benjamin linard

Présentation

Publications

Article dans une revue (28)

Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species Ismael Blanchard,Quynh Trang Bui,Alexis Mergez,Sukanya Denni,Amandine Cornilleet al. Horticulture research, In press, ⟨10.1093/hr/uhag104⟩ Article dans une revue hal-05577186v1
Computing Phylo-k-mers Nikolai Romashchenko,Benjamin Linard,Eric Rivals,Fabio Pardi IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 20 (5), pp.2889-2897. ⟨10.1109/TCBB.2023.3278049⟩ Article dans une revue lirmm-03778953v2
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, 2023, 32 (23), pp.6147-6160. ⟨10.1111/mec.16747⟩ Article dans une revue hal-04102313v1
EPIK: Precise and scalable evolutionary placement with informative k-mers Nikolai Romashchenko,Benjamin Linard,Fabio Pardi,Eric Rivals Bioinformatics, 2023, 39 (12), pp. btad692. ⟨10.1093/bioinformatics/btad692⟩ Article dans une revue lirmm-04308461v1
Ten years of collaborative progress in the Quest for Orthologs Benjamin Linard,Ingo Ebersberger,Shawn Mcglynn,Natasha Glover,Tomohiro Mochizukiet al. Molecular Biology and Evolution, 2021, pp.msab098. ⟨10.1093/molbev/msab098⟩ Article dans une revue hal-03217851v1
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⟩ Article dans une revue hal-03094833v1
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. Emersonet al. Molecular Biology and Evolution, 2020, 37 (3), pp.683-694. ⟨10.1093/molbev/msz255⟩ Article dans une revue hal-02385328v1
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⟩ Article dans une revue hal-02905244v1
OrthoInspector 3.0: open portal for comparative genomics Yannis Nevers,Arnaud Kress,Audrey Defosset,Raymond Ripp,Benjamin Linardet al. Nucleic Acids Research, 2019, 47 (D1), pp.D411-D418. ⟨10.1093/nar/gky1068⟩ Article dans une revue hal-01984857v1
New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencing Carmelo Andujar,Paula Arribas,Michal Motyka,Mathew Bocek,Ladislav Bocaket al. Mitochondrial DNA Part B Resources, 2019, 4 (2), pp.2447-2450. ⟨10.1080/23802359.2019.1637289⟩ Article dans une revue hal-02922399v1
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⟩ Article dans une revue lirmm-02410441v1
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 Andujaret al. Molecular Phylogenetics and Evolution, 2018, 128, pp.1-11. ⟨10.1016/j.ympev.2018.07.008⟩ Article dans une revue hal-01984910v1
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 Altenhoffet al. Bioinformatics, 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩ Article dans une revue hal-01758841v1
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 Bocaket al. Mitochondrial DNA Part A, 2017, 28 (2), pp.156-158. ⟨10.3109/19401736.2015.1115488⟩ Article dans une revue hal-01636908v1
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⟩ Article dans une revue hal-01636904v1
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 Timmermanset al. PLoS ONE, 2016, 11 (9), pp.e0161841. ⟨10.1371/journal.pone.0161841⟩ Article dans une revue hal-01636900v1
Standardized benchmarking in the quest for orthologs Adrian M Altenhoff,Brigitte Boeckmann,Salvador Capella-Gutiérrez,Daniel A Dalquen,Todd Delucaet al. Nature Methods, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩ Article dans une revue hal-01636892v1
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⟩ Article dans une revue hal-01636888v1
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⟩ Article dans une revue hal-01636899v1
OrthoInspector 2.0: Software and database updates Benjamin Linard,Alexis Allot,Raphaël Schneider,Can Morel,Raymond Rippet al. Bioinformatics, 2015, 31 (3), pp.447-448. ⟨10.1093/bioinformatics/btu642⟩ Article dans une revue hal-01636893v1
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 Pireset al. Molecular Ecology Resources, 2015, 15 (4), pp.880-892. ⟨10.1111/1755-0998.12364⟩ Article dans une revue hal-01636897v1
Functional insights into the core-TFIIH from a comparative survey Florence Bedez,Benjamin Linard,Xavier Brochet,Raymond Ripp,Julie D. Thompsonet al. Genomics, 2013, 101 (3), pp.178-186. ⟨10.1016/j.ygeno.2012.11.003⟩ Article dans une revue hal-01636894v1
KD4v: comprehensible knowledge discovery system for missense variant Tien-Dao Luu,Alin Rusu,Vincent Walter,Benjamin Linard,Laetitia Poidevinet al. Nucleic Acids Research, 2012, 40 (W1), pp.W71-W75. ⟨10.1093/nar/gks474⟩ Article dans une revue hal-01636871v1
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⟩ Article dans une revue inserm-00682055v1
Toward community standards in the quest for orthologs Christophe Dessimoz,Toni Gabaldon,David Roos,Erik L L Sonnhammer,Javier Herreroet al. Bioinformatics, 2012, 28 (6), pp.900-904. ⟨10.1093/bioinformatics/bts050⟩ Article dans une revue hal-01636872v1
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⟩ Article dans une revue hal-01636866v1
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⟩ Article dans une revue hal-01636867v1
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⟩ Article dans une revue inserm-00663697v1

