Chromosome‐level genome assembly of Triplophysa tibetana , a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Centromere evolution and CpG methylation during vertebrate speciation

(2017) Kazuki Ichikawa et al.   Nature Communications

Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments

(2016) Qian Zhang et al.   Genome Biology and Evolution

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

(2016) Olivier Rey et al.   TRENDS IN ECOLOGY & EVOLUTION

The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

(2016) Qin Qiao et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds

(2015) Jung-Woo Choi et al.   DNA RESEARCH

Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes

(2015) Ying Wang et al.   Genome Biology and Evolution

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

Genetic Convergence in the Adaptation of Dogs and Humans to the High-Altitude Environment of the Tibetan Plateau

(2014) Guo-Dong Wang et al.   Genome Biology and Evolution

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

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

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

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

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

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau

(2013) Yanhua Qu et al.   Nature Communications

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

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

(2012) Adam C. English et al.   PLoS One

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE