Li Lab:Publications

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Peer Reviewed Publications

($ Selected Publications; ^ (Co-)first authors; * (Co-)corresponding authors; H-index = 21)

In preparation

1. Li W^, Liu XS, Struhl K and Wade JT: Distinguishing function from noise: identification of functional protein-DNA interactions from genome-wide binding profiles. Submitted.
   
   2011
   
   
2. Xi Y, Yao J, Chen R*, Li W*, He X*: Nucleosome fragility marks novel functional states of nucleosomes throughout the yeast genome.
   $ Genome Res (2011). Accepted.
   
   
3. Klisch T^, Xi Y^, Flora A, Wang L, Li W*, Zoghbi H*: The Atoh1 in vivo targetome: a new approach to neurodevelopmental studies.
   $ PNAS (2011). Accepted
   
   
4. Daines B^, Wang H^, Wang L^, Li Y, Emmert D, Gelbart W, Li W, Gibbs R, Chen RA: The Drosophila melanogaster Transcriptome by Paired-End RNA-Sequencing.
   $ Genome Res (2011).
   
   
5. Chen Y, Meyer CA, Liu T, Taing L, Li W, Liu JS, Liu XS: MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip/seq data.
   Genome Biology (2011). Accepted.
   
   2010
   
   
6. Wang L, Xi Y, Yu J, Dong L, Yen L, Li W*: A Statistical Method for the Detection of Alternative Splicing using RNA-seq.
   $ PLoS ONE 5 (2010) e8529.Full Article; Highlighted in This Week in PLoS in GenomeWeb.com
   
   
7. Chen Z^, Wang L^, Wang Q*, Li W*: Histone modifications and chromatin organization in prostate cancer (Invited Review).
   $ Epigenomics 2 (2010) 551-560. Full Article
   
   
8. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF: Sequencing-Based Sequence-based profiling of DNA methylation: comparisons of methods and catalogue of allelic epigenetic modifications.
   $ Nature Biotechnology 28 (2010) 1097-1105.
   
   
9. Lanz RB, Bulynko Y, Malovannaya A, Labhart P, Wang L, Li W, Qin J, Harper M, O'Malley BW: Global Characterization of Transcriptional Impact of the SRC-3 Coregulator.
   Mol Endocrinol 24 (2010) 859-872.
   
   
10. Kim BJ, Li Y, Zhang J, Xi Y, Yang T, Jung SY, Pan X, Chen R, Li W, Wang Y, Qin J: Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells.
    J Biol Chem 285 (2010) 22784-22792.
    
    
11. Wang M, Song X, Han P, Li W, Jiang B: Couplet- syntax: an improved syntax to represent pre-miRNA’s local continuous structure-sequence information.
    Journal of Theoretical Biology. 264 (2010) 578-584.
    
    2009
    
    
12. Xi Y, Li W*: BSMAP: whole genome Bisulfite Sequence MAPping program.
    $ BMC Bioinformatics (2009) 10:232.Full Article; BioMed Central Highly Accessed
    
    
13. Wang Q^, Li W^, Zhang Y, Yuan X, ..., Kantoff PW, Liu XS*, Brown M*: Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer.
    $ Cell 138 (2009) 245-256 Full Article; Faculty of 1000 Must Read; Prostate-cancer Research Highlights in Nature Review Cancer ; Spotlight in ACS Chem. Biol
    
    
14. Huang J, Chen T, Liu X, Jiang J, Li J, Li D, Liu XS, Li W, Kang J, Pei G: More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells.
    Cell Res (2009)
    
    
15. Xia X, Lemieux M, Li W, Carroll JS, Brown M, Liu XS and Kung A: Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis.
    Proc Natl Acad Sci U S A 106 (2009) 4260-4265.
    
