Gateways to the FANTOM5 promoter level mammalian expression atlas

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

(2014) H. Kawaji et al.   GENOME RESEARCH

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

Preserving sequence annotations across reference sequences

(2014) Zuotian Tatum et al.   Journal of Biomedical Semantics

Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain

(2012) George P. Patrinos et al.   HUMAN MUTATION

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Toward interoperable bioscience data

(2012) Susanna-Assunta Sansone et al.   NATURE GENETICS

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

(2012) Hazuki Takahashi et al.   Nature Protocols

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery

(2012) Jun-ichi Takeda et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts

(2012) Takahiro Suzuki et al.   PLoS One

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer

(2012) Masayoshi Itoh et al.   PLoS One

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

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

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

The value of data

(2011) Barend Mons et al.   NATURE GENETICS

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

(2011) R. Yamashita et al.   NUCLEIC ACIDS RESEARCH

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

(2011) P. L. Whetzel et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

(2009) Hideya Kawaji et al.   BMC BIOINFORMATICS

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

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Gene Expression Atlas at the European Bioinformatics Institute

(2009) Misha Kapushesky et al.   NUCLEIC ACIDS RESEARCH

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji et al.   GENOME BIOLOGY

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

BodyParts3D: 3D structure database for anatomical concepts

(2008) N. Mitsuhashi et al.   NUCLEIC ACIDS RESEARCH