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 The following list is outdated.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)