TreeFam: a curated database of phylogenetic trees of animal gene families. - Heng Li 002; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-Karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang 002; Lars Bolund; Gane Ka-Shu Wong; Wei-Mou Zheng; et al. (Nucleic Acids Res., 2006)

A cross-species alignment tool (CAT). - Heng Li 002; Liang Guan; Tao Liu; Yiran Guo; Wei-Mou Zheng; Gane Ka-Shu Wong; Jun Wang 004 (BMC Bioinform., 2007)

Snap: an integrated SNP annotation platform. - Shengting Li; Lijia Ma; Heng Li 002; Søren Vang; Yafeng Hu; Lars Bolund; Jun Wang 004 (Nucleic Acids Res., 2007)

PigGIS: Pig Genomic Informatics System. - Jue Ruan; Yiran Guo; Heng Li 002; Yafeng Hu; Fei Song; Xin Huang; Karsten Kristiansen; Lars Bolund; Jun Wang 004 (Nucleic Acids Res., 2007)

TreeFam: 2008 Update. - Jue Ruan; Heng Li 002; Zhongzhong Chen; Avril Coghlan; Lachlan James M. Coin; Yiran Guo; Jean-Karim Hériché; Yafeng Hu; Karsten Kristiansen; Ruiqiang Li; Tao Liu; Alan Moses; et al. (Nucleic Acids Res., 2008)

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. - Kathryn E. Holt; Yik Y. Teo; Heng Li 002; Satheesh Nair; Gordon Dougan; John Wain; Julian Parkhill (Bioinform., 2009)

Fast and accurate short read alignment with Burrows-Wheeler transform. - Heng Li 002; Richard Durbin (Bioinform., 2009)

The Sequence Alignment/Map format and SAMtools. - Heng Li 002; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor T. Marth; Gonçalo R. Abecasis; Richard Durbin (Bioinform., 2009)

A survey of sequence alignment algorithms for next-generation sequencing. - Heng Li 002; Nils Homer (Briefings Bioinform., 2010)

Fast and accurate long-read alignment with Burrows-Wheeler transform. - Heng Li 002; Richard Durbin (Bioinform., 2010)

Evolutionary Transients in the Rice Transcriptome. - Jun Wang 004; Jianguo Zhang; Ruiqiang Li; Hongkun Zheng; Jun Li 051; Yong Zhang 036; Heng Li 002; Peixiang Ni; Songgang Li; Shengting Li; Jingqiang Wang; Dongyuan Liu; et al. (Genom. Proteom. Bioinform., 2010)

Tabix: fast retrieval of sequence features from generic TAB-delimited files. - Heng Li 002 (Bioinform., 2011)

Improving SNP discovery by base alignment quality. - Heng Li 002 (Bioinform., 2011)

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. - Heng Li 002 (Bioinform., 2011)

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. - Heng Li 002 (Bioinform., 2012)

Toward better understanding of artifacts in variant calling from high-coverage samples. - Heng Li 002 (Bioinform., 2014)

Fast construction of FM-index for long sequence reads. - Heng Li 002 (Bioinform., 2014)

BFC: correcting Illumina sequencing errors. - Heng Li 002 (Bioinform., 2015)

FermiKit: assembly-based variant calling for Illumina resequencing data. - Heng Li 002 (Bioinform., 2015)

BGT: efficient and flexible genotype query across many samples. - Heng Li 002 (Bioinform., 2016)

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. - Heng Li 002 (Bioinform., 2016)

Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. - Md. Vasimuddin; Sanchit Misra; Heng Li 002; Srinivas Aluru (IPDPS, 2019)

Identifying centromeric satellites with dna-brnn. - Heng Li 002 (Bioinform., 2019)

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. - Shilpa Garg; John Aach; Heng Li 002; Isaac Sebenius; Richard Durbin; George M. Church (Bioinform., 2020)

New strategies to improve minimap2 alignment accuracy. - Heng Li 002 (Bioinform., 2021)

Bedtk: finding interval overlap with implicit interval tree. - Heng Li 002; Jiazhen Rong (Bioinform., 2021)

Real-time mapping of nanopore raw signals. - Haowen Zhang; Haoran Li; Chirag Jain; Haoyu Cheng; Kin Fai Au; Heng Li 002; Srinivas Aluru (Bioinform., 2021)