Evgenia V. Kriventseva
A5038335924- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Insect symbiosis and bacterial influences
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Protein Structure and Dynamics
- Insect Resistance and Genetics
- Insect-Plant Interactions and Control
- Insect and Arachnid Ecology and Behavior
- RNA Research and Splicing
- Evolution and Genetic Dynamics
- Cancer-related molecular mechanisms research
- Microbial Natural Products and Biosynthesis
- Infections and bacterial resistance
- Clostridium difficile and Clostridium perfringens research
- CRISPR and Genetic Engineering
- Invertebrate Immune Response Mechanisms
- Advanced Proteomics Techniques and Applications
- Microbial Community Ecology and Physiology
- MicroRNA in disease regulation
- Mosquito-borne diseases and control
- RNA modifications and cancer
University of Geneva
2011-2024
SIB Swiss Institute of Bioinformatics
2012-2024
Imperial College London
2008
University Hospital of Geneva
2008
European Bioinformatics Institute
2000-2007
Wellcome Trust
2001-2007
Johns Hopkins University
2007
University of California, Riverside
2007
Broad Institute
2007
Virginia Tech
2007
Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.We propose a measure for quantitative genome assembly annotation completeness based on evolutionarily informed expectations gene content. We implemented procedure in open-source software, with sets Benchmarking Universal Single-Copy Orthologs, named BUSCO.Software Python datasets available download from...
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies expanding data volumes make evaluation completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying genomic sets in terms the expected gene content Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements complete refactoring code to it more flexible extendable facilitate high-throughput...
To understand the biology and evolution of ruminants, cattle genome was sequenced to about sevenfold coverage. The contains a minimum 22,000 genes, with core set 14,345 orthologs shared among seven mammalian species which 1217 are absent or undetected in noneutherian (marsupial monotreme) genomes. Cattle-specific evolutionary breakpoint regions chromosomes have higher density segmental duplications, enrichment repetitive elements, species-specific variations genes associated lactation immune...
We describe the draft genome of microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count a consequence an elevated rate duplication resulting in tandem clusters. More than third Daphnia's genes have no detectable homologs any other available proteome, most amplified families are specific to lineage. coexpansion interacting within metabolic pathways suggests that maintenance duplicated not random, analysis expression under different...
We present a draft sequence of the genome Aedes aegypti, primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times size malaria Anopheles gambiae. Nearly 50% Ae. aegypti consists transposable elements. These contribute to factor 4 6 increase in average gene length sizes intergenic regions relative An. gambiae Drosophila melanogaster. Nonetheless, chromosomal synteny generally maintained among all three insects, although conservation...
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up the resource coverage, sampling genomic diversity 1271 eukaryotes, 6013 prokaryotes 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, 404 archaeal genomes, picking best sequenced annotated representatives for each species or operational taxonomic unit. relies on concept hierarchy...
Parasitoid Wasp Genomes wasps, which prey on and reproduce in host insect species, play important roles plant herbivore interactions, may provide valuable tools the biological control of pest species. The Nasonia Genome Working Group (p. 343 ; see news story by Pennisi ) presents genome three very closely related species: vitripennis, N. giraulti , longicornis . findings document rapid evolution between a endosymbiont that can cause nuclear-cytoplasmic incompatibilities affect speciation.
Mosquitoes are vectors of parasitic and viral diseases immense importance for public health. The acquisition the genome sequence yellow fever Dengue vector, Aedes aegypti (Aa), has enabled a comparative phylogenomic analysis insect immune repertoire: in Aa, malaria vector Anopheles gambiae (Ag), fruit fly Drosophila melanogaster (Dm). Analysis signaling pathways response modules reveals both conservative rapidly evolving features associated with different functional gene categories...
As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences its primary bacterial endosymbiont Candidatus Riesia pediculicola. The has smallest known insect genome, spanning 108 Mb. Despite status as obligate parasite, it retains a remarkably complete basal repertoire 10,773 protein-coding genes 57 microRNAs. Representing hemimetabolous...
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from single gene in their last common ancestor. In 2016 reached its 9th release, growing to over 22 million 5000 species, now adding plants, archaea and viruses. this update we focused on usability fast-growing wealth data: updating the user programmatic interfaces browse query data, further enhancing already extensive integration available functional annotations. Collating annotations 100 resources, enabled...
