Ensembl 2006

The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

• Publication year

  2005

• Venue

  Nucleic Acids Res.

• Publication date

  2005-12-28

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkj133PMID 16381931PMCID 1347495
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Pfam protein families database

  2007cited by this paper
• Automated generation of heuristics for biological sequence comparison

  2005cited by this paper
• Adding Some SPICE to DAS

  2005cited by this paper
• BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

  2005cited by this paper
• Haploview: analysis and visualization of LD and haplotype maps

  2005cited by this paper
• [International HapMap project].

  2005cited by this paper
• Whole-Genome Patterns of Common DNA Variation in Three Human Populations

  2005cited by this paper
• Dasty and UniProt DAS: a perfect pair for protein feature visualization

  2005cited by this paper
• Large-scale analysis of pseudogenes in the human genome.

  2004cited by this paper
• Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

  2004cited by this paper
• The Ensembl automatic gene annotation system.

  2004cited by this paper
• GeneWise and Genomewise.

  2004cited by this paper
• Ensembl 2005

  2004cited by this paper
• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

  2004cited by this paper
• The ENCODE (ENCyclopedia Of DNA Elements) Project

  2004cited by this paper
• The Pfam protein families database

  2004cited by this paper
• Gene annotation: prediction and testing.

  2003cited by this paper
• The International HapMap Project

  2003cited by this paper
• EnsMart: a generic system for fast and flexible access to biological data.

  2003cited by this paper
• MicroRNA targets in Drosophila

  2003cited by this paper
• The International HapMap Consortium. The International HapMap Project (Co-PI of Hong Kong Centre which responsible for 2.5% of genome)

  2003cited by this paper
• A genome-wide survey of human pseudogenes.

  2003cited by this paper
• MicroRNA Targets in Drosophila

  2003cited by this paper
• The Distributed Annotation System

  2001cited by this paper

• Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer

  2025cites this paper
• Data Science Driven Drug Repurposing for Metabolic Disorders

  2019cites this paper
• Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

  2018cites this paper
• Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle

  2017cites this paper
• Analyses of Gingival Adhesion Molecules in Periodontitis: Theoretical In Silico, Comparative In Vivo, and Explanatory In Vitro Models.

  2016cites this paper
• Functional exploration of antisense long non-coding RNAs containing transposable elements : a bioinformatics approach

  2016cites this paper
• Association of C5L2 genetic polymorphisms with coronary artery disease in a Han population in Xinjiang, China

  2016cites this paper
• A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways

  2016cites this paper
• Expression of Concern: Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability

  2015cites this paper
• Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

  2015cites this paper
• Roles of small RNAs in the effects of nutrition on apoptosis and spermatogenesis in the adult testis

  2015cites this paper
• Association of C5aR1genetic polymorphisms with coronary artery disease in a Han population in Xinjiang, China

  2015cites this paper
• Host susceptibility to malaria in human and mice: compatible approaches to identify potential resistant genes.

  2014cites this paper
• Ensemble-based classification approach for micro-RNA mining applied on diverse metagenomic sequences

  2014cites this paper
• Gene Expression Profile of NF-κB, Nrf2, Glycolytic, and p53 Pathways During the SH-SY5Y Neuronal Differentiation Mediated by Retinoic Acid

  2014cites this paper
• Influence of component 5a receptor 1 (C5AR1) -1330T/G polymorphism on nonsedating H1-antihistamines therapy in Chinese patients with chronic spontaneous urticaria.

  2014cites this paper
• ARH-seq: identification of differential splicing in RNA-seq data

  2014cites this paper
• Pregnancy-Induced Gingivitis and OMICS in Dentistry: In Silico Modeling and in Vivo Prospective Validation of Estradiol-Modulated Inflammatory Biomarkers

  2014cites this paper
• MMPREDOX/NO Interplay in Periodontitis and Its Inhibition with Satureja hortensis L. Essential Oil

  2013cites this paper
• Database tools in genetic diseases research.

  2013cites this paper
• Updates on Mapping Quantitative Trait Loci Host susceptibility to malaria in human and mice : compatible approaches to identify potential resistant genes

  2013cites this paper
• International Union of Basic and Clinical Pharmacology. LXXXVII. Complement Peptide C5a, C4a, and C3a Receptors

  2013cites this paper
• Semi-Global Inference in Phenotype-Protein Network

  2013cites this paper
• Major Components of Energy Drinks (Caffeine, Taurine, and Guarana) Exert Cytotoxic Effects on Human Neuronal SH-SY5Y Cells by Decreasing Reactive Oxygen Species Production

  2013cites this paper
• The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

  2013cites this paper
• Comparative evolutionary genomics of the STAT family of transcription factors

  2012cites this paper
• Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation

  2012cites this paper
• Genomic perspectives in inter-individual adverse responses following nanomedicine administration: The way forward.

  2012cites this paper
• Transcriptomic Signature of Leishmania Infected Mice Macrophages: A Metabolic Point of View

  2012cites this paper
• OrbId: Origin-based identification of microRNA targets.

  2012cites this paper
• Nested Hierarchal Organization of Conservation for MicroRNAs and Their Putative Targets to Drosophila melanogaster

  2012cites this paper
• The GH18 family of chitinases: their domain architectures, functions and evolutions.

  2012cites this paper
• Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach.

  2012cites this paper
• Genome-wide analysis of mobile genetic element insertion sites

  2011cites this paper
• The large-scale evolution by generating new genes from gene duplication; similarity and difference between monoploid and diploid organisms.

  2011cites this paper
• Bioinformatic analysis of human membrane proteins for antibody-based proteomics

  2011cites this paper
• Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances

  2011cites this paper
• Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins

  2011cites this paper
• NFκB inhibitors induce cell death in glioblastomas.

  2011cites this paper
• Identification of Parkinson’s disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson’s disease patients

  2011cites this paper
• ARH: predicting splice variants from genome-wide data with modified entropy

  2010cites this paper
• Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode

  2010cites this paper
• The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

  2010cites this paper
• Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome

  2010cites this paper
• The Chaperone-Like Protein HYPK Acts Together with NatA in Cotranslational N-Terminal Acetylation and Prevention of Huntingtin Aggregation

  2010cites this paper
• PathEx: a novel multi factors based datasets selector web tool

  2010cites this paper
• Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

  2010cites this paper
• An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

  2010cites this paper
• Molecular characterization and evolutionary plasticity of protein-protein interfaces

  2010cites this paper
• Expression patterns of microRNAs in the chorioamniotic membranes: a role for microRNAs in human pregnancy and parturition

  2009cites this paper
• Human capacitance to dosage imbalance: coping with inefficient selection.

  2009cites this paper
• Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models

  2009cites this paper
• A systematic review of human antioxidant genes.

  2009cites this paper
• cAMP Response Element Binding Protein Is Required for Mouse Neural Progenitor Cell Survival and Expansion

  2009cites this paper
• PLIPS, an automatically collected database of protein lists reported by proteomics studies.

  2009cites this paper
• Identification of candidate genes for congenital ventricular septal defects with HSA22q11 loss of heterozygosity.

  2009cites this paper
• PPI spider: A tool for the interpretation of proteomics data in the context of protein–protein interaction networks

  2009cites this paper
• Exercise behavior and mental health : A genetic perspective

  2009cites this paper
• Ensembl’s 10th year

  2009cites this paper
• An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications

  2009cites this paper
• GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists

  2009cites this paper
• Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties.

  2009cites this paper
• Meta-basic estimates the size of druggable human genome

  2009cites this paper
• A Computation to Integrate the Analysis of Genetic Variations Occurring within Regulatory Elements and Their Possible Effects

  2009influential citation
• Berkeley PHOG: PhyloFacts orthology group prediction web server

  2009cites this paper
• Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

  2009cites this paper
• Molecular basis of gene dosage sensitivity

  2009cites this paper
• Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

  2009cites this paper
• Identificación de genes candidatos en las comunicaciones interventriculares congénitas con pérdida de heterocigosis de HSA22q11

  2009cites this paper
• Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery

  2009cites this paper
• MicroRNA‐122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma

  2009cites this paper
• HAPPI: an online database of comprehensive human annotated and predicted protein interactions

  2009cites this paper
• Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates

  2009cites this paper
• A novel human NatA Nα-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1)

  2009cites this paper
• DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System

  2009cites this paper
• Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

  2009cites this paper
• Analysis of genomic DNA with the UCSC genome browser.

  2009cites this paper
• A systematic strategy for the discovery of candidate genes responsible for phenotypic variation.

  2009cites this paper
• Do Alu repeats drive the evolution of the primate transcriptome?

  2008cites this paper
• Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells

  2008cites this paper
• The fellowship of the RING: the RING-B-box linker region interacts with the RING in TRIM21/Ro52, contains a native autoantigenic epitope in Sjögren syndrome, and is an integral and conserved region in TRIM proteins.

  2008cites this paper
• Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

  2008cites this paper
• POPE—a tool to aid high-throughput phylogenetic analysis

  2008cites this paper
• Comparative genomics-based prediction of protein function.

  2008cites this paper
• Just how versatile are domains?

  2008cites this paper
• Genome annotation.

  2008cites this paper
• MetWAMer: eukaryotic translation initiation site prediction

  2008cites this paper
• Reduced purifying selection prevails over positive selection in human copy number variant evolution.

  2008cites this paper
• Prediction of regulatory elements.

  2008cites this paper
• Functional protein divergence in the evolution of Homo sapiens

  2008cites this paper
• Innate immunity genes as candidate genes: searching for relevant natural polymorphisms in databases and assessing family-based association of polymorphisms with human diseases.

  2008cites this paper
• Searching the protein interaction space through the MINT database.

  2008cites this paper
• Dissection of Functional Residues in Receptor Activity-Modifying Proteins Through Phylogenetic and Statistical Analyses

  2008cites this paper
• Identification of kinetin riboside as a repressor of CCND1 and CCND2 with preclinical antimyeloma activity.

  2008cites this paper
• Structure–function relationships in the 2‐oxo acid dehydrogenase family: Substrate‐specific signatures and functional predictions for the 2‐oxoglutarate dehydrogenase‐like proteins

  2008cites this paper
• Meta-Analysis Approach identifies Candidate Genes and associated Molecular Networks for Type-2 Diabetes Mellitus

  2008cites this paper
• MACHOS: Markov clusters of homologous subsequences

  2008cites this paper
• Factoring local sequence composition in motif significance analysis.

  2008cites this paper
• Pitfalls of the most commonly used models of context dependent substitution

  2008cites this paper
• Gene discovery and the genetic basis of calcium consumption.

  2008cites this paper