The UCSC Genome Browser database: update 2010.
paper
Cited
Public
- Authors
- Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M; Hinrichs, Angie S; Zweig, Ann S; Fujita, Pauline A; Diekhans, Mark; Smith, Kayla E; Rosenbloom, Kate R; Raney, Brian J; Pohl, Andy; Pheasant, Michael; Meyer, Laurence R; Learned, Katrina; Hsu, Fan; Hillman-Jackson, Jennifer; Harte, Rachel A; Giardine, Belinda; Dreszer, Timothy R; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James
- Year
- 2010
- Journal
- Nucleic acids research
- PMID
- 19906737
- DOI
- 10.1093/nar/gkp939
- PMCID
- PMC2808870
The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
Main Genome Browser display page on the hg18 human assembly, showing the Wiki track, OMIM Genes, UCSC Genes and the 44-species Conservation track, with all six conservation score tracks visible. The highlighted region shows drag-and-zoom in action. When the mouse button is released, the browser will redraw at the new coordinates listed in the position/search box.
Details page of SNP rs4987121 from the SNPs (130) track, showing the new โpredicted function relative to selected gene tracksโ feature using UCSC Genes, RefSeq Genes and Ensembl Genes. The window on the right is the Chimera 3D protein structure viewer, opened by clicking on the โChimeraโ link in the first window. The selected SNP is highlighted in red, while other non-synonymous SNPs are highlighted in gold.
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| Effect of 17ฮฒ-estradiol and flavonoids on the regulation of expression of newly identified oestrogen responsive genes in a rat raphe nuclei-derived cell line. | Amer DA et al. | โ | 2012 | โ |
| Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis. | Walsh SW et al. | โ | 2012 | โ |
| Epigenetic analysis: ChIP-chip and ChIP-seq. | Pellegrini M et al. | โ | 2012 | โ |
| Epigenetic regulation of human cis-natural antisense transcripts. | Conley AB et al. | โ | 2012 | โ |
| Evolutionary forces shaping genomic islands of population differentiation in humans. | Hofer T et al. | โ | 2012 | โ |
| Evolutionary relationships between miRNA genes and their activity. | Zhu Y et al. | โ | 2012 | โ |
| Evolution of the human-specific microRNA miR-941. | Hu HY et al. | โ | 2012 | โ |
| Expression profile of genes involved in pathogenesis of pediatric Crohn's disease. | Sim WH et al. | โ | 2012 | โ |
| Fast computation and applications of genome mappability. | Derrien T et al. | โ | 2012 | โ |
| Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease. | Masud R et al. | โ | 2012 | โ |
| Genetic association of SLC2A14 polymorphism with Alzheimer's disease in a Han Chinese population. | Wang W et al. | โ | 2012 | โ |
| Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions. | Schwarzbauer K et al. | โ | 2012 | โ |
| Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. | Vavouri T et al. | โ | 2012 | โ |
| Identification of 3' gene ends using transcriptional and genomic conservation across vertebrates. | Morgan M et al. | โ | 2012 | โ |
| Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. | Oh YM et al. | โ | 2012 | โ |
| Identification of gene-oriented exon orthology between human and mouse. | Fu GC et al. | โ | 2012 | โ |
| Identification of imprinted loci by transcriptome sequencing. | Babak T | โ | 2012 | โ |
| Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. | Hemberg M et al. | โ | 2012 | โ |
| Large-scale computational identification of regulatory SNPs with rSNP-MAPPER. | Riva A | โ | 2012 | โ |
| Lengthening of 3'UTR increases with morphological complexity in animal evolution. | Chen CY et al. | โ | 2012 | โ |
| Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. | Wrzodek C et al. | โ | 2012 | โ |
| Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability. | Thu KL et al. | โ | 2012 | โ |
| Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. | Kim Guisbert KS et al. | โ | 2012 | โ |
| MetaMirClust: discovery of miRNA cluster patterns using a data-mining approach. | Chan WC et al. | โ | 2012 | โ |
| Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period. | Pluta K et al. | โ | 2012 | โ |
| More single-nucleotide mutations surround small insertions than small deletions in primates. | Huang S et al. | โ | 2012 | โ |
| Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants. | Sun K et al. | โ | 2012 | โ |
| Obesity-insulin targeted genes in the 3p26-25 region in human studies and LG/J and SM/J mice. | Kraja AT et al. | โ | 2012 | โ |
