A Quick Guide to Large-Scale Genomic Data Mining

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction

(2009) Curtis Huttenhower et al.   BIOINFORMATICS

Unifying biological image formats with HDF5

(2009) Matthew T. Dougherty et al.   COMMUNICATIONS OF THE ACM

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory

(2009) M. D. Brazas et al.   NUCLEIC ACIDS RESEARCH

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Web services at the European Bioinformatics Institute-2009

(2009) H. Mcwilliam et al.   NUCLEIC ACIDS RESEARCH

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

(2009) Guy R. Cochrane et al.   NUCLEIC ACIDS RESEARCH

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Atlas at the European Bioinformatics Institute

(2009) Misha Kapushesky et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Data reporting standards: making the things we use better

(2009) John Quackenbush   Genome Medicine

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB

(2008) T. F. Rayner et al.   BIOINFORMATICS

Integrating biological data – the Distributed Annotation System

(2008) Andrew M Jenkinson et al.   BMC BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Interoperability with Moby 1.0--It's better than sharing your toothbrush!

(2008)   BRIEFINGS IN BIOINFORMATICS

Experience using web services for biological sequence analysis

(2008) H. Stockinger et al.   BRIEFINGS IN BIOINFORMATICS

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

(2008) S. Kumar et al.   BRIEFINGS IN BIOINFORMATICS

Network integration and graph analysis in mammalian molecular systems biology

(2008) A. Ma'ayan   IET Systems Biology

International genome project launched

(2008) Erika Check Hayden   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services—an example with ChIP-chip data

(2008) Olivier Sand et al.   Nature Protocols

ENDEAVOUR update: a web resource for gene prioritization in multiple species

(2008) L.-C. Tranchevent et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

(2008) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Getting Started in Biological Pathway Construction and Analysis

(2008) Ganesh A Viswanathan et al.   PLoS Computational Biology

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS