Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

(2013) J. H. Graber et al.   GENOME RESEARCH

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts

(2013) Z. Moqtaderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

(2012) J. E. Collins et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

(2012) H. Stroud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis

(2012) Yukio Kurihara et al.   G3-Genes Genomes Genetics

Zebrafish as a genomics model for human neurological and polygenic disorders

(2011) Thomas S. Becker et al.   Developmental Neurobiology

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

(2011) Cailin E. Joyce et al.   HUMAN MOLECULAR GENETICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Double-stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV-dependent siRNA levels in Arabidopsis

(2011) T. Pelissier et al.   RNA

Single-molecule direct RNA sequencing without cDNA synthesis

(2011) Fatih Ozsolak et al.   Wiley Interdisciplinary Reviews-RNA

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome reannotation of Escherichia coli CFT073 with new insights into virulence

(2009) Chengwei Luo et al.   BMC GENOMICS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

(2009) C. Cole et al.   RNA

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead 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