A beginner's guide to eukaryotic genome annotation

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming

(2011) Sanne Nygaard et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

(2011) C. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNA in genome regulation

(2011) Tiffany Hung et al.   RNA Biology

Solving the Problem: Genome Annotation Standards before the Data Deluge

(2011) William Klimke et al.   Standards in Genomic Sciences

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

(2011) Garret Suen et al.   PLoS Genetics

A vertebrate case study of the quality of assemblies derived from next-generation sequences

(2011) Liang Ye et al.   GENOME BIOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Long non-coding RNAs: Guardians of development

(2010) Selina van Leeuwen et al.   DIFFERENTIATION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

(2010) M. C. Munoz-Torres et al.   NUCLEIC ACIDS RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

(2010) James Rodney Brister et al.   Viruses-Basel

Meeting report: a workshop on Best Practices in Genome Annotation

(2010) R. Madupu et al.   Database-The Journal of Biological Databases and Curation

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Alu repeats increase local recombination rates

(2009) David J Witherspoon et al.   BMC GENOMICS

mGene: Accurate SVM-based gene finding with an application to nematode genomes

(2009) G. Schweikert et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction

(2008) Qian Liu et al.   BIOINFORMATICS

Splign: algorithms for computing spliced alignments with identification of paralogs

(2008) Yuri Kapustin et al.   Biology Direct

nGASP - the nematode genome annotation assessment project

(2008) Avril Coghlan et al.   BMC BIOINFORMATICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

(2008) Nicolas Buisine et al.   GENOMICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

VectorBase: a data resource for invertebrate vector genomics

(2008) D. Lawson et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY