A5050349949- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Amyotrophic Lateral Sclerosis Research
- Epigenetics and DNA Methylation
- Cancer-related gene regulation
- Biomedical Text Mining and Ontologies
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Neurogenetic and Muscular Disorders Research
- Biotechnology and Related Fields
- Genetics and Neurodevelopmental Disorders
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- RNA Research and Splicing
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic Mapping and Diversity in Plants and Animals
- Metabolomics and Mass Spectrometry Studies
- Chromosomal and Genetic Variations
- Intestinal Malrotation and Obstruction Disorders
- Autism Spectrum Disorder Research
- CRISPR and Genetic Engineering
Carnegie Mellon University
2025
Princess Margaret Cancer Centre
2020
University Health Network
2020
University of Toronto
2020
European Bioinformatics Institute
2010-2019
University of California, San Francisco
2004-2017
Wellcome Trust
2014-2017
Genomics (United Kingdom)
2017
Wellcome Sanger Institute
2008-2016
Open Targets
2016
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based for human and mouse GENCODE sets. is based on alignment biological sequences, including cDNAs, proteins RNA-seq reads, target in order construct candidate transcript models. Careful assessment filtering these transcripts ultimately leads final set, which made available website. Here, we describe...
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)...
Gorillas are humans' closest living relatives after chimpanzees, and of comparable importance for the study human origins evolution. Here we present assembly analysis a genome sequence western lowland gorilla, compare whole genomes all extant great ape genera. We propose synthesis genetic fossil evidence consistent with placing human–chimpanzee human–chimpanzee–gorilla speciation events at approximately 6 10 million years ago. In 30% genome, gorilla is closer to or chimpanzee than latter...
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains from over 7000 public sequencing and 42 000 array-based studies comprising 1.5 million assays in total. proportion sequencing-based submissions has grown significantly last few years doubled 18 months,...
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...
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal plant samples of different cell types, organism parts, developmental stages, diseases other conditions. It consists selected microarray RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality processed using standardised analysis methods. Since the last update, has grown seven-fold (1572 as August 2015),...
We have designed and developed a data integration visualization platform that provides evidence about the association of known potential drug targets with diseases. The is to support identification prioritization biological for follow-up. Each target linked disease using integrated genome-wide from broad range sources. either target-centric workflow identify diseases may be associated specific target, or disease-centric disease. Users can easily transition between these target- workflows....
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species contexts, such as tissue, developmental stage, disease or cell type. The available public controlled access data sets from sources are curated re-analysed using standardized, open source pipelines made for queries, download visualization. As of August 2017, holds 3,126 studies across 33 species, including 731 plants. Data large-scale RNA...
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and DDBJ Omics Archive, supporting peer-reviewed publications. It accepts generated by sequencing or array-based technologies currently contains from almost a million assays, over 30 000 experiments. proportion sequencing-based submissions has grown significantly last 2 years reached, in...
Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases other biological experimental conditions. The consists of selected high-quality microarray RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms processed using standardized analysis methods. new version...
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...
Autosomal dominant mutations of the RNA/DNA binding protein FUS are linked to familial amyotrophic lateral sclerosis (FALS); however, it is not clear how cause neurodegeneration. Using transgenic mice expressing a common FALS-associated mutation (FUS-R521C mice), we found that mutant proteins formed stable complex with WT and interfered normal interactions between histone deacetylase 1 (HDAC1). Consequently, FUS-R521C exhibited evidence DNA damage as well profound dendritic synaptic...
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous paralogous classification, whole-genome alignments, synteny. Additional annotations include ontology-based protein structure function; genetic, epigenetic, phenotypic diversity; pathway associations....
X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 was recently shown to play an important role DNA methylation CpG islands (CGIs), late step the pathway that is required for long-term maintenance gene silencing. Here we show inactive (Xi) CGI can occur via either Smchd1-dependent or -independent pathways. methylation, primary pathway, acquired gradually over...
Significance Both overexpression of wild-type fused in sarcoma (FUS) protein and missense mutations can be pathogenic a group related neurodegenerative disorders that includes amyotrophic lateral sclerosis frontotemporal lobar degeneration. It is unclear how FUS cause disease human patients. In this work, we generated novel transgenic mouse models expressing low levels mutant FUS, both which recapitulate aspects the diseases. We found profound difference underlying mechanisms by mutation...
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) pathways (The Plant Reactome archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The section features 39 fully assembled reference that integrated using ontology-based annotation analyses, accessed through both visual programmatic...
The Smchd1 gene encodes a large protein with homology to the SMC family of proteins involved in chromosome condensation and cohesion. Previous studies have found that has an important role CpG island (CGI) methylation on inactive X (Xi) stable silencing some Xi genes. In this study, using genome-wide expression analysis, we showed is required for around 10% genes Xi, apparently independent CGI hypomethylation, and, moreover, these nonrandomly occur clusters. Additionally, at cluster four...
Transcriptional control by beta-catenin and lymphoid enhancer-binding factor 1 (LEF1)/T cell regulates proliferation in stem cells tumorigenesis. Here we provide evidence that transcriptional co repressor homeodomain interacting protein kinase 2 (HIPK2) controls the number of progenitor skin susceptibility to develop squamous carcinoma. Loss HIPK2 leads increased proliferative potential, more rapid G1-S transition cycle, expansion epidermal compartment. Among critical regulators only cyclin...
In female mammals, one of the two X chromosomes is transcriptionally silenced to equalize X-linked gene dosage relative XY males, a process termed chromosome inactivation. Mechanistically, this thought occur via directed recruitment chromatin modifying factors by master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along entire length chromosome. A well-studied example polycomb repressive complex 2 (PRC2), for there evidence direct interaction involving PRC2...
Highlights•Loss of TGF-β1 regulates excitatory-inhibitory inputs in DA neurons via autocrine mechanism•TGF-β signaling reduces axonal and dendritic growth neurons•Mice lacking TGF-β are persistently hyperactive•Mice exhibit reversal-learning deficitsSummaryNeural circuits involving midbrain dopaminergic (DA) regulate reward goal-directed behaviors. Although local GABAergic input is known to modulate circuits, the mechanism that controls excitatory/inhibitory synaptic balance remains unclear....
The Pit1-Oct1-Unc86 domain (POU domain) transcription factor Brn3a controls sensory neuron survival by regulating the expression of Trk receptors and members Bcl-2 family. Loss leads to a dramatic increase in apoptosis severe loss neurons ganglia. Although recent evidence suggests that Brn3a-mediated can be modified additional cofactors, exact mechanisms are not known. Here, we report homeodomain interacting protein kinase 2 (HIPK2) is pro-apoptotic transcriptional cofactor suppresses gene...
X chromosome inactivation is the mechanism used in mammals to achieve dosage compensation of X-linked genes XX females relative XY males. Chromosome silencing triggered cis by expression non-coding RNA Xist. As such, correct regulation Xist gene promoter required establish appropriate activity both males and females. Studies date have demonstrated co-transcription an antisense Tsix low-level sense transcription prior onset inactivation. The balance important determining probability that a...
Expanded GGGGCC repeats in the first intron of C9orf72 gene represent most common cause familial amyotrophic lateral sclerosis (ALS), but mechanisms underlying repeat-induced disease remain incompletely resolved. One proposed gain-of-function mechanism is that repeat-containing RNA forms aggregates sequester binding proteins, leading to altered metabolism motor neurons. Here, we identify zinc finger protein Zfp106 as a specific repeat-binding protein, and using affinity purification-mass...