Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

(2020) Qun-Jie Zhang et al.   Molecular Plant

A platinum standard pan-genome resource that represents the population structure of Asian rice

(2020) Yong Zhou et al.   Scientific Data

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

(2020) Julian Catchen et al.   G3-Genes Genomes Genetics

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis

(2019) Jin Liu et al.   Molecular Plant

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Retrotranspositional landscape of Asian rice revealed by 3000 genomes

(2018) Marie-Christine Carpentier et al.   Nature Communications

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

(2016) X. Lan et al.   SCIENCE

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

(2015) Dario Copetti et al.   BMC GENOMICS

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Rice blast resistance gene Pikahei-1(t), a member of a resistance gene cluster on chromosome 4, encodes a nucleotide-binding site and leucine-rich repeat protein

(2014) Xin Xu et al.   MOLECULAR BREEDING

Rice by the numbers: A good grain

(2014) Emily Elert   NATURE

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

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

(2012) Hongjian Wan et al.   BMC GENOMICS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Cytokinin Activity of cis-Zeatin and Phenotypic Alterations Induced by Overexpression of Putative cis-Zeatin-O-glucosyltransferase in Rice

(2012) T. Kudo et al.   PLANT PHYSIOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Recent advances in rice blast effector research

(2010) Barbara Valent et al.   CURRENT OPINION IN PLANT BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Refunctionalization of the ancient rice blast disease resistance genePitby the recruitment of a retrotransposon as a promoter

(2008) Keiko Hayashi et al.   PLANT JOURNAL

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

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

(2008) Brian J Haas et al.   GENOME BIOLOGY