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Mathieu Seppey
Swiss Institute of Bioinformatics
GenomeGenomicsGeneticsBenchmarkingBiology
12Publications
6H-index
899Citations
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Publications 12
Newest
#1Frederic B. Bastian (Swiss Institute of Bioinformatics)H-Index: 9
#2Julien Roux (University of Basel)H-Index: 15
Last. Marta Rosikiewicz (Swiss Institute of Bioinformatics)H-Index: 5
view all 23 authors...
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as "healthy" or not). Data are integrated and made...
Source
#1Mathieu Seppey (Swiss Institute of Bioinformatics)H-Index: 6
#2Panagiotis Ioannidis (FORTH: Foundation for Research & Technology – Hellas)H-Index: 21
Last. Nadir Alvarez (UNIL: University of Lausanne)H-Index: 29
view all 13 authors...
The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene ...
2 CitationsSource
#1Mathieu Seppey (University of Geneva)H-Index: 6
#2Mosè Manni (University of Geneva)H-Index: 14
Last. Evgeny M. Zdobnov (University of Geneva)H-Index: 58
view all 3 authors...
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy gen...
6 CitationsSource
#1Robert M. Waterhouse (Swiss Institute of Bioinformatics)H-Index: 38
#2Mathieu Seppey (Swiss Institute of Bioinformatics)H-Index: 6
Last. Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
view all 4 authors...
The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of cr...
Source
#1Mathieu Seppey (Swiss Institute of Bioinformatics)H-Index: 6
#2Mosè Manni (Swiss Institute of Bioinformatics)H-Index: 14
Last. Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
view all 3 authors...
Metagenomics promotes our understanding of microbial communities. The methodology profoundly relies on computational interpretation of the sequencing reads in the light of our evolving understanding of microbial taxonomy. The fast growing volumes of such readouts and the reference databases prompted development of a multitude of computational procedures over recent years. Only a subset of these has appeared in independent benchmarking assessments, which are also quickly becoming obsolete. This i...
5 CitationsSource
#1Mathieu Seppey (UNIL: University of Lausanne)H-Index: 6
#2Panagiotis Ioannidis (Swiss Institute of Bioinformatics)H-Index: 21
Last. Nadir Alvarez (AMNH: American Museum of Natural History)H-Index: 29
view all 13 authors...
The diversity and evolutionary success of beetles (Coleoptera) are proposed to have arisen from millions of years of specialized trophic interactions with land plants. In particular, ingestion of toxic plant allelochemicals may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by these interactions remains largely anecdotal and without explicit hypothesis testing. To address this, w...
Source
#1Robert M. Waterhouse (Swiss Institute of Bioinformatics)H-Index: 38
#2Mathieu Seppey (Swiss Institute of Bioinformatics)H-Index: 6
Last. Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
view all 8 authors...
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more fle...
345 CitationsSource
#1Robert M. Waterhouse (UNIL: University of Lausanne)H-Index: 38
#2Mathieu Seppey (Swiss Institute of Bioinformatics)H-Index: 6
Last. Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
view all 8 authors...
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). Now in its third release, BUSCO utilities extend beyond quality control to applications in comparative genomics, ...
21 CitationsSource
#1Panagiotis Ioannidis (Swiss Institute of Bioinformatics)H-Index: 21
#2Felipe A. Simão (Swiss Institute of Bioinformatics)H-Index: 9
Last. Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
view all 9 authors...
Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the ge...
28 CitationsSource
#1Evgeny M. Zdobnov (Swiss Institute of Bioinformatics)H-Index: 58
#2Fredrik Tegenfeldt (Swiss Institute of Bioinformatics)H-Index: 6
Last. Evgenia V. Kriventseva (Swiss Institute of Bioinformatics)H-Index: 31
view all 9 authors...
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene fun...
169 CitationsSource
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