-01758841v1
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The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera

Benjamin Linard , Alex Crampton-Platt , Jerome Moriniere , Martijn J T N Timmermans , Carmelo Andujar
Molecular Phylogenetics and Evolution, 2018, 128, pp.1-11. ⟨10.1016/j.ympev.2018.07.008⟩
Journal articles hal-01984910v1
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The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles

Carmelo Andujar , Paula Arribas , Benjamin Linard , Robin Kundrata , Ladislav Bocak
Mitochondrial DNA Part A, 2017, 28 (2), pp.156-158. ⟨10.3109/19401736.2015.1115488⟩
Journal articles hal-01636908v1
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Lessons from genome skimming of arthropod-preserving ethanol

Benjamin Linard , P. Arribas , C. Andújar , A. Crampton-Platt , A. P. Vogler
Molecular Ecology Resources, 2016, 16 (6), pp.1365-1377. ⟨10.1111/1755-0998.12539⟩
Journal articles hal-01636888v1
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Standardized benchmarking in the quest for orthologs

Adrian M Altenhoff , Brigitte Boeckmann , Salvador Capella-Gutiérrez , Daniel A Dalquen , Todd Deluca
Nature Methods, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Journal articles hal-01636892v1
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Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents

Débora P Paula , Benjamin Linard , Alex Crampton-Platt , Amrita Srivathsan , Martijn J T N Timmermans
PLoS ONE, 2016, 11 (9), pp.e0161841. ⟨10.1371/journal.pone.0161841⟩
Journal articles hal-01636900v1
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The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera

Benjamin Linard , P. Arribas , C. Andújar , A. Crampton-Platt , A. P. Vogler
Mitochondrial DNA Part A, 2016, 28 (1), pp.71-72. ⟨10.3109/19401736.2015.1110803⟩
Journal articles hal-01636904v1
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Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics

Benjamin Linard , Alex Crampton-Platt , Conrad P D T Gillett , Martijn J T N Timmermans , Alfried P Vogler
Genome Biology and Evolution, 2015, 7 (6), pp.1474-1489. ⟨10.1093/gbe/evv086⟩
Journal articles hal-01636899v1
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OrthoInspector 2.0: Software and database updates

Benjamin Linard , Alexis Allot , Raphaël Schneider , Can Morel , Raymond Ripp
Bioinformatics, 2015, 31 (3), pp.447-448. ⟨10.1093/bioinformatics/btu642⟩
Journal articles hal-01636893v1
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Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

Débora P. Paula , Benjamin Linard , David A Andow , Edison R Sujii , Carmen S S Pires
Molecular Ecology Resources, 2015, 15 (4), pp.880-892. ⟨10.1111/1755-0998.12364⟩
Journal articles hal-01636897v1
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Functional insights into the core-TFIIH from a comparative survey

Florence Bedez , Benjamin Linard , Xavier Brochet , Raymond Ripp , Julie D. Thompson
Genomics, 2013, 101 (3), pp.178-186. ⟨10.1016/j.ygeno.2012.11.003⟩
Journal articles hal-01636894v1
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EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

Benjamin Linard , Ngoc Hoan Nguyen , Francisco Prosdocimi , Olivier Poch , Julie D. Thompson
Evolutionary Bioinformatics, 2012, 8, pp.61-77. ⟨10.4137/EBO.S8814⟩
Journal articles hal-01636866v1
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Toward community standards in the quest for orthologs

Christophe Dessimoz , Toni Gabaldon , David Roos , Erik L L Sonnhammer , Javier Herrero
Bioinformatics, 2012, 28 (6), pp.900-904. ⟨10.1093/bioinformatics/bts050⟩
Journal articles hal-01636872v1
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KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu , Alin Rusu , Vincent Walter , Benjamin Linard , Laetitia Poidevin
Nucleic Acids Research, 2012, 40 (W1), pp.W71-W75. ⟨10.1093/nar/gks474⟩
Journal articles hal-01636871v1
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Controversies in modern evolutionary biology: the imperative for error detection and quality control.

Francisco Prosdocimi , Benjamin Linard , Pierre Pontarotti , Olivier Poch , Julie Thompson
BMC Genomics, 2012, 13 (1), pp.5. ⟨10.1186/1471-2164-13-5⟩
Journal articles inserm-00682055v1
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OrthoInspector: comprehensive orthology analysis and visual exploration.

Benjamin Linard , Julie Thompson , Olivier Poch , Odile Lecompte
BMC Bioinformatics, 2011, 12 (1), pp.11. ⟨10.1186/1471-2105-12-11⟩
Journal articles inserm-00663697v1
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A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

Julie D. Thompson , Benjamin Linard , Odile Lecompte , Olivier Poch
PLoS ONE, 2011, 6 (3), pp.18093 - 18093. ⟨10.1371/journal.pone.0018093⟩
Journal articles hal-01636867v1

Rapid alignment-free phylogenec placement via ancestral k-mers

Benjamin Linard , Krister M. Swenson , Fabio Pardi
MCEB: Mathematical and Computational Evolutionary Biology, Jun 2018, St Martin de Londres, France
Conference papers lirmm-01964481v1