List of works - Heng Li

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A Draft Sequence of the Neandertal Genome

scientific article

A cross-species alignment tool (CAT)

scientific article

A direct characterization of human mutation based on microsatellites

scientific article (publication date: October 2012)

A draft human pangenome reference

scientific article published on 10 May 2023

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

scientific article

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

scientific article

A high-coverage genome sequence from an archaic Denisovan individual

scientific article

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data ⬇️

scientific article published on September 8, 2011

A survey of sequence alignment algorithms for next-generation sequencing

scientific article

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

scientific article published on 12 August 2019

Accurate whole human genome sequencing using reversible terminator chemistry

scientific article

Ancient human genomes suggest three ancestral populations for present-day Europeans

scientific article

BFC: correcting Illumina sequencing errors

scientific article published on 6 May 2015

BGT: efficient and flexible genotype query across many samples

scientific article

Chromosome-scale, haplotype-resolved assembly of human genomes

scientific article published on 07 December 2020

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth

scientific article

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

scientific article published on 13 October 2009

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

scientific article published on 3 June 2009

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

scientific article

Evolutionary transients in the rice transcriptome

scientific article published on December 2010

Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly ⬇️

scientific article published on May 7, 2012

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

scientific article published on 20 May 2012

Fast and accurate long-read alignment with Burrows-Wheeler transform

scientific article (publication date: March 2010)

Fast and accurate long-read assembly with wtdbg2

scientific article published on 09 December 2019

Fast and accurate short read alignment with Burrows-Wheeler transform

scientific article

Fast construction of FM-index for long sequence reads ⬇️

scientific article published on 8 August 2014

FermiKit: assembly-based variant calling for Illumina resequencing data

scientific article published on 27 July 2015

Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

scientific article published on 10 February 2004

Genetic history of an archaic hominin group from Denisova Cave in Siberia

scientific article

Genome sequence of a 45,000-year-old modern human from western Siberia

scientific article

Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups

scientific article

Haplotype-resolved assembly of diploid genomes without parental data

scientific article published in 2022

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

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

scientific article

Improving SNP discovery by base alignment quality ⬇️

scientific article published on February 13, 2011

Inference of human population history from individual whole-genome sequences ⬇️

scientific article (publication date: 13 July 2011)

Mapping short DNA sequencing reads and calling variants using mapping quality scores

scientific article

Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes

scientific article published on 08 August 2013

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

scientific article published on 19 March 2016

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

scientific article

Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis

article

PigGIS: Pig Genomic Informatics System

scientific article

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

scientific article

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology

scientific article

SOAPindel: efficient identification of indels from short paired reads

scientific article

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).

scientific article

Snap: an integrated SNP annotation platform

scientific article published on 29 November 2006

Tabix: fast retrieval of sequence features from generic TAB-delimited files

scientific article

Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome

article

The Genomes of Oryza sativa: a history of duplications

scientific article

The Sequence Alignment/Map format and SAMtools

scientific article (publication date: 15 August 2009)

The anatomy of successful computational biology software

scientific article

The complete genome sequence of a Neanderthal from the Altai Mountains

scientific article

The contribution of rare variation to prostate cancer heritability

scientific article

The date of interbreeding between Neandertals and modern humans

scientific article published in 2012

The design and construction of reference pangenome graphs with minigraph

scientific article published on 16 October 2020

The diploid genome sequence of an Asian individual

scientific article

The sequence and de novo assembly of the giant panda genome

scientific article

Three-dimensional genome structures of single diploid human cells

scientific article

Toward better understanding of artifacts in variant calling from high-coverage samples ⬇️

scientific article published on 27 June 2014

TreeFam: 2008 Update

scientific article

TreeFam: a curated database of phylogenetic trees of animal gene families

scientific article

Using population admixture to help complete maps of the human genome

scientific article published on 24 February 2013

Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans

article

pIRS: Profile-based Illumina pair-end reads simulator

scientific article

List of works by Heng Li

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

A Draft Sequence of the Neandertal Genome

A cross-species alignment tool (CAT)

A direct characterization of human mutation based on microsatellites

A draft human pangenome reference

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

A high-coverage genome sequence from an archaic Denisovan individual

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data ⬇️

A survey of sequence alignment algorithms for next-generation sequencing

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Accurate whole human genome sequencing using reversible terminator chemistry

Ancient human genomes suggest three ancestral populations for present-day Europeans

BFC: correcting Illumina sequencing errors

BGT: efficient and flexible genotype query across many samples

Chromosome-scale, haplotype-resolved assembly of human genomes

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Evolutionary transients in the rice transcriptome

Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly ⬇️

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

Fast and accurate long-read alignment with Burrows-Wheeler transform

Fast and accurate long-read assembly with wtdbg2

Fast and accurate short read alignment with Burrows-Wheeler transform

Fast construction of FM-index for long sequence reads ⬇️

FermiKit: assembly-based variant calling for Illumina resequencing data

Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Genome sequence of a 45,000-year-old modern human from western Siberia

Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups

Haplotype-resolved assembly of diploid genomes without parental data

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

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

Improving SNP discovery by base alignment quality ⬇️

Inference of human population history from individual whole-genome sequences ⬇️

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis

PigGIS: Pig Genomic Informatics System

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology

SOAPindel: efficient identification of indels from short paired reads

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).

Snap: an integrated SNP annotation platform

Tabix: fast retrieval of sequence features from generic TAB-delimited files

Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome

The Genomes of Oryza sativa: a history of duplications

The Sequence Alignment/Map format and SAMtools

The anatomy of successful computational biology software

The complete genome sequence of a Neanderthal from the Altai Mountains

The contribution of rare variation to prostate cancer heritability

The date of interbreeding between Neandertals and modern humans

The design and construction of reference pangenome graphs with minigraph

The diploid genome sequence of an Asian individual

The sequence and de novo assembly of the giant panda genome

Three-dimensional genome structures of single diploid human cells

Toward better understanding of artifacts in variant calling from high-coverage samples ⬇️

TreeFam: 2008 Update

TreeFam: a curated database of phylogenetic trees of animal gene families

Using population admixture to help complete maps of the human genome

Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans

pIRS: Profile-based Illumina pair-end reads simulator