相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads
Wei Li et al.
PLANT GENOME (2020)
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Joshua C. Stein et al.
NATURE GENETICS (2018)
Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice
Qiang Zhao et al.
NATURE GENETICS (2018)
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution
Zhigang Wu et al.
COMMUNICATIONS BIOLOGY (2018)
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
Minoru Kanehisa et al.
JOURNAL OF MOLECULAR BIOLOGY (2016)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication
Muhua Wang et al.
NATURE GENETICS (2014)
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)
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Joshua N. Burton et al.
NATURE BIOTECHNOLOGY (2013)
Genome Size Variation among and within Camellia Species by Using Flow Cytometric Analysis
Hui Huang et al.
PLOS ONE (2013)
Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution
Jinfeng Chen et al.
NATURE COMMUNICATIONS (2013)
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Yoshihiro Kawahara et al.
RICE (2013)
Hi-C: A comprehensive technique to capture the conformation of genomes
Jon-Matthew Belton et al.
METHODS (2012)
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Ruibang Luo et al.
GIGASCIENCE (2012)
Scaffolding pre-assembled contigs using SSPACE
Marten Boetzer et al.
BIOINFORMATICS (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
Carlos Llorens et al.
NUCLEIC ACIDS RESEARCH (2011)
miRBase: integrating microRNA annotation and deep-sequencing data
Ana Kozomara et al.
NUCLEIC ACIDS RESEARCH (2011)
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)
Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments
Liang Tang et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2010)
agriGO: a GO analysis toolkit for the agricultural community
Zhou Du et al.
NUCLEIC ACIDS RESEARCH (2010)
Infernal 1.0: inference of RNA alignments
Eric P. Nawrocki et al.
BIOINFORMATICS (2009)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
genBlastA: Enabling BLAST to identify homologous gene sequences
Rong She et al.
GENOME RESEARCH (2009)
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable et al.
SCIENCE (2009)
Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
Brian J. Haas et al.
GENOME BIOLOGY (2008)
The Pfam protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2008)
Clustal W and clustal X version 2.0
M. A. Larkin et al.
BIOINFORMATICS (2007)
RNAmmer:: consistent and rapid annotation of ribosomal RNA genes
Karin Lagesen et al.
NUCLEIC ACIDS RESEARCH (2007)
Doubling genome size without polyploidization:: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
Benoit Piegu et al.
GENOME RESEARCH (2006)
Comparison of four nuclear isolation buffers for plant DNA flow cytometry
Joao Loureiro et al.
ANNALS OF BOTANY (2006)
AUGUSTUS:: ab initio prediction of alternative transcripts
Mario Stanke et al.
NUCLEIC ACIDS RESEARCH (2006)
Advances in the study of systematics and evolution of the tribe Oryzeae (Poaceae)
YL Guo et al.
ACTA PHYTOTAXONOMICA SINICA (2006)
The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
JSS Ammiraju et al.
GENOME RESEARCH (2006)
The map-based sequence of the rice genome
T Matsumoto et al.
NATURE (2005)
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
M Stanke et al.
NUCLEIC ACIDS RESEARCH (2005)
De novo identification of repeat families in large genomes
AL Price et al.
BIOINFORMATICS (2005)
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
TD Wu et al.
BIOINFORMATICS (2005)
Automated generation of heuristics for biological sequence comparison
GS Slater et al.
BMC BIOINFORMATICS (2005)
Repbase update, a database of eukaryotic repetitive elements
J Jurka et al.
CYTOGENETIC AND GENOME RESEARCH (2005)
Rfam: annotating non-coding RNAs in complete genomes
S Griffiths-Jones et al.
NUCLEIC ACIDS RESEARCH (2005)
AUGUSTUS: a web server for gene finding in eukaryotes
M Stanke et al.
NUCLEIC ACIDS RESEARCH (2004)
GeneWise and genomewise
E Birney et al.
GENOME RESEARCH (2004)
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
BJ Haas et al.
NUCLEIC ACIDS RESEARCH (2003)
LTR_STRUC: a novel search and identification program for LTR retrotransposons
EM McCarthy et al.
BIOINFORMATICS (2003)
Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
T Thiel et al.
THEORETICAL AND APPLIED GENETICS (2003)
Automated de novo identification of repeat sequence families in sequenced genomes
ZR Bao et al.
GENOME RESEARCH (2002)
A draft sequence of the rice genome (Oryza sativa L. ssp japonica)
SA Goff et al.
SCIENCE (2002)
Low levels of genetic diversity within populations and high differentiation among populations of a wild rice, Oryza granulata Nees et Arn. ex Watt., from China
LZ Gao et al.
INTERNATIONAL JOURNAL OF PLANT SCIENCES (2000)
Using GeneWise in the Drosophila annotation experiment
E Birney et al.
GENOME RESEARCH (2000)