    2008
    
    
16. Zhang Y^, Liu T^, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W*, Liu XS*: Model-based Analysis of ChIP-Seq (MACS).
    $ Genome Biol. 9 (2008) R137 Full Article; BioMed Central Highly Accessed; Recommended by the AB/SOLiD
    
    
17. Johnson D^, Li W^, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P et al.: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
    $ Genome Res. 18 (2008) 393-403. Abstract Full Article; Highlights in Nature Method
    
    
18. Li W, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides.
    $ BMC Genomics (2008). Abstract Full Article; News in Bioinform
    
    
19. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS and Brown M: FoxA1 translates epigenetic signatures into lineage-specific transcription.
    $ Cell 132 (2008) 958-970 Abstract
    
    
20. Agoulnik IU, Bingman WE, Nakka M, Li W, Wang Q, Brown M, Liu XS, Weigel NL: Target Gene Specific Regulation of Androgen Receptor Activity by p42/p44 MAPK.
    Mol Endocrinol 22 (2008) 2420-2432.
    
    
21. Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Ohgane J, Tanaka S et al: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression.
    Genome Res 18 (2008) 1969-1978
    
    
22. Gottardo R, Li W, Liu XS and Johnson WE: A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments.
    Biometrics 64 (2008) 468-478. Abstract
    
    2007
    
    
23. Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK, Chinnaiyan AM, Pienta KJ and Brown M: A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.(Featured Article)
    $ Mol Cell 27 (2007) 380-392. Abstract; Faculty of 1000 Recommended
    
    
24. O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser R, Wong KK, Li W, KcKenna K, Liu XS, Neuberg D, Silverman L, DeAngelo D, Kutok J, Rothstein R, DePinho R, Chin L, Lee C and Look AT: Tandem Duplication as a Novel Mechanism of MYB Activation in Human T-ALL.
    J Exp Med 204 (2007) 3059-3066.
    
    
25. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R and Liu XS: Model-based analysis of two-color arrays (MA2C).
    Genome Biol 8 (2007) R178. Abstract
    
    
26. Song J, Maghsoudi K, Li W, Fox E, Quackenbush J and Liu XS: Microarray Blob-Defect Removal Improves Array Analysis.
    Bioinformatics 23 (2007) 966-971. Abstract Full Article
    
    
27. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.(list author)
    Genome Biol 8 (2007) R45. Abstract Full Article
    
    2006
    
    
28. Johnson WE^, Li W^, Meyer CA^, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip.
    $ Proc. Natl. Acad. Sci. U S A 103 (2006) 12457-12462. Abstract Full Article
    
    
29. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS and Brown M: Genome-wide analysis of estrogen receptor binding sites.
    $ Nat. Genet. 38 (2006) 1289-1297. Abstract
    
    
30. Ji X^, Li W^, Song J, Wei L and Liu XS: CEAS: cis-regulatory element annotation system.
    $ Nucleic Acids Res. 34 (2006) W551-554. Abstract Full Article
    
    
31. Nelson EA, Walker SR, Li W, Liu XS and Frank DA: Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology.
    J. Biol. Chem. 281 (2006) 26216-26224. Abstract Full Article
    
    
32. Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA and Look AT: Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.
    Blood 108 (2006) 986-992. Abstract Full Article
    
    
33. The DNA sequence, annotation and analysis of human chromosome 3. (list author)
    Nature 440 (2006) 1194-1198. Abstract
    
    2005
    
    
34. Li W, Meyer CA and Liu XS: A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.
    $ Bioinformatics 21 Suppl 1 (ISMB2005) i274-i282. Abstract
    
    
35. Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA and Brown M: Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1.
    $ Cell 122 (2005) 33-43. Abstract
    
    
36. Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. (list author)
    BMC Genomics 6 (2005) 70. Abstract Full Article
    
    
37. Yu Z, Li Y, Meng Q, Yuan J, Zhao Z, Li W, Hu X, Yan B, Fan B, Yu S and Li N: Comparative analysis of the pig BAC sequence involved in the regulation of myostatin gene. Sci.
    China C Life Sci. 48 (2005) 168-180. Abstract
    