Communication dans un congrès (4)

Towards a phylo-k-mer meta-index and classifier for phylogenetic placements in a collection of trees Benjamin Linard,Fabio Pardi SeqBim2025, CNRS; Nantes Université; Laboratoire des Sciences du Numériques de Nantes, Nov 2025, Nantes (France), France Communication dans un congrès hal-05555562v1
Simplified pangenome graph traversals with PSSM scoring : search for motifs differentials Julien Guidihounme,Simon De Givry,Benjamin Linard Methods for Interfacing with Graphs of Genomic Sequences, camille marchet; guillaume gautreau, Sep 2024, Lille, France Communication dans un congrès hal-04803005v1
Towards an edit distance between pangenome graphs Siegfried Dubois,Benjamin Linard,Matthias Zytnicki,Claire Lemaitre,Thomas Faraut SeqBIM 2023 - Journées sur les Séquences en Bioinformatique, Informatique et Mathématiques, Nov 2023, Lille, France. pp.1-2 Communication dans un congrès hal-04320771v1
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 Communication dans un congrès lirmm-01964481v1

Poster de conférence (4)

MSpangepop: Simulating complex structural variants under advanced demographic scenarios using the coalescent Lucien Piat,Sukanya Denni,Siegfried Dubois,Florent Couturier,Nicolas Lapaluet al. JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-1, 2025 Poster de conférence hal-05219528v1
Benchmarking pangenome graph mapping with strobemer-based seeding Marouane Boumlik,Benjamin Linard,Matthias Zytnicki JOBIM 2024JOBIM 2024, Jun 2024, JOBIM 2024, France Poster de conférence hal-04656363v1
Simplified pangenome graph traversals with PSSM scoring : search for motifs differentials Julien Guidihounme,Simon De Givry,Benjamin Linard JOBIM 2024, Jun 2024, Toulouse, France Poster de conférence hal-04656256v1
Benchmarking read mapping on pangenomic variation graphs Hajar Bouhamout,Benjamin Linard,Matthias Zytnicki jobim 2023, Jun 2023, Nice, France Poster de conférence hal-04150552v1

Pré-publication, Document de travail (5)

A roadmap for the adoption of pangenomics in agronomy Stéphanie Bocs,Camille Carrette,Johann Confais,Siegfried Dubois,Ludovic Duvauxet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05357866v2
Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species Ismael Blanchard,Quynh Trang Bui,Alexis Mergez,Sukanya Denni,Amandine Cornilleet al. 2026 Pré-publication, Document de travail hal-05450185v1
Bioinfomics days : introduction to variation graphs Benjamin Linard 2024 Pré-publication, Document de travail hal-04828607v1
Rapid alignment-free phylogenetic identification of metagenomic sequences Benjamin Linard,Krister M. Swenson,Fabio Pardi 2019 Pré-publication, Document de travail lirmm-01964474v2
EvoKEN: evolutionary knowledge extraction in networks Benjamin Linard,Ngoc Thanh Nguyen,Odile Lecompte,Olivier Poch,Julie D. Thompson 2017 Pré-publication, Document de travail hal-01636898v1

Thèse (1)

Development of evolutionary knowledge extraction methods and their application in biological complex systems Benjamin Linard Biochemistry, Molecular Biology. Université de Strasbourg, 2012. English. ⟨NNT : 2012STRAJ044⟩ Thèse tel-00766182v1

Logiciel (1)

RAPPAS Benjamin Linard 2023, ⟨swh:1:dir:1902e071bfa74c8998065dac7edda0098f23b3ea;origin=https://hal.archives-ouvertes.fr/lirmm-04171414;visit=swh:1:snp:4a3bdb3e600d9228330f167436da52334324d603;anchor=swh:1:rel:3337ba01c204f1c91956cc701b4267e655e1d959;path=/⟩ Logiciel lirmm-04171414v1