Publications

I have moved the list of journal papers here. The following list is outdated.

Li H. Tabix: Fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, accepted.
1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature, 467:1061-73. [PMID: 20981092]
Li H. and Homer N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform, 11:473-83. [PMID: 20460430]
Green R.E., Krause J., Briggs A.W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M.H. et al. (2010) A draft sequence of the Neandertal genome. Science, 328:680-4. [PMID: 20448178]
Li H. and Durbin R. (2010) Fast and accurate long read alignment with Burrows-Wheeler Transform. Bioinformatics, 26:589-95. [PMID: 20080505]
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z et al. (2009) The sequence and de novo assembly of the giant panda genome. Nature, 463:311-7. [PMID: 20010809]
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]
Holt K.E., Teo Y.Y., Li H., Nair S., Dougan G., Wain J. and Parkhill J. (2009) Detecting SNPs and estimating allele frequency in clonal bacterial populations by sequencing pooled DNA. Bioinformatics, 25:2074-5. [PMID: 19497932]
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
Vilella A.J., Severin J., Ureta-Vidal A., Li H., Durbin R. and Birney E. (2009) EnsemblCompara GeneTrees: complete, duplication aware phylogenetic trees in vertebrates. Genome Res., 19:327-35. [PMID: 19029536]
Li J., Gromov P., Gromova I., Moreira J.M., Timmermans-Wielenga V., Rank F., Wang K., Li S., Li H., Wiuf C., Yang H., et al. (2008) Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics, 8:5038-52. [PMID: 19003862]
Wang J.*, Wang W.*, Li R.*, Li Y.*, Tian G., Goodman L., Fan W., Zhang J., Li J., Zhang J., et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456:60-5. [PMID: 18987735]
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]
Down T.a.*, Rakyan V.K.*, Turner D.J., Flicek P., Li H., Thorne N.P., Kulesha E., Gräf S., Tomazou E.M., Bäckdahl L., ..., Tavaré S. and Beck S. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylation analysis. Nat. Biotech., 26:779-85 [PMID: 18612301]
Campbell P.J.*, Stephens P.*, Pleasance E.D.*, O'Meara S., Li H., Santarius T., Stebbings L.A., Leroy C., Edkins S., Hardy C., ..., Stratton M.R. and Futreal P.A. (2008) Identification of somatically acquired rearrangement in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet., 40:722-9 [PMID: 18438408]
Ruan J.*, Li H.*, Chen Z., Coghlan A., Coin L.J., Guo Y., H ériché J.K., Hu Y., Kristiansen K., Li R., ..., Bolund L., Wang J. and Durbin R. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36:D735-40. [PMID: 18056084]
Li H.*, Guan L.*, Liu T.*, Guo Y.*, Zheng W., Wong G. and Wang J. (2007) A cross-species alignment tool (CAT). BMC Bioinformatics, 8:439. [PMID: 17880681]
Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M. J., Panitz, F., Jorgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., ... and Fredholm, M. (2007) Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol., 8:R45. [PMID: 17407547]
Li S.*, Ma L.*, Li H.*, Vang S., Hu Y., Bolund L. and Wang J. (2007) Snap: an integrated SNP annotation platform. Nucleic Acids Res., 35:D707-10. [PMID: 17135198]
Ruan J.*, Guo Y.*, Li H.*, Hu Y., Song F., Huang X., Kristiensen K., Bolund L. and Wang J. (2007) PigGIS: Pig Genomic Informatics System. Nucleic Acids Res., 35:D654-7. [PMID: 17090590]
Li H.*, Coghlan A.*, Ruan J.*, Coin L.J., Hériché J.K., Osmotherly L., Li R., Liu T., Zhang Z., Bolund L., ..., Wang J. and Durbin R. (2006) Treefam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res., 34:D572-80. [PMID: 16381935]
Yu J.*, Wang J.*, Lin W.*, Li S.*, Li, H.*, Zhou J.*, Ni P.*, Dong W., Hu S., Zeng C., ..., Wang J., Wong G. and Yang H. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 3:e25. [PMID: 15685292]
Li H., Liu J.*, Xu Z*., Jin J., Fang L., Gao L., Li Y., Xing Z., Gao S., Liu T., ..., Xie H., Zheng W. and Hao B. (2005) Test data sets and evaluation of gene prediction programs on the rice genome. J Comput Sci & Technol, 20:446-53. [SpringerLink]
Wong G., Liu B., Wang J., Zhang Y., Yang X., Zhang Z., Meng Q., Zhou J., Li D., Zhang J., ..., Yu J., Wang J. and Yang H. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature, 432:717-22. [PMID: 15592405]
Xia Q., Zhou Z., Lu C., Cheng D., Dai F., Li B., Zhao P., Zha X., Cheng T., Chai C., ..., Wang J., Wong G. and Yang H. (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 306:1937-40. [PMID: 15591204]
Wang J., Zhang J., Zheng H., Li J., Liu D., Li H., Samudrala R., Yu J. and Wong G. (2004) Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature, 431. (Comments) [PMID: 15495343]
Li C., Ni P., Francki M., Hunter A., Zhang Y., Schibeci D., Li H., Tarr A., Wang J., Cakir M., ... and Appels,R. (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Funct Integr Genomics, 4:84-93. [PMID: 14770301]

Thesis

Li H. (2006) Constructing the TreeFam database. PhD thesis, the Institute of Theoretical Physics, Chinese Academy of Science. [PDF in English or in Chinese]

Presentations

Challenges and Solutions in the Analysis of Next Generation Sequence Data. 2nd CHOP/PENN NGS Symposium. The Abramson Research Center, Philadelphia, US. (Keynote; slides)
Aligning new-sequencing reads with BWA. Next-Generation Sequencing Workshop. Broad Institute, Boston, US. (Talk; slides and videos available here)
Quest for standard -- Sequence Alignment/Map format. GMOD Aug2009 meeting. Oxford university, UK. (Talk; slides available here)
Towards accurate gene trees. Workshop on Quest of Orthologs. European Bioinformatics Institute (EBI), UK, 2009-07-04. (Talk)
Short-read Alignment with MAQ and BWA. Workshop on short read informatics. European Bioinformatics Institute (EBI), UK, 2009-05-01. (slides)
SAMTools: Generic Utilities for Alignments. Workshop on next generation sequencing. European Bioinformatics Institute (EBI), UK, 2008-12-19. (Talk)
MAQ: Mapping and Assembly with Qualities. Conference on the Biology of Genomes. Cold Spring Harbor Laboratory, US, 2008-05-08. (poster)
Inference of human population history from the whole genome sequence of a single individual. Conference on the Biology of Genomes. Cold Spring Harbor Laboratory, US, 2008-05-08. (Talk)
Read mapping. Meeting on 1000 Genomes Project. Cold Spring Harbor Laboratory, US, 2008-05-06. (5-min informal talk. Part of slides)
Modeling gene trees with Context-Free Grammar. Workshop on Current Challenges & Problems in Phylogenetics. Issac Newton Institute, Cambridge UK, 2007-09-03. (Slides and video can be found here for the time being)