Benjamin Linard

Benjamin Linard
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE

PhD bioinformatics

About

40
Publications
20,948
Reads
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1,086
Citations
Citations since 2017
19 Research Items
796 Citations
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2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
Introduction
Environemental bioinformatics, biodiversity, environmental DNA, metabarcoding / metagenomics, phylogeny
Additional affiliations
October 2019 - present
SPYGEN
SPYGEN
Position
  • Researcher
Description
  • Research officer in Spygen. Hosted by the LIRMM and the University of Montpellier. Worldwide Biodiversity Observatory Project. Algorithm & software development, setup of the bioinformatic platform, transfers to production, devops.
January 2018 - September 2019
Institut des Sciences de l'Evolution de Montpellier
Position
  • PostDoc Position
March 2016 - December 2017
Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM)
Position
  • PostDoc Position

Publications

Publications (40)
Article
Full-text available
The accurate determination of orthology and inparalogy relationships is essential for comparative sequence analysis, functional gene annotation and evolutionary studies. Various methods have been developed based on either simple blast all-versus-all pairwise comparisons and/or time-consuming phylogenetic tree analyses. We have developed OrthoInspec...
Article
Full-text available
Field-collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA...
Article
Full-text available
Motivation Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever pre...
Article
Full-text available
Motivation: Phylogenetic placement (PP) is a process of taxonomic identification for which several tools are now available. However, it remains difficult to assess which tool is more adapted to particular genomic data or a particular reference taxonomy. We developed PEWO, the first benchmarking tool dedicated to PP assessment. Its automated workfl...
Article
Full-text available
To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of...
Preprint
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and assuming a phylogenetic model of sequence evolution, we can compute a probability score for any given k-mer at any gi...
Article
Full-text available
The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis)...
Article
Full-text available
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology - evolutionary relatedness - is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplicati...
Article
Full-text available
Motivation Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically-distinct viral types. Here, we consider the task of screening large collections o...
Preprint
Full-text available
Motivation: Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically-distinct viral types. Here, we consider the task of screening large collections...
Article
Full-text available
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites...
Article
Full-text available
High-throughput DNA methods hold great promise for the study of the hyperdiverse arthropod fauna of the soil. We used the mitochondrial metagenomic approach to generate 39 mitochondrial genomes from adult and larval specimens of Coleoptera collected from soil samples. The mitogenomes correspond to species from the families Carabidae (6), Chrysomeli...
Article
Full-text available
OrthoInspector is one of the leading software suites for orthology relations inference. In this paper, we describe a major redesign of the OrthoInspector online resource along with a significant increase in the number of species: 4753 organisms are now covered across the three domains of life, making OrthoInspector the most exhaustive orthology res...
Preprint
Full-text available
A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen sam...
Preprint
Full-text available
Motivation Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever pre...
Article
Full-text available
We introduce a multi-factorial, multi-level approach to build and explore evolutionary scenarios of complex protein networks. EvoKEN combines a unique formalism for integrating multiple types of data associated with network molecular components and knowledge extraction techniques for detecting cohesive/anomalous evolutionary processes. We analyzed...
Article
Full-text available
Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challeng...
Article
Full-text available
The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochon...
Article
Full-text available
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess t...
Article
Full-text available
We describe the mitochondrial genome of Hydropsyche pellucidula Curtis 1834, which is first described for the suborder Annulipalpia and the first in the order Trichoptera to show a non-canonical gene order. The mitogenome was obtained by de novo assembly of shotgun sequenced total genomic DNA using Illumina Miseq technology, which produced an avera...
Article
Full-text available
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low coverage sequencing by "genome skimming", which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of ~200 speci...
Article
Full-text available
DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct s...
Article
Full-text available
We previously developed OrthoInspector, a package incorporating an original algorithm for the detection of orthology and inparalogy relations between different species. We have added new functionalities to the package. While its original algorithm was not modified, performing similar orthology predictions, we facilitated the prediction of very larg...
Article
Full-text available
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk Activating Kinase) and the core-TFIIH. The core-TFIIH, composed of seven subunits (XPB, XPD, P62, P52, P44, P34, P8), plays a crucial role in transcription and repair. Here, we performed an extended sequence analysis to establish the accurate phylogenetic distribution of the c...
Article
Full-text available
Systems biology has developed enormously over the 10 last years, with studies covering diverse biological levels (molecule, network, tissue, organism, ecology...). From an evolutionary point of view, systems biology provides unequalled opportunities. This thesis describes new methodologies and tools to study the evolution of biological systems, tak...
Thesis
Full-text available
Systems biology, an opportunity for evolutionary biologyEvolution is a principle inherent to life and a fundamental aspect of biology. Life is not fixed or stable,instead all species are slowly transformed over time. These transformations can be observed at themolecular level, with the selection of genetic mutations, the conservation/modification o...
Article
Full-text available
A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides...
Article
Full-text available
The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is h...
Article
Full-text available
The data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biology, for example, has led to many interesting, but often controversial studies. It has been suggested that part of the conflict may be due to...
Article
Full-text available
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutiona...
Conference Paper
Full-text available
High throughput genomics technologies are providing huge amounts of raw genomic sequence data. As a consequence, it is now feasible to compare sequences from hundreds of diverse organisms, to perform detailed studies of the evolutionary patterns and forces that shaped extant proteins and to understand the effect of the genetic changes that are resp...
Article
Full-text available
Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used...
Data
Full-text available
Figure S2. Aligment of the VHS domains of GGA and TOM proteins. (A) The sequences of the VHS domain of Metazoa, Fungi, Plantae and Prostists GGA were aligned and the secondary structure of human GGA1 is shown above the sequence alignment (PDB ID code 1JWF). (B) The sequences of the VHS domain of Metazoa TOM were aligned and the secondary structure...
Article
Although the number of antiepileptic drugs (AEDs) is increasing, none displays neuroprotective or antiepileptogenic properties that could prevent status epilepticus (SE)-induced drug-resistant epilepsy. Ketogenic diet (KD) and calorie restriction (CR) are proposed as alternative treatments in epilepsy. Our goal was to assess the neuroprotective or...

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Projects

Projects (3)
Project
Bioinformatic and methodological developments to tackle the latest challenges in environmental genomics, with a focus on non-model clades and biodiversity studies.
Project
VIROGENESIS is a research project under the EC H2020 framework (2015-2018), that will develop bioinformatics software applications to fully exploit the potential of high-throughput Next-Generation-Sequencing (NGS) technologies in the field of virology. With the advent of NGS analysis pipelines becoming part of the routine repertoire of research, clinical and public health laboratories in the public sector and private industry, this project will improve viral pathogen discovery and detection, clinical diagnostics as well as disease control and prevention. The consortium consists of computational biologists, statisticians, epidemiological modellers, clinical and molecular virologists, from Belgium, The Netherlands, France, the United Kingdom, the Republic of South Africa and the United States of America.