Li Lab:