The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani 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

Data use under the NIH GWAS Data Sharing Policy and future directions

(2014)   NATURE GENETICS

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

(2014) Scott Federhen et al.   Standards in Genomic Sciences

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

(2014) Toshiaki Katayama et al.   Journal of Biomedical Semantics

Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing

(2013) Koichiro Doi et al.   BIOINFORMATICS

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

(2013) H. Nagasaki et al.   DNA RESEARCH

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Assembly information services in the European Nucleotide Archive

(2013) Nima Pakseresht et al.   NUCLEIC ACIDS RESEARCH

DDBJ progress report: a new submission system for leading to a correct annotation

(2013) Takehide Kosuge et al.   NUCLEIC ACIDS RESEARCH

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

Identification and Characterization of Cancer Mutations in Japanese Lung Adenocarcinoma without Sequencing of Normal Tissue Counterparts

(2013) Ayako Suzuki et al.   PLoS One

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

DDBJ new system and service refactoring

(2012) Osamu Ogasawara et al.   NUCLEIC ACIDS RESEARCH

The International Nucleotide Sequence Database Collaboration

(2012) Y. Nakamura et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

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

Prepublication data sharing

(2009)   NATURE

Web API for biology with a workflow navigation system

(2009) Y. Kwon et al.   NUCLEIC ACIDS RESEARCH

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS