Monitoring transcription initiation activities in rat and dog

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

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The frequent evolutionary birth and death of functional promoters in mouse and human

(2015) Robert S. Young et al.   GENOME RESEARCH

Paradigm shifts in genomics through the FANTOM projects

(2015) Michiel de Hoon et al.   MAMMALIAN GENOME

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

(2015) Xingquan Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

EpiFactors: a comprehensive database of human epigenetic factors and complexes

(2015) Yulia A. Medvedeva et al.   Database-The Journal of Biological Databases and Curation

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

(2014) Jessica Severin et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS