Emily Perry
A5083196883- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Genetic Associations and Epidemiology
- Machine Learning in Bioinformatics
- Plant Virus Research Studies
- BRCA gene mutations in cancer
- Ethics in Clinical Research
- Genetics, Bioinformatics, and Biomedical Research
- Cancer-related gene regulation
- Plant Pathogens and Resistance
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Identification and Quantification in Food
- Animal Genetics and Reproduction
- Plant Disease Resistance and Genetics
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
European Bioinformatics Institute
2014-2022
Jackson Laboratory
2021
Wellcome Trust
2014-2017
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of draft human genome, with aim accelerating genomics research through rapid open distribution public data. Large amounts raw data are thus transformed into knowledge, which is made available via a multitude channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded multiple directions. First, resources describe fields genomics, gene...
Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed efficiently deliver annotation at scale all eukaryotic life, it also provides deep comprehensive key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the new assemblies. Here, report release greatest annual number newly annotated genomes history...
Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed comprehensive annotation of gene structures, regulatory elements variants, enable comparative genomics by inferring the evolutionary history genes genomes. Our integrated are made available in a variety ways, including genome browsers, search interfaces, specialist tools such as Variant Effect Predictor, download files programmatic interfaces....
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates key model organisms. It provides data 87 species across our main early Pre! websites. This year we introduced three newly annotated released numerous updates supported with concentration on latest assemblies human, mouse, zebrafish rat. We also provided two previous human assembly, GRCh37, through dedicated...
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions variation) on new human assembly, GRCh38, although continue to support researchers using GRCh37.p13 assembly through dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped identify of interest...
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation comparative genomics across the vertebrate subphylum key model organisms. pipeline capable of integrating experimental reference data from multiple providers into single integrated resource. Here, we present 94 newly annotated re-annotated genomes, bringing total number genomes offered by to 227. This represents largest expansion resource since its...
The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. seeks be a fundamental resource driving progress by creating, maintaining and updating reference genome annotation comparative genomics resources. This year we describe our new expanded gene, variant capabilities, which led 50% increase in number of vertebrate genomes support. We have also doubled human variants added regulatory regions for many mouse...
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate integrate diverse collection of large-scale reference data to create more comprehensive view biology than would be possible from any individual dataset. Our extensive resources include evidence-based gene regulatory region annotation, variation trees. An accompanying suite tools, infrastructure programmatic access methods ensure uniform analysis distribution all...
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,...
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 project (http://www.ensembl.org). Together, two provide a consistent set of programmatic and interactive interfaces to rich range including genome sequence, gene models, transcript genetic variation, comparative analysis. This paper provides update previous publications about resource, with focus on recent...
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 interfaces to genomic across tree life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform...
Abstract To sustain and develop the largest fully open human genomic resources International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on foundation of 1000 Genomes Project, which created openly accessible catalogue variation developed from samples spanning five continents. IGSR (i) maintains access to Project resources, (ii) updates GRCh38 reference assembly, (iii) adds new data generated cell lines, (iv) shares with a similarly consent...
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from 1000 Genomes Project. IGSR represents largest open collection of human variation provides easy access to these resources. was established 2015 maintain extend Project data, which has been widely used as a reference set by researchers developing analysis methods. mapped all sequence newest (GRCh38), will release updated variant calls ensure...
Abstract Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the project (https://www.ensembl.org). The two collectively present genome annotation through a consistent set of interfaces spanning tree life presenting sequence, annotation, variation, transcriptomic data comparative analysis. Here, we our largest increase in plant, metazoan fungal since project's inception creating one world's...
New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. Ensembl project collects maintains the regulation data resources on epigenetic transcription factor binding methylation for human mouse, well microarray probe mappings annotations variety chordate...
The Ensembl Variant Effect Predictor (VEP) is a freely available, open-source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequences using Ensembl/GENCODE or RefSeq gene sets. also reports phenotype associations from databases such as ClinVar, allele frequencies studies including gnomAD, predictions deleteriousness tools Sorting Intolerant From Tolerant Combined Annotation Dependent Depletion. VEP includes options to customize prioritization....
The Ensembl Genome Browser provides a wealth of freely available genomic data that can be accessed for many purposes by genetics, genomics, and molecular biology researchers. Herein we present two protocols exploring different aspects these data: phenotype its associated variants genes, promoter the epigenetic marks protein-binding activity with it. These workflows illustrate subset types through Browser, considered springboard further exploration.
Abstract Background Variant interpretation is dependent on transcript annotation and remains time consuming challenging. There are major obstacles for historical data reuse of new variants. First, both RefSeq Ensembl/GENCODE produce sets in common use, but there currently no easy way to translate between the two. Second, resources often used variant (e.g. ClinVar, gnomAD, UniProt) do not use same set, nor default or protein sequence. Method Ensembl ran a survey 2018 sample attitudes choosing...
As part of our Q&A series, Genome Biology spoke to four scientists about their personal experiences as parents in careers highlight the challenges researchers having children and support they need this regard. Our participants also included a couple (Kristin Tessmar-Raible Florian Raible), we were interested know whether both being active can have an impact. One wishes remain anonymous.
The Ensembl Variant Effect Predictor (VEP) is a freely available, open source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequence using Ensembl/GENCODE or RefSeq gene sets. also reports phenotype associations from databases such as ClinVar, allele frequencies studies including gnomAD, predictions deleteriousness tools SIFT CADD. VEP includes options to customise prioritisation. well supported updated roughly quarterly incorporate latest gene,...
Variant interpretation is dependent on transcript annotation and remains time consuming challenging. There are major obstacles for historical data reuse of new variants. First, both RefSeq Ensembl/GENCODE produce sets in common use, but there currently no easy way to translate between the two. Second, resources often used variant (e.g. ClinVar, gnomAD, UniProt) do not use same set, nor default or protein sequence. Ensembl ran a survey 2018 assay attitudes choosing one per locus, gather...
Variant interpretation is dependent on transcript annotation and remains time consuming challenging. There are major obstacles for historical data reuse of new variants. First, both RefSeq Ensembl/GENCODE produce sets in common use, but there currently no easy way to translate between the two. Second, resources often used variant (e.g., ClinVar, gnomAD, UniProt) do not use same set, nor default or protein sequence. Ensembl ran a survey 2018 sample attitudes choosing one per locus, gather...