Building a Chinese pan-genome of 486 individuals

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

Association of Rare PTGIS Variants With Susceptibility and Pulmonary Vascular Response in Patients With Idiopathic Pulmonary Arterial Hypertension

(2020) Xiao-Jian Wang et al.   JAMA Cardiology

Identifying centromeric satellites with dna-brnn

(2019) Heng Li   BIOINFORMATICS

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Towards pan-genome read alignment to improve variation calling

(2018) Daniel Valenzuela et al.   BMC GENOMICS

Characteristics of genomic alterations of lung adenocarcinoma in young never-smokers

(2018) Wenxin Luo et al.   INTERNATIONAL JOURNAL OF CANCER

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Germline BMP9 mutation causes idiopathic pulmonary arterial hypertension

(2018) Xiao-Jian Wang et al.   EUROPEAN RESPIRATORY JOURNAL

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Diversity in non-repetitive human sequences not found in the reference genome

(2017) Birte Kehr et al.   NATURE GENETICS

Deep whole-genome sequencing of 90 Han Chinese genomes

(2017) Tianming Lan et al.   GigaScience

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Novel CLCN7 mutation identified in a Han Chinese family with autosomal dominant osteopetrosis-2

(2016) Hao Deng et al.   Molecular Pain

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

RPAN: rice pan-genome browser for ∼3000 rice genomes

(2016) Chen Sun et al.   NUCLEIC ACIDS RESEARCH

An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

(2016) Yun Sung Cho et al.   Nature Communications

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

(2016) Jayne Y. Hehir-Kwa et al.   Nature Communications

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

PopIns: population-scale detection of novel sequence insertions

(2015) Birte Kehr et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Identification of a Novel Mutation in the Titin Gene in a Chinese Family with Limb-Girdle Muscular Dystrophy 2J

(2015) Wen Zheng et al.   MOLECULAR NEUROBIOLOGY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

The Genome of a Mongolian Individual Reveals the Genetic Imprints of Mongolians on Modern Human Populations

(2014) Haihua Bai et al.   Genome Biology and Evolution

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation

(2013) Emmanuel F Mongodin et al.   BMC GENOMICS

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Revising the human mutation rate: implications for understanding human evolution

(2012) Aylwyn Scally et al.   NATURE REVIEWS GENETICS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene

(2009) David Reich et al.   PLoS Genetics

Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress

(2008) Jie Yang et al.   PLoS One