About me
My name is Heng Li, a research scientist at the Broad Institute, working with David Reich and David Altshuler. My current interests include the analysis of new sequencing data, population genetics and phylogenetics. I am the principal developer of several projects including SAMtools, BWA, MAQ, TreeSoft and TreeFam with most of them started when I was a postdoctoral fellow of Richard Durbin at the Wellcome Trust Sanger Institute. I was also involved in several projects when I was in BGI (Beijing Genomics Institute, Chinese Academy of Science) between 2002 and 2006. These projects include rice finishing, silkworm sequencing, chicken variation study, heterozygote detection for capillary reads, gene finding and CAT alignment software.
At the time I am writing this page my wife, my little daughter and I
are living in Boston, United States. Our motherland is China,
forever.
Selected Publications
- Li H. and Durbin R. (2010) Fast and accurate long read alignment with Burrows-Wheeler Transform. Bioinformatics, 26:589-95. [PMID: 20080505]
- Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25:2078-9. [PMID: 19505943]
- Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
- Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P.,
Milton J., Brown C.G., Hall K.P., Evers D.J., Barnes C.L., et
al. (2008) Accurate whole human genome sequencing using reversible
terminator
chemistry. Nature, 456:53-9. [PMID: 18987734]
- Li H., Ruan J. and Durbin R. (2008) Mapping short DNA
sequencing reads and calling variants using mapping quality
scores. Genome
Res., 18:1851-8. [PMID: 18714091]
- Ruan J.*, Li H.*, Chen Z., Coghlan A., Coin L.J., Guo Y., Hériché J.K., Hu Y., Kristiansen K., Li R., et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36:D735-40. [PMID: 18056084]
- Li H., Liu J.*, Xu Z*., Jin J., Fang L., Gao L., Li Y., Xing Z., Gao S., Liu T., et al. (2005) Test data sets and evaluation of gene prediction programs on the rice genome. J Comput Sci & Technol, 20:446-53. [SpringerLink]
- Yu J.*, Wang J.*, Lin W.*, Li S.*, Li, H.*, Zhou J.*, Ni P.*, Dong W., Hu S., Zeng C., et al. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol., 3:e25. [PMID: 15685292]