The sequence and de novo assembly of Oxygymnocypris stewartii genome

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A new partnership for an impactful future

(2016) Weimin Zhong et al.   Science China-Life Sciences

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

(2015) Yaping Wang et al.   NATURE GENETICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Polyphyletic origins of schizothoracine fish (Cyprinidae, Osteichthyes) and adaptive evolution in their mitochondrial genomes

(2015) Takahiro Yonezawa et al.   GENES & GENETIC SYSTEMS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Tectonic evolution of the Qinghai-Tibet Plateau

(2012) Guitang Pan et al.   JOURNAL OF ASIAN EARTH SCIENCES

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Threatened fishes of the world: Oxygymnocypris stewartii (Lloyd 1908) (Cyprinidae)

(2009) De-Lin Qi et al.   ENVIRONMENTAL BIOLOGY OF FISHES

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Rapidly evolving fish genomes and teleost diversity

(2008) Vydianathan Ravi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY