Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

(2016) Alan Derr et al.   GENOME RESEARCH

The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing

(2015) O. Bartok et al.   EMBO JOURNAL

Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis

(2015) D.-P. Lai et al.   HUMAN MOLECULAR GENETICS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

(2015) Eleonora de Klerk et al.   TRENDS IN GENETICS

Differentiation of Human Parthenogenetic Pluripotent Stem Cells Reveals Multiple Tissue- and Isoform-Specific Imprinted Transcripts

(2015) Yonatan Stelzer et al.   Cell Reports

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes

(2014) G. Ji et al.   BRIEFINGS IN BIOINFORMATICS

High-resolution mapping defines the cooperative architecture of Polycomb response elements

(2014) G. A. Orsi et al.   GENOME RESEARCH

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Genome-guided transcript assembly by integrative analysis of RNA sequence data

(2014) Nathan Boley et al.   NATURE BIOTECHNOLOGY

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites

(2014) Kyoko Matsumoto et al.   NUCLEIC ACIDS RESEARCH

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Transcription Factor Networks in Drosophila melanogaster

(2014) David Y. Rhee et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier

(2013) Sarah Sheppard et al.   BIOINFORMATICS

Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

(2013) B Gurudatta et al.   CELL CYCLE

The Drosophila Transcription Factor Adf-1 (nalyot) Regulates Dendrite Growth by Controlling FasII and Staufen Expression Downstream of CaMKII and Neural Activity

(2013) C. Timmerman et al.   JOURNAL OF NEUROSCIENCE

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS 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

Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs

(2013) O. Bartok et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

(2012) Simon Haenni et al.   NUCLEIC ACIDS RESEARCH

Genome-wide alternative polyadenylation in animals: insights from high-throughput technologies

(2012) Y. Sun et al.   Journal of Molecular Cell Biology

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing

(2011) Y. Fu et al.   GENOME RESEARCH

Temperature Entrainment of the Circadian Cuticle Deposition Rhythm in Drosophila melanogaster

(2011) Chihiro Ito et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

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

(2010) Fatih Ozsolak et al.   CELL

A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence

(2010) Nuno Miguel Nunes et al.   EMBO JOURNAL

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes

(2009) Takashi Tadokoro et al.   FEBS Journal

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

(2009) Elizabeth A Rach et al.   GENOME BIOLOGY

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

The DRE/DREF transcriptional regulatory system: a master key for cell proliferation

(2007) A MATSUKAGE et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms