标题
The state of play in higher eukaryote gene annotation
作者
关键词
-
出版物
NATURE REVIEWS GENETICS
Volume 17, Issue 12, Pages 758-772
出版商
Springer Nature
发表日期
2016-10-24
DOI
10.1038/nrg.2016.119
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
- (2016) Xinping Yang et al. CELL
- Ribosome Footprint Profiling of Translation throughout the Genome
- (2016) Nicholas T. Ingolia CELL
- The life history of retrocopies illuminates the evolution of new mammalian genes
- (2016) Francesco Nicola Carelli et al. GENOME RESEARCH
- Alternative Polyadenylation of mRNAs: 3′-Untranslated Region Matters in Gene Expression
- (2016) MOLECULES AND CELLS
- Evolution to the rescue: using comparative genomics to understand long non-coding RNAs
- (2016) Igor Ulitsky NATURE REVIEWS GENETICS
- Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
- (2016) Andrew D. Foote et al. Nature Communications
- Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
- (2016) James C. Wright et al. Nature Communications
- Ensembl regulation resources
- (2016) Daniel R. Zerbino et al. Database-The Journal of Biological Databases and Curation
- Ribosomal profiling adds new coding sequences to the proteome
- (2015) M. A. S. Mumtaz et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.
- (2015) Katharina J. Hoff et al. BIOINFORMATICS
- The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome
- (2015) Tanya Z. Berardini et al. GENESIS
- Linking RNA biology to lncRNAs
- (2015) Loyal A. Goff et al. GENOME RESEARCH
- Functional and genetic diversity of leukocyte immunoglobulin-like receptor and implication for disease associations
- (2015) Kouyuki Hirayasu et al. JOURNAL OF HUMAN GENETICS
- The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes
- (2015) David J. Adams et al. MAMMALIAN GENOME
- Mouse genome annotation by the RefSeq project
- (2015) Kelly M. McGarvey et al. MAMMALIAN GENOME
- Creating reference gene annotation for the mouse C57BL6/J genome assembly
- (2015) Jonathan M. Mudge et al. MAMMALIAN GENOME
- Regulation of Splicing Factors by Alternative Splicing and NMD Is Conserved between Kingdoms Yet Evolutionarily Flexible
- (2015) Liana F. Lareau et al. MOLECULAR BIOLOGY AND EVOLUTION
- Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin
- (2015) Benjamin S. Scruggs et al. MOLECULAR CELL
- CTCF Binding Polarity Determines Chromatin Looping
- (2015) Elzo de Wit et al. MOLECULAR CELL
- Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events
- (2015) Hagen Tilgner et al. NATURE BIOTECHNOLOGY
- The landscape of long noncoding RNAs in the human transcriptome
- (2015) Matthew K Iyer et al. NATURE GENETICS
- Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
- (2015) Borbala Mifsud et al. NATURE GENETICS
- A copy number variation map of the human genome
- (2015) Mehdi Zarrei et al. NATURE REVIEWS GENETICS
- The selection and function of cell type-specific enhancers
- (2015) Sven Heinz et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- WormBase 2016: expanding to enable helminth genomic research
- (2015) Kevin L. Howe et al. NUCLEIC ACIDS RESEARCH
- RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling
- (2015) Shang-Qian Xie et al. NUCLEIC ACIDS RESEARCH
- Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
- (2015) Nuala A. O'Leary et al. NUCLEIC ACIDS RESEARCH
- An update on LNCipedia: a database for annotated human lncRNA sequences
- (2015) P.J. Volders et al. NUCLEIC ACIDS RESEARCH
- NONCODE 2016: an informative and valuable data source of long non-coding RNAs
- (2015) Yi Zhao et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2016
- (2015) Andrew Yates et al. NUCLEIC ACIDS RESEARCH
- FlyBase: establishing a Gene Group resource forDrosophila melanogaster
- (2015) Helen Attrill et al. NUCLEIC ACIDS RESEARCH
- The awesome power of ribosome profiling
- (2015) Richard Jackson et al. RNA
- The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
- (2015) et al. SCIENCE
- Tissue-based map of the human proteome
- (2015) M. Uhlen et al. SCIENCE
- Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins
- (2015) Yanqi Hao et al. Cell Reports
- Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
- (2015) Hadas Hezroni et al. Cell Reports
- Avianbase: a community resource for bird genomics
- (2015) Lél Eöry et al. GENOME BIOLOGY
- Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
- (2015) Leif Andersson et al. GENOME BIOLOGY
- Non-coding RNA: what is functional and what is junk?
