Genomic divergence of Stellera chamaejasme through local selection across the Qinghai–Tibet plateau and northern China

Expansion of Cyclophyllidea Biodiversity in Rodents of Qinghai-Tibet Plateau and the “Out of Qinghai-Tibet Plateau” Hypothesis of Cyclophyllideans

(2022) Yao-Dong Wu et al.   Frontiers in Microbiology

Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis

(2021) Satoshi Kidokoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Study on life histroy traits of Stellera chamaejasme provide insights into its control on degraded typical steppe

(2021) Lizhu Guo et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Evolutionary origin of species diversity on the Qinghai‐Tibet Plateau

(2021) Kangshan Mao et al.   Journal of Systematics and Evolution

Genome‐wide analysis of butterfly bush ( Buddleja alternifolia ) in three uplands provides insights into biogeography, demography and speciation

(2021) Yong‐Peng Ma et al.   NEW PHYTOLOGIST

Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation

(2021) Quanjun Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

(2020) Xupo Ding et al.   GigaScience

Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)

(2020) Xu Zhang et al.   NEW PHYTOLOGIST

Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau

(2020) Meiling Song et al.   PeerJ

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

OUP accepted manuscript

(2018)   National Science Review

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

(2017) Fan Han et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

(2017) Tao Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era

(2016) Feng Gao et al.   G3-Genes Genomes Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

Genetic diversity of the weed species,Stellera chamaejasme, in China inferred from amplified fragment length polymorphism analysis

(2015) Yong-Hong Zhang et al.   WEED BIOLOGY AND MANAGEMENT

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

(2013) Sebastien Renaut et al.   MOLECULAR ECOLOGY

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The reproductive biology of Stellera chamaejasme (Thymelaeaceae): A self-incompatible weed with specialized flowers

(2011) Zhi-Qiang Zhang et al.   FLORA

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2010) A. McKenna et al.   GENOME RESEARCH

Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions

(2010) Yong-Hong Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

A Polyadenylation Factor Subunit Implicated in Regulating Oxidative Signaling in Arabidopsis thaliana

(2008) Jingxian Zhang et al.   PLoS One