4.6 Article

Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Review Plant Sciences

Progress, challenges and the future of crop genomes

Todd P. Michael et al.

CURRENT OPINION IN PLANT BIOLOGY (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Qun-Jie Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biotechnology & Applied Microbiology

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Joshua N. Burton et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemistry & Molecular Biology

The Pfam protein families database

Marco Punta et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

Adam C. English et al.

PLOS ONE (2012)

Article Biochemical Research Methods

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

Sante Gnerre et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Genome sequencing and analysis of the model grass Brachypodium distachyon

John P. Vogel et al.

NATURE (2010)

Editorial Material Multidisciplinary Sciences

Increased Food and Ecosystem Security via Perennial Grains

J. D. Glover et al.

SCIENCE (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

Regina S. Baucom et al.

GENOME RESEARCH (2009)

Article Biochemistry & Molecular Biology

genBlastA: Enabling BLAST to identify homologous gene sequences

Rong She et al.

GENOME RESEARCH (2009)

Editorial Material Multidisciplinary Sciences

Perspective - Synteny and collinearity in plant genomes

Haibao Tang et al.

SCIENCE (2008)

Article Biochemical Research Methods

Clustal W and clustal X version 2.0

M. A. Larkin et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biotechnology & Applied Microbiology

LTR retrotransposons in rice (Oryza sativa, L.):: recent burst amplifications followed by rapid DNA loss

Clementine Vitte et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Zhao Xu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

BIOINFORMATICS (2006)

Article Plant Sciences

Comparison of four nuclear isolation buffers for plant DNA flow cytometry

Joao Loureiro et al.

ANNALS OF BOTANY (2006)

Article Biochemical Research Methods

CAFE: a computational tool for the study of gene family evolution

T De Bie et al.

BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

The map-based sequence of the rice genome

T Matsumoto et al.

NATURE (2005)

Article Biochemical Research Methods

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

TD Wu et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

AUGUSTUS: a web server for gene finding in eukaryotes

M Stanke et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders

WH Majoros et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

GeneWise and genomewise

E Birney et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Biochemical Research Methods

LTR_STRUC: a novel search and identification program for LTR retrotransposons

EM McCarthy et al.

BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Automated de novo identification of repeat sequence families in sequenced genomes

ZR Bao et al.

GENOME RESEARCH (2002)

Review Multidisciplinary Sciences

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

S Kaul et al.

NATURE (2000)