NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

(2014) H. Kawaji et al.   GENOME RESEARCH

Paired-End Analysis of Transcription Start Sites inArabidopsisReveals Plant-Specific Promoter Signatures

(2014) Taj Morton et al.   PLANT CELL

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

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

(2012) P. Batut et al.   GENOME RESEARCH

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

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies

(2010) Matthew S. Hestand et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A transcription factor affinity-based code for mammalian transcription initiation

(2009) M. Megraw et al.   GENOME RESEARCH

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

(2009) Yoshiharu Y. Yamamoto et al.   PLANT JOURNAL