| On the presence and role of human gene-body DNA methylation. | Jjingo D et al. | โ | 2012 | โ |
| Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. | Gray VE et al. | โ | 2012 | โ |
| PhyLAT: a phylogenetic local alignment tool. | Sun H et al. | โ | 2012 | โ |
| PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse. | Pott S et al. | โ | 2012 | โ |
| Retrotransposon profiling of RNA polymerase III initiation sites. | Qi X et al. | โ | 2012 | โ |
| Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network. | Su J et al. | โ | 2012 | โ |
| RNA editing of protein sequences: a rare event in human transcriptomes. | Kleinman CL et al. | โ | 2012 | โ |
| Sexually dimorphic effects of oxytocin receptor gene (OXTR ) variants on Harm Avoidance. | Stankova T et al. | โ | 2012 | โ |
| Strategies to explore functional genomics data sets in NCBI's GEO database. | Wilhite SE et al. | โ | 2012 | โ |
| The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites. | Riva A | โ | 2012 | โ |
| The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. | Jenal M et al. | โ | 2012 | โ |
| The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family. | Karn RC et al. | โ | 2012 | โ |
| The transcription factor encyclopedia. | Yusuf D et al. | โ | 2012 | โ |
| The UCSC Archaeal Genome Browser: 2012 update. | Chan PP et al. | โ | 2012 | โ |
| Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. | Duitama J et al. | โ | 2012 | โ |
| Transcription initiation arising from E-cadherin/CDH1 intron2: a novel protein isoform that increases gastric cancer cell invasion and angiogenesis. | Pinheiro H et al. | โ | 2012 | โ |
| Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms. | Chiang CW et al. | โ | 2012 | โ |
| Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. | Pei J et al. | โ | 2012 | โ |
| Upstream distal regulatory elements contact the Lmo2 promoter in mouse erythroid cells. | Bhattacharya A et al. | โ | 2012 | โ |
| URPD: a specific product primer design tool. | Chuang LY et al. | โ | 2012 | โ |
| Vitamin D receptor polymorphisms in patients with cutaneous melanoma. | Orlow I et al. | โ | 2012 | โ |
| 17p13.3 microduplications are associated with split-hand/foot malformation and long-bone deficiency (SHFLD). | Armour CM et al. | โ | 2011 | โ |
| A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression. | Farrell JJ et al. | โ | 2011 | โ |
| A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. | Liu S et al. | โ | 2011 | โ |
| A comprehensive map of mobile element insertion polymorphisms in humans. | Stewart C et al. | โ | 2011 | โ |
| Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. | Roux J et al. | โ | 2011 | โ |
| AlleleSeq: analysis of allele-specific expression and binding in a network framework. | Rozowsky J et al. | โ | 2011 | โ |
| Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. | Gertz J et al. | โ | 2011 | โ |
| Annotating genes and genomes with DNA sequences extracted from biomedical articles. | Haeussler M et al. | โ | 2011 | โ |
| A novel compression tool for efficient storage of genome resequencing data. | Wang C et al. | โ | 2011 | โ |
| AREM: aligning short reads from ChIP-sequencing by expectation maximization. | Newkirk D et al. | โ | 2011 | โ |
| AREsite: a database for the comprehensive investigation of AU-rich elements. | Gruber AR et al. | โ | 2011 | โ |
| Aryl hydrocarbon receptor-mediated induction of Stearoyl-CoA desaturase 1 alters hepatic fatty acid composition in TCDD-elicited steatosis. | Angrish MM et al. | โ | 2011 | โ |
| Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. | Lekprasert P et al. | โ | 2011 | โ |
| A tissue-specific landscape of sense/antisense transcription in the mouse intestine. | Klostermeier UC et al. | โ | 2011 | โ |
| A transcriptomic atlas of mouse neocortical layers. | Belgard TG et al. | โ | 2011 | โ |
| A user's guide to the encyclopedia of DNA elements (ENCODE). | ENCODE Project Consortium | โ | 2011 | โ |
| Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. | Edmonson MN et al. | โ | 2011 | โ |
| Both size and GC-content of minimal introns are selected in human populations. | Wang D et al. | โ | 2011 | โ |
| Bovine Genome Database: integrated tools for genome annotation and discovery. | Childers CP et al. | โ | 2011 | โ |
| Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications. | Muranen TA et al. | โ | 2011 | โ |
| Characterization of postsynaptic Ca2+ signals at the Drosophila larval NMJ. | Desai SA et al. | โ | 2011 | โ |
| Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. | Vavouri T et al. | โ | 2011 | โ |
| Chromosome 3 anomalies investigated by genome wide SNP analysis of benign, low malignant potential and low grade ovarian serous tumours. | Birch AH et al. | โ | 2011 | โ |
| Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. | Yegnasubramanian S et al. | โ | 2011 | โ |
| Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. | Nguyen DK et al. | โ | 2011 | โ |
| Comparative analysis of algorithms for next-generation sequencing read alignment. | Ruffalo M et al. | โ | 2011 | โ |
| Comparative analysis of neural transcriptomes and functional implication of unannotated intronic expression. | Sun Y et al. | โ | 2011 | โ |
| Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. | Suzuki H et al. | โ | 2011 | โ |
| Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. | Hillmer AM et al. | โ | 2011 | โ |
| Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. | Chung WJ et al. | โ | 2011 | โ |
| Computational discovery of human coding and non-coding transcripts with conserved splice sites. | Rose D et al. | โ | 2011 | โ |
| Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. | McPherson A et al. | โ | 2011 | โ |
| Conceptual thinking for in silico prioritization of candidate disease genes. | Tiffin N | โ | 2011 | โ |
| Conservation of an RNA regulatory map between Drosophila and mammals. | Brooks AN et al. | โ | 2011 | โ |
| Conserved RNA structures in the non-canonical Hac1/Xbp1 intron. | Hooks KB et al. | โ | 2011 | โ |
| Context-dependent robustness to 5' splice site polymorphisms in human populations. | Lu ZX et al. | โ | 2011 | โ |
| Current concepts of follicle-stimulating hormone receptor gene regulation. | George JW et al. | โ | 2011 | โ |
| Dalliance: interactive genome viewing on the web. | Down TA et al. | โ | 2011 | โ |
| Databases and resources for human small non-coding RNAs. | Agirre E et al. | โ | 2011 | โ |
| dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. | Liu X et al. | โ | 2011 | โ |
| Deep resequencing of the voltage-gated potassium channel subunit KCNE3 gene in chronic tinnitus. | Sand PG et al. | โ | 2011 | โ |
| Delay in feedback repression by cryptochrome 1 is required for circadian clock function. | Ukai-Tadenuma M et al. | โ | 2011 | โ |
| Deletion and duplication of 11p13-11p14: reciprocal aberrations derived from a paternal insertion. | Dolan M et al. | โ | 2011 | โ |
| Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length. | Lou SK et al. | โ | 2011 | โ |
| Developing a community-based genetic nomenclature for anole lizards. | Kusumi K et al. | โ | 2011 | โ |
| Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. | Chung D et al. | โ | 2011 | โ |
| DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. | Karimi MM et al. | โ | 2011 | โ |
| DNA secondary structures and epigenetic determinants of cancer genome evolution. | De S et al. | โ | 2011 | โ |
| dPORE-miRNA: polymorphic regulation of microRNA genes. | Schmeier S et al. | โ | 2011 | โ |
| DPY19L2 deletion as a major cause of globozoospermia. | Koscinski I et al. | โ | 2011 | โ |
| Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. | Pencovich N et al. | โ | 2011 | โ |
| Effect of the transposable element environment of human genes on gene length and expression. | Jjingo D et al. | โ | 2011 | โ |
| Efficient internal exon recognition depends on near equal contributions from the 3' and 5' splice sites. | Shepard PJ et al. | โ | 2011 | โ |
| ELAV-mediated 3'-end processing of ewg transcripts is evolutionarily conserved despite sequence degeneration of the ELAV-binding site. | Haussmann IU et al. | โ | 2011 | โ |
| Enhancers regulate progression of development in mammalian cells. | Kranz AL et al. | โ | 2011 | โ |
| Epigenetic regulation of microRNA genes and the role of miR-34b in cell invasion and motility in human melanoma. | Mazar J et al. | โ | 2011 | โ |
| Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments. | McIver LJ et al. | โ | 2011 | โ |
| Evolution of promoter affinity for transcription factors in the human lineage. | Molineris I et al. | โ | 2011 | โ |
| Functional screening of Alzheimer pathology genome-wide association signals in Drosophila. | Shulman JM et al. | โ | 2011 | โ |
| genenames.org: the HGNC resources in 2011. | Seal RL et al. | โ | 2011 | โ |
| Genetic effects at pleiotropic loci are context-dependent with consequences for the maintenance of genetic variation in populations. | Lawson HA et al. | โ | 2011 | โ |
| Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. | Shu W et al. | โ | 2011 | โ |
| Genome-wide computational analysis of dioxin response element location and distribution in the human, mouse, and rat genomes. | Dere E et al. | โ | 2011 | โ |
| Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. | Martin D et al. | โ | 2011 | โ |
| Genome-wide depletion of replication initiation events in highly transcribed regions. | Martin MM et al. | โ | 2011 | โ |
| Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. | Tang B et al. | โ | 2011 | โ |
| Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. | Uren PJ et al. | โ | 2011 | โ |
| Genomic characteristics of cattle copy number variations. | Hou Y et al. | โ | 2011 | โ |
| Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. | Carette JE et al. | โ | 2011 | โ |
| High density DNA methylation array with single CpG site resolution. | Bibikova M et al. | โ | 2011 | โ |
| Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription. | Numata K et al. | โ | 2011 | โ |
| Human piRNAs are under selection in Africans and repress transposable elements. | Lukic S et al. | โ | 2011 | โ |
| Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. | Munoz-Torres MC et al. | โ | 2011 | โ |
| Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. | Subramanian RP et al. | โ | 2011 | โ |
| Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. | Thiagarajan RD et al. | โ | 2011 | โ |
| Identification of human-specific transcript variants induced by DNA insertions in the human genome. | Kim DS et al. | โ | 2011 | โ |
| Identification of improved IL28B SNPs and haplotypes for prediction of drug response in treatment of hepatitis C using massively parallel sequencing in a cross-sectional European cohort. | Smith KR et al. | โ | 2011 | โ |
| Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. | Sephton CF et al. | โ | 2011 | โ |
| Identification of novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease. | Airavaara M et al. | โ | 2011 | โ |
| Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. | Zhang F et al. | โ | 2011 | โ |
| Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. | Chien CH et al. | โ | 2011 | โ |
| Integrated expression profiling and genome-wide analysis of ChREBP targets reveals the dual role for ChREBP in glucose-regulated gene expression. | Jeong YS et al. | โ | 2011 | โ |
| Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer. | Oyama M et al. | โ | 2011 | โ |
| Integration of genome-wide computation DRE search, AhR ChIP-chip and gene expression analyses of TCDD-elicited responses in the mouse liver. | Dere E et al. | โ | 2011 | โ |
| Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes. | Beck D et al. | โ | 2011 | โ |
| Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. | Zuvich RL et al. | โ | 2011 | โ |
| In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. | Lai HC et al. | โ | 2011 | โ |
| IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. | Kim H et al. | โ | 2011 | โ |
| Jarid1b targets genes regulating development and is involved in neural differentiation. | Schmitz SU et al. | โ | 2011 | โ |
| Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins. | Golbert DC et al. | โ | 2011 | โ |
| Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. | Carmi S et al. | โ | 2011 | โ |
| lncRNAdb: a reference database for long noncoding RNAs. | Amaral PP et al. | โ | 2011 | โ |
| Mapping association between long-range cis-regulatory regions and their target genes using synteny. | Mongin E et al. | โ | 2011 | โ |
| Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. | Zhang C et al. | โ | 2011 | โ |
| Meiotic recombination favors the spreading of deleterious mutations in human populations. | Necลulea A et al. | โ | 2011 | โ |
| Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. | Rabani M et al. | โ | 2011 | โ |
| MicroRNA expression and regulation in human, chimpanzee, and macaque brains. | Hu HY et al. | โ | 2011 | โ |
| MicroRNA gene dosage alterations and drug response in lung cancer. | Enfield KS et al. | โ | 2011 | โ |
| MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. | Yuan Z et al. | โ | 2011 | โ |
| MicroRNA profiling of rhesus macaque embryonic stem cells. | Sun Z et al. | โ | 2011 | โ |
| miRTar: an integrated system for identifying miRNA-target interactions in human. | Hsu JB et al. | โ | 2011 | โ |
| miRTarBase: a database curates experimentally validated microRNA-target interactions. | Hsu SD et al. | โ | 2011 | โ |
| ModBase, a database of annotated comparative protein structure models, and associated resources. | Pieper U et al. | โ | 2011 | โ |
| MotifMap: integrative genome-wide maps of regulatory motif sites for model species. | Daily K et al. | โ | 2011 | โ |
| MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. | Gupta R et al. | โ | 2011 | โ |
| NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. | Shirdel EA et al. | โ | 2011 | โ |
| NCBI Epigenomics: a new public resource for exploring epigenomic data sets. | Fingerman IM et al. | โ | 2011 | โ |
| Network analysis of microRNAs and their regulation in human ovarian cancer. | Schmeier S et al. | โ | 2011 | โ |
| New tools and methods for direct programmatic access to the dbSNP relational database. | Saccone SF et al. | โ | 2011 | โ |
| New words in human mutagenesis. | Panchin AY et al. | โ | 2011 | โ |
| Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. | Fullwood MJ et al. | โ | 2011 | โ |
| Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. | Hackl M et al. | โ | 2011 | โ |
| Novel clinical finding in MECP2 duplication syndrome. | Budisteanu M et al. | โ | 2011 | โ |
| NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq. | Xia Z et al. | โ | 2011 | โ |
| Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. | Reumers J et al. | โ | 2011 | โ |
| Ordered progression of stage-specific miRNA profiles in the mouse B2 B-cell lineage. | Spierings DC et al. | โ | 2011 | โ |
| p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins. | Bรถhlig L et al. | โ | 2011 | โ |
| PHAST and RPHAST: phylogenetic analysis with space/time models. | Hubisz MJ et al. | โ | 2011 | โ |
| Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. | Martin DI et al. | โ | 2011 | โ |
| Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. | Enderle D et al. | โ | 2011 | โ |
| Population transcriptomics of Drosophila melanogaster females. | Mรผller L et al. | โ | 2011 | โ |
| PPARฮณ disease gene network and identification of therapeutic targets for prostate cancer. | Venkatachalam G et al. | โ | 2011 | โ |
| Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. | Chen Y et al. | โ | 2011 | โ |
| Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). | Baranov PV et al. | โ | 2011 | โ |
| Proteomic patterns of cervical cancer cell lines, a network perspective. | Higareda-Almaraz JC et al. | โ | 2011 | โ |
| QDMR: a quantitative method for identification of differentially methylated regions by entropy. | Zhang Y et al. | โ | 2011 | โ |
| Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 ยตg total RNA. | Christodoulou DC et al. | โ | 2011 | โ |
| Quantitative genetic study of the circulating osteopontin in community-selected families. | Ermakov S et al. | โ | 2011 | โ |
| Rampant purifying selection conserves positions with posttranslational modifications in human proteins. | Gray VE et al. | โ | 2011 | โ |
| Reactome: a database of reactions, pathways and biological processes. | Croft D et al. | โ | 2011 | โ |
| Regulation of alternative splicing by the core spliceosomal machinery. | Saltzman AL et al. | โ | 2011 | โ |
| Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. | Rebollo R et al. | โ | 2011 | โ |
| RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression. | Lalonde E et al. | โ | 2011 | โ |
| Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees. | Renaud G et al. | โ | 2011 | โ |
| SigCS base: an integrated genetic information resource for human cerebral stroke. | Park YK et al. | โ | 2011 | โ |
| Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. | Pierron D et al. | โ | 2011 | โ |
| SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3' splice site. | Doktor TK et al. | โ | 2011 | โ |
| Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. | Jiang J et al. | โ | 2011 | โ |
| SNP uniqueness problem: a proof-of-principle in HapMap SNPs. | Doron S et al. | โ | 2011 | โ |
| Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. | de Almeida SF et al. | โ | 2011 | โ |
| starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. | Yang JH et al. | โ | 2011 | โ |
| Statistical inference of allelic imbalance from transcriptome data. | Nothnagel M et al. | โ | 2011 | โ |
| Strategic approaches to unraveling genetic causes of cardiovascular diseases. | Marian AJ et al. | โ | 2011 | โ |
