Eugene Kulesha
A5015292353- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Machine Learning in Bioinformatics
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Glycosylation and Glycoproteins Research
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Genetic Mapping and Diversity in Plants and Animals
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- RNA regulation and disease
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Plant Disease Resistance and Genetics
- RNA Research and Splicing
- Nutrition, Genetics, and Disease
- Zoonotic diseases and public health
European Bioinformatics Institute
2007-2016
Wellcome Trust
2006-2016
Wellcome Sanger Institute
2006-2016
Oxford Metrics (United Kingdom)
2015
MRC Laboratory of Molecular Biology
2013
Cold Spring Harbor Laboratory
2013
Cornell University
2013
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing diverse individuals from multiple populations. Here we report completion the project, having reconstructed genomes 2,504 26 populations using combination low-coverage sequencing, deep exome and dense microarray genotyping. We characterized broad spectrum variation, in total over 88 million variants (84.7 single nucleotide polymorphisms (SNPs), 3.6...
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms farm animals. Over the past year we have increased number of that support 77 expanded our genome browser a new scrollable overview improved variation phenotype views. We also report updates core datasets improvements gene homology relationships from addition species. Our REST service has been extended additional for...
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets all supported species; large-scale whole multiple species alignments across vertebrates clade-specific eutherian mammals, primates, birds fish; variation data 17 regulation annotations based ENCODE other sets. are accessible through the browser at http://www.ensembl.org tools...
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human data as well key model organisms such mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) Tasmanian devil (Sarcophilus harrisii) bringing total number of supported to 61 release 64 (September 2011). Of these, 55 appear main website six are provided preview site (Pre!Ensembl; http://pre.ensembl.org)...
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases, and other for chordate, selected model organism disease vector genomes. As release 51 (November 2008), fully supports 45 species, three additional species have preliminary support. New in the past year include orangutan six low coverage mammalian Major additions improvements to since our previous report major redesign website; generation multiple...
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation chordate genome sequences. Over the past year number genomes available from has increased 15 to 33, with addition sites for mammalian elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat european hedgehog; fish stickleback medaka second example sea squirt (Ciona savignyi) mosquito (Aedes aegypti). Some major features added during include first...
The Ensembl project ( http://www.ensembl.org ) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations set of includes additional data focused variation, comparative, evolutionary, functional regulatory annotation. most advanced resources are provided for key including human, mouse, rat zebrafish...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set programmatic and interactive interfaces to rich range including reference sequence, gene models, transcriptional data, genetic variation comparative analysis. This paper provides update previous publications about resource,...
Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets homologous genes other relevant datasets in order evaluate answer evolutionary-related questions. However, complexity computational requirements producing such are substantial: this has led only a small number reference resources that used for most analyses. Ensembl one set...
The 1000 Genomes Project was launched as one of the largest distributed data collection and analysis projects ever undertaken in biology. In addition to primary scientific goals creating both a deep catalog human genetic variation extensive methods accurately discover characterize using new sequencing technologies, project makes all its publicly available. Members coordination center have developed deployed several tools enable widespread access.
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases and other for chordate selected model organism disease vector genomes. As release 47 (October 2007), fully supports 35 species, with preliminary support six additional species. New species in the past year include platypus horse. Major additions improvements to since our previous report extensive functional genomics data form specialized database,...
We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists three fully integrated parts, reference 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, visualization tool that has been with the Ensembl genome browser new algorithm analysis immunoprecipitation-based demonstrate utility our by identifying first comprehensive set differentially methylated regions (tDMRs) may play role in...
Abstract The Structural Classification of Proteins (SCOP) database is a classification protein domains organised according to their evolutionary and structural relationships. We report major effort increase the coverage data, aiming provide almost all domain superfamilies with representatives in PDB. have also improved schema, provided new API modernised web interface. This by far most significant update since SCOP 1.75 builds on advances schema from 2 prototype. accessible...
We present a prototype of new structural classification proteins, SCOP2 (http://scop2.mrc-lmb.cam.ac.uk/), that we have developed recently. is successor to the Structural Classification Proteins (SCOP, http://scop.mrc-lmb.cam.ac.uk/scop/) database. Similarly SCOP, main focus organize structurally characterized proteins according their and evolutionary relationships. was designed provide more advanced framework for protein structure annotation classification. It defines approach essentially...
Ensembl(http://www.ensembl.org)integrates genomic information for a comprehensive set of chordate genomes with particular focus on resources human, mouse, rat, zebrafish and other high-value sequenced genomes.We provide complete gene annotations all supported species in addition to specific that target genome variation, function evolution.Ensembl data is accessible variety formats including via our browser, API BioMart.This year marks the tenth anniversary Ensembl time project has grown...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies genome annotation, analysis dissemination, developed in the context of vertebrate-focused project, provides a complementary set resources species through consistent programmatic interactive interfaces. These provide access to including reference sequence, gene models, transcriptional data, polymorphisms comparative...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis dissemination) developed in the context of (vertebrate-focused) provides a complementary set resources species through consistent programmatic interactive interfaces. These provide access to including reference sequence, gene models, transcriptional data, polymorphisms comparative analysis....
Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the genome annotation and visualisation platform. consists five sub-portals (for bacteria, protists, fungi, plants invertebrate metazoa) designed complement availability vertebrate genomes in Ensembl. Many databases supporting have been built close collaboration with community, which we consider as essential for...
Abstract Background The maturing field of genomics is rapidly increasing the number sequenced genomes and producing more information from those previously sequenced. Much this additional variation data derived sampling multiple individuals a given species with goal discovering new variants characterising population frequencies that are already known. These have immense value for many studies, including designed to understand evolution connect genotype phenotype. Maximising utility requires...
Abstract Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, time-to-result can be protracted because of fixed-time runs and cumbersome bioinformatics workflows. This limits utility approach settings where rapid species identification is crucial, such as quality control food-chain components, or during outbreak infectious disease. Here we What’s my Pot? (WIMP), a laboratory analysis...
The field of non-coding RNA biology has been hampered by the lack availability a comprehensive, up-to-date collection accessioned sequences. Here we present first release RNAcentral, database that collates and integrates information from an international consortium established sequence databases. initial contains over 8.1 million sequences, including representatives all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality,...
The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response new challenges facing integrative bioinformatics. Here we describe the various infrastructure components present extended version specification. Version 1.53E incorporates several recent developments, including extension serve types an ontology protein features. Our...