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, thus forms the cornerstone comparative genomics, phylogenomics metagenomics. We present update OrthoDB—the hierarchical catalog orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation at varying resolution by explicitly referring to hierarchy species radiations, now also adopted other resources. current release comprehensive coverage animals fungi representing...
Orthology, refining the concept of homology, is cornerstone evolutionary comparative studies. With ever-increasing availability genomic data, inference orthology has become instrumental for generating hypotheses about gene functions crucial to many This update OrthoDB hierarchical catalog orthologs (http://www.orthodb.org) covers 3027 complete genomes, including most comprehensive set 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling representative genomes from over 11,000...
Abstract OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling eukaryotes, prokaryotes, viruses. Genomics continues to accelerate our exploration gene diversity orthology is the most precise way bridging knowledge with rapidly expanding universe genomic sequences. samples organisms best quality genomics data provide leading coverage species diversity. This update underlying over 18 000 prokaryotes almost 2000 eukaryotes 100 million propels another level....
We report the whole-genome sequence of common marmoset (Callithrix jacchus). The 2.26-Gb genome a female was assembled using Sanger read data (6×) and shotgun strategy. A first analysis has permitted comparison with genomes apes Old World monkeys identification specific features that might contribute to unique biology this diminutive primate, including genetic changes may influence body size, frequent twinning chimerism. observed positive selection in growth hormone/insulin-like factor genes...
Genomes of eusocial insects code for dramatic examples phenotypic plasticity and social organization. We compared the genomes seven ants, honeybee, various solitary to examine whether lineages share distinct features genomic Each ant lineage contains ∼4000 novel genes, but only 64 these genes are conserved among all ants. Many gene families have been expanded in notably those involved chemical communication (e.g., desaturases odorant receptors). Alignment revealed reduced purifying selection...
ABSTRACT Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies expanding data volumes make evaluation completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying in terms the expected gene content Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org ). Now its third release, BUSCO utilities extend beyond control to applications comparative genomics, predictor training,...
Abstract OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number available organisms. is leading in the coverage genomic diversity sampling Eukaryotes, Prokaryotes Viruses, Bacteria further set to increase three-fold. The user interface has been enhanced response massive growth data. three views on data: (i) list orthologous groups related query, which are now arranged visualize their hierarchical relations, (ii) detailed view an group, featuring...
The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes.Using publicly available proteome mammary expressed tags, 197 protein genes over 6,000 were identified in genome. Intersection these 238 production quantitative trait loci curated from literature decreased search space for effectors by more than an order magnitude. Genome location analysis revealed a tendency to be clustered genes. Using genomes monotreme...
The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present web accessible OrthoDB database that catalogs groups orthologous in a hierarchical manner, at each radiation phylogeny, from more general fine-grained delineations between closely related species. We COG-like Inparanoid-like ortholog delineation procedure on all-against-all Smith-Waterman sequence comparisons...
The concept of homology drives speculation on a gene's function in any given species when its biological roles other are characterized. With reference to specific radiation homologous relations define orthologs, i.e. descendants from single gene the ancestor. large-scale delineation genealogies is challenging task, and numerous approaches problem reflect importance orthology as cornerstone for comparative studies. Here, we present updated OrthoDB catalog eukaryotic orthologs delineated at...
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification proteins into groups related proteins. clustering is based on analysis all pairwise comparisons between protein sequences. Analysis has been carried out for different levels similarity, yielding a hierarchical organisation clusters. provides links to InterPro, which integrates information families, domains functional sites from PROSITE, PRINTS, Pfam ProDom. Links the InterPro graphical...
A collection of transmembrane proteins with annotated regions, for which good experimental evidence exist, was created as a test or training set algorithms to predict regions in proteins.
Delineating ancestral gene relations among a large set of sequenced eukaryotic genomes allowed us to rigorously examine links between evolutionary and functional traits. We classified 86% over 1.36 million protein-coding genes from 40 vertebrates, 23 arthropods, 32 fungi into orthologous groups linked 90% them Gene Ontology or InterPro annotations. Quantifying properties ortholog phyletic retention, copy-number variation, sequence conservation, we examined correlations with essentiality More...
MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation metazoan genes. The mature ∼22-nt long RNA molecules processed from genome-encoded stem-loop structured precursor Hundreds such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers estimated. miROrtho database (http://cegg.unige.ch/mirortho) presents results a comprehensive...