| Systematic analysis of human microRNA divergence based on evolutionary emergence. | Wang QH et al. | โ | 2011 | โ |
| Systematic CpG islands methylation profiling of genes in the wnt pathway in epithelial ovarian cancer identifies biomarkers of progression-free survival. | Dai W et al. | โ | 2011 | โ |
| T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. | Burren OS et al. | โ | 2011 | โ |
| Tabix: fast retrieval of sequence features from generic TAB-delimited files. | Li H | โ | 2011 | โ |
| TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. | Williams K et al. | โ | 2011 | โ |
| The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression. | Wang Y et al. | โ | 2011 | โ |
| The characterisation of piRNA-related 19mers in the mouse. | Oey HM et al. | โ | 2011 | โ |
| The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. | Ringwald M et al. | โ | 2011 | โ |
| The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. | Hallen L et al. | โ | 2011 | โ |
| The mouse Gene Expression Database (GXD): 2011 update. | Finger JH et al. | โ | 2011 | โ |
| The Pancreatic Expression database: 2011 update. | Cutts RJ et al. | โ | 2011 | โ |
| The putative RNA helicase HELZ promotes cell proliferation, translation initiation and ribosomal protein S6 phosphorylation. | Hasgall PA et al. | โ | 2011 | โ |
| The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. | Fischer S et al. | โ | 2011 | โ |
| The UCSC Genome Browser database: update 2011. | Fujita PA et al. | โ | 2011 | โ |
| TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology. | Hong D et al. | โ | 2011 | โ |
| Transcriptional regulation of neural retina leucine zipper (Nrl), a photoreceptor cell fate determinant. | Montana CL et al. | โ | 2011 | โ |
| tRNA genes protect a reporter gene from epigenetic silencing in mouse cells. | Ebersole T et al. | โ | 2011 | โ |
| UMARS: Un-MAppable Reads Solution. | Li SC et al. | โ | 2011 | โ |
| Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. | Garcia DM et al. | โ | 2011 | โ |
| Widespread establishment and regulatory impact of Alu exons in human genes. | Shen S et al. | โ | 2011 | โ |
| Widespread expression of piRNA-like molecules in somatic tissues. | Yan Z et al. | โ | 2011 | โ |
| ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. | Rashid NU et al. | โ | 2011 | โ |
| A candidate subspecies discrimination system involving a vomeronasal receptor gene with different alleles fixed in M. m. domesticus and M. m. musculus. | Karn RC et al. | โ | 2010 | โ |
| A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. | Ramagopalan SV et al. | โ | 2010 | โ |
| Alternative splicing is frequent during early embryonic development in mouse. | Revil T et al. | โ | 2010 | โ |
| Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. | Ye ZQ et al. | โ | 2010 | โ |
| Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. | Stacey SN et al. | โ | 2010 | โ |
| An Examination of KCNE1 Mutations and Common Variants in Chronic Tinnitus. | Sand PG et al. | โ | 2010 | โ |
| ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. | Wang K et al. | โ | 2010 | โ |
| A quick guide to large-scale genomic data mining. | Huttenhower C et al. | โ | 2010 | โ |
| ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. | Law MJ et al. | โ | 2010 | โ |
| BigWig and BigBed: enabling browsing of large distributed datasets. | Kent WJ et al. | โ | 2010 | โ |
| BiologicalNetworks 2.0--an integrative view of genome biology data. | Kozhenkov S et al. | โ | 2010 | โ |
| Canonical and alternate functions of the microRNA biogenesis machinery. | Chong MM et al. | โ | 2010 | โ |
| Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression. | Cunnington MS et al. | โ | 2010 | โ |
| Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. | Chavez L et al. | โ | 2010 | โ |
| De novo assembly and analysis of RNA-seq data. | Robertson G et al. | โ | 2010 | โ |
| Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes. | Wang J et al. | โ | 2010 | โ |
| Emergence of mammals by emergency: exaptation. | Okada N et al. | โ | 2010 | โ |
| Gene regulation and the origins of human biological uniqueness. | Sholtis SJ et al. | โ | 2010 | โ |
| Genome-wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure. | Boellmann F et al. | โ | 2010 | โ |
| Genome-wide association between branch point properties and alternative splicing. | Corvelo A et al. | โ | 2010 | โ |
| Genome-wide functional analysis of human 5' untranslated region introns. | Cenik C et al. | โ | 2010 | โ |
