The state of play in higher eukaryote gene annotation

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

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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