- (2015) Alexander F. Palazzo et al. Frontiers in Genetics
- Finding the missing honey bee genes: lessons learned from a genome upgrade
- (2014) Christine G Elsik et al. BMC GENOMICS
- Enhancer RNAs: the new molecules of transcription
- (2014) Fan Lai et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Regulation of Natural mRNAs by the Nonsense-Mediated mRNA Decay Pathway
- (2014) Megan Peccarelli et al. EUKARYOTIC CELL
- Widespread intron retention in mammals functionally tunes transcriptomes
- (2014) Ulrich Braunschweig et al. GENOME RESEARCH
- Progranulin Transcripts with Short and Long 5′ Untranslated Regions (UTRs) Are Differentially Expressed via Posttranscriptional and Translational Repression
- (2014) Anja Capell et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- A draft map of the human proteome
- (2014) Min-Sik Kim et al. NATURE
- A promoter-level mammalian expression atlas
- (2014) NATURE
- Genome-guided transcript assembly by integrative analysis of RNA sequence data
- (2014) Nathan Boley et al. NATURE BIOTECHNOLOGY
- Function-based identification of mammalian enhancers using site-specific integration
- (2014) Diane E Dickel et al. NATURE METHODS
- Proteogenomics: concepts, applications and computational strategies
- (2014) Alexey I Nesvizhskii NATURE METHODS
- Targeted sequencing for gene discovery and quantification using RNA CaptureSeq
- (2014) Tim R Mercer et al. Nature Protocols
- Ribosome profiling: new views of translation, from single codons to genome scale
- (2014) Nicholas T. Ingolia NATURE REVIEWS GENETICS
- CTCF: an architectural protein bridging genome topology and function
- (2014) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- Transcriptional enhancers: from properties to genome-wide predictions
- (2014) Daria Shlyueva et al. NATURE REVIEWS GENETICS
- Genenames.org: the HGNC resources in 2015
- (2014) Kristian A. Gray et al. NUCLEIC ACIDS RESEARCH
- lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
- (2014) Xiu Cheng Quek et al. NUCLEIC ACIDS RESEARCH
- VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases
- (2014) Gloria I. Giraldo-Calderón et al. NUCLEIC ACIDS RESEARCH
- RNAcentral: an international database of ncRNA sequences
- (2014) NUCLEIC ACIDS RESEARCH
- Rfam 12.0: updates to the RNA families database
- (2014) Eric P. Nawrocki et al. NUCLEIC ACIDS RESEARCH
- High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
- (2014) Hyunghoon Cho et al. PLoS One
- Comparative analysis of pseudogenes across three phyla
- (2014) Cristina Sisu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Impact of regulatory variation from RNA to protein
- (2014) A. Battle et al. SCIENCE
- Comparative genomics reveals insights into avian genome evolution and adaptation
- (2014) G. Zhang et al. SCIENCE
- Application of resequencing to rice genomics, functional genomics and evolutionary analysis
- (2014) Longbiao Guo et al. Rice
- Considerations when investigating lncRNA function in vivo
- (2014) Andrew R Bassett et al. eLife
- Major Histocompatibility Complex Genomics and Human Disease
- (2013) John Trowsdale et al. Annual Review of Genomics and Human Genetics
- Structural and functional annotation of the porcine immunome
- (2013) Harry D Dawson et al. BMC GENOMICS
- Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation
- (2013) Justin J.-L. Wong et al. CELL
- On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE
- (2013) D. Graur et al. Genome Biology and Evolution
- Functional transcriptomics in the post-ENCODE era
- (2013) J. M. Mudge et al. GENOME RESEARCH
- Tackling Structures of Long Noncoding RNAs
- (2013) Irina Novikova et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Assessment of transcript reconstruction methods for RNA-seq
- (2013) Tamara Steijger et al. NATURE METHODS
- Current status and new features of the Consensus Coding Sequence database
- (2013) Catherine M. Farrell et al. NUCLEIC ACIDS RESEARCH
- miRBase: annotating high confidence microRNAs using deep sequencing data
- (2013) Ana Kozomara et al. NUCLEIC ACIDS RESEARCH
- Gene Expression Regulation by Upstream Open Reading Frames and Human Disease
- (2013) Cristina Barbosa et al. PLoS Genetics
- Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs
- (2013) Matthew J. Hangauer et al. PLoS Genetics
- Web Apollo: a web-based genomic annotation editing platform
- (2013) Eduardo Lee et al. GENOME BIOLOGY
- Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
- (2013) Mar Gonzàlez-Porta et al. GENOME BIOLOGY
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements
- (2012) Lucy W. Barrett et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Function of alternative splicing
- (2012) Olga Kelemen et al. GENE
- High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- (2012) P. Batut et al. GENOME RESEARCH
- A quantitative atlas of polyadenylation in five mammals
- (2012) Adnan Derti et al. GENOME RESEARCH
- The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- (2012) T. Derrien et al. GENOME RESEARCH
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Hi–C: A comprehensive technique to capture the conformation of genomes
- (2012) Jon-Matthew Belton et al. METHODS
- Structural variation: the genome's hidden architecture
- (2012) Monya Baker NATURE METHODS
- A beginner's guide to eukaryotic genome annotation
- (2012) Mark Yandell et al. NATURE REVIEWS GENETICS
- Protein–RNA interactions: new genomic technologies and perspectives
- (2012) Julian König et al. NATURE REVIEWS GENETICS
- APPRIS: annotation of principal and alternative splice isoforms
- (2012) Jose Manuel Rodriguez et al. NUCLEIC ACIDS RESEARCH
- GenBank
- (2012) Dennis A. Benson et al. NUCLEIC ACIDS RESEARCH
- Community gene annotation in practice
- (2012) J. E. Loveland et al. Database-The Journal of Biological Databases and Curation
- Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
- (2012) Claudia Kutter et al. PLoS Genetics
- The GENCODE pseudogene resource
- (2012) Baikang Pei et al. GENOME BIOLOGY
- PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
- (2011) M. F. Lin et al. BIOINFORMATICS
- Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
- (2011) T. Carver et al. BIOINFORMATICS
- Synthetic spike-in standards for RNA-seq experiments
- (2011) L. Jiang et al. GENOME RESEARCH
- The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates
- (2011) J. M. Mudge et al. MOLECULAR BIOLOGY AND EVOLUTION
- Pig genome sequence - analysis and publication strategy
- (2010) Alan L Archibald et al. BMC GENOMICS
- Widespread transcription at neuronal activity-regulated enhancers
- (2010) Tae-Kyung Kim et al. NATURE
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Locus Reference Genomic sequences: an improved basis for describing human DNA variants
- (2010) Raymond Dalgleish et al. Genome Medicine
- Most “Dark Matter” Transcripts Are Associated With Known Genes
- (2010) Harm van Bakel et al. PLOS BIOLOGY
- Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
- (2010) Joseph K. Pickrell et al. PLoS Genetics
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- Genome-wide mapping of alternative splicing in Arabidopsis thaliana
- (2009) S. A. Filichkin et al. GENOME RESEARCH
- ChIP-based methods for the identification of long-range chromatin interactions
- (2009) Melissa J. Fullwood et al. JOURNAL OF CELLULAR BIOCHEMISTRY
- An oestrogen-receptor-α-bound human chromatin interactome
- (2009) Melissa J. Fullwood et al. NATURE
- Biogenesis of small RNAs in animals
- (2009) V. Narry Kim et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
- (2009) N. T. Ingolia et al. SCIENCE
- Using native and syntenically mapped cDNA alignments to improve de novo gene finding
- (2008) Mario Stanke et al. BIOINFORMATICS
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