    
38. The Chinese Human Genome Sequencing Consortium: #Beijing Region# (3pter-D3S3397) of the human genome: Complete sequence and analysis. Sci.(list author)
    China C Life Sci. 48 (2005) 311-329. Abstract
    
    2004
    
    
39. Li W, Shi J, Wang X, Han Y, Tong W, Ma L, Liu B and Cai B: Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6.
    $ Gene 336 (2004) 231-240. Abstract
    
    
40. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. (list author)
    Nature 431 (2004) 931-945. Abstract
    
    
41. Li Y, Luo C, Li W, Xu Z, Zeng C, Bi S, Yu J, Wu J and Yang H: Structure-based preliminary analysis of immunity and virulence of SARS coronavirus.
    Viral Immunol. 17 (2004) 528-534. Abstract
    
    
42. Wang J, Xue Y, Feng X, Li X, Wang H, Li W, Zhao C, Cheng X, Ma Y, Zhou P, Yin J, Bhatnagar A, Wang R and Liu S: An Analysis of the Proteomic Profile for Thermoanaerobacter Tengcongensis under Optimal Culture Conditions.
    Proteomics 4 (2004) 136-150. Abstract
    
    
43. Lu H, Zhao Y, Zhang J, Wang Y, Li W, Zhu X, Sun S, Xu J, Ling L, Cai L, Bu D and Chen R: Date of origin of the SARS coronavirus strains.
    BMC Infect. Dis. 4 (2004). Abstract Full Article
    
    2003
    
    
44. Wang J, Wen J, Li J, Yin J, Zhu Q, Wang H, Yang Y, Qin E, You B, Li W, Li X, Huang S, Yang R, Zhang X, Yang L, Zhang T, Yin Y, Cui X, Tang X, Wang L, He B, Ma L, Lei T, Zeng C, Fang J, Yu J, Yang H, West MB, Bhatnagar A, Lu Y, Xu N and Liu S: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus.
    Clin. Chem. 49 (2003) 1989-1996. Abstract Full Article
    
    
45. A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China.(joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 101-107. Abstract
    
    
46. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).(joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 180-192. Abstract
    
    
47. Evolution and Variation of the SARS-CoV Genome. (joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 216-225. Abstract
    
    
48. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). (joint first author)
    Chin. Sci. Bull. 48 (2003) 941-948. Abstract
    
    
49. Qi Z, Hu Y, Li W, Chen Y, Zhang Z, Sun S, Hu H, Zhang J, Bu D, Ling L and Chen R: Phylogeny of SARS-CoV as Inferred from Complete Genome Comparison.
    Chin. Sci. Bull. 48 (2003) 1175-1178. Abstract
    
    2002
    
    
50. Bao Q^, Tian Y^, Li W^, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J and Yang H: A Complete Sequence of the T. tengcongensis Genome.
    $ Genome Res. 12 (2002) 689-700. Abstract Full Article
    
    
51. Li W, Fang W, Ling L, Wang J, Xuan Z and Chen R: Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis.
    $ J. Biol. Phys. 28 (2002) 439-447. Abstract
    
    
52. Ling L, Wang J, Cui Y, Li W and Chen R: Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms. Mol. Phylogenet. Evol. 25 (2002) 101-111.
    Abstract Full Article
    
    
53. Zhong L, Wang K, Tan J, Li W and Li S: Putative cytochrome P450 genes in rice genome (Oryza sativa L. ssp. indica) and their EST evidence.
    Sci. China C Life Sci. 45 (2002) 512-517. Abstract
    
    
54. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). (list author)
    Science 296 (2002) 79-92. Abstract
    
    2001
    
    
55. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. (list author)
    $ Nature 409 (2001) 860-921. Abstract
    
    
56. A draft sequence of the rice (Oryza sativa ssp. indica) genome. (list author)
    Chin. Sci. Bull. 46 (2001) 1937-1942.