| Genomic information infrastructure after the deluge. | Parkhill J et al. | โ | 2010 | โ |
| Genomic-scale capture and sequencing of endogenous DNA from feces. | Perry GH et al. | โ | 2010 | โ |
| genoPlotR: comparative gene and genome visualization in R. | Guy L et al. | โ | 2010 | โ |
| Gerontome: a web-based database server for aging-related genes and analysis pipelines. | Kwon J et al. | โ | 2010 | โ |
| High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors. | Cattoglio C et al. | โ | 2010 | โ |
| High-resolution human genome structure by single-molecule analysis. | Teague B et al. | โ | 2010 | โ |
| Human-chimpanzee promoter comparisons: property-conserved evolution? | Deyneko IV et al. | โ | 2010 | โ |
| Human functional genetic studies are biased against the medically most relevant primate-specific genes. | Hao L et al. | โ | 2010 | โ |
| Identification and characterization of a promoter cassette conferring adipocyte-specific gene expression. | Wang ZV et al. | โ | 2010 | โ |
| Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. | Wetterbom A et al. | โ | 2010 | โ |
| Identifying a high fraction of the human genome to be under selective constraint using GERP++. | Davydov EV et al. | โ | 2010 | โ |
| Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. | Chari R et al. | โ | 2010 | โ |
| interPopula: a Python API to access the HapMap Project dataset. | Antao T | โ | 2010 | โ |
| Large copy-number variations are enriched in cases with moderate to extreme obesity. | Wang K et al. | โ | 2010 | โ |
| Leiden Open Variation Database of the MUTYH gene. | Out AA et al. | โ | 2010 | โ |
| ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. | Zhang Y et al. | โ | 2010 | โ |
| Next generation sequencing based approaches to epigenomics. | Hirst M et al. | โ | 2010 | โ |
| Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. | Kalay G et al. | โ | 2010 | โ |
| Pharmacogenomics and bioinformatics: PharmGKB. | Thorn CF et al. | โ | 2010 | โ |
| PI3 kinase signalling blocks Foxp3 expression by sequestering Foxo factors. | Merkenschlager M et al. | โ | 2010 | โ |
| PriorsEditor: a tool for the creation and use of positional priors in motif discovery. | Klepper K et al. | โ | 2010 | โ |
| Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. | Leleu M et al. | โ | 2010 | โ |
| Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress. | Lardenois A et al. | โ | 2010 | โ |
| ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. | Ling Y et al. | โ | 2010 | โ |
| Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins. | Holmes RS et al. | โ | 2010 | โ |
| Reverse engineering the yeast RNR1 transcriptional control system. | Mao G et al. | โ | 2010 | โ |
| Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. | Aerts S et al. | โ | 2010 | โ |
| SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. | Shetty AC et al. | โ | 2010 | โ |
| SeqWare Query Engine: storing and searching sequence data in the cloud. | O'Connor BD et al. | โ | 2010 | โ |
| Slam haplotypes modulate the response to lipopolysaccharide in vivo through control of NKT cell number and function. | Aktan I et al. | โ | 2010 | โ |
| SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. | Saccone SF et al. | โ | 2010 | โ |
| Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology. | Mocellin S et al. | โ | 2010 | โ |
| The case for cloud computing in genome informatics. | Stein LD | โ | 2010 | โ |
| The Genomedata format for storing large-scale functional genomics data. | Hoffman MM et al. | โ | 2010 | โ |
| The RNA structurome: high-throughput probing. | Westhof E et al. | โ | 2010 | โ |
| The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation. | Tuch BB et al. | โ | 2010 | โ |
| Transcribed dark matter: meaning or myth? | Ponting CP et al. | โ | 2010 | โ |
| Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. | Xu G et al. | โ | 2010 | โ |
| Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. | Sรกnchez-Gracia A et al. | โ | 2010 | โ |
| Two new ArrayTrack libraries for personalized biomedical research. | Xu J et al. | โ | 2010 | โ |
| Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. | Wood HM et al. | โ | 2010 | โ |
| Visualizing biological data-now and in the future. | O'Donoghue SI et al. | โ | 2010 | โ |
| What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. | Kelkar YD et al. | โ | 2010 | โ |
| Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. | Kenigsberg E et al. | โ | 2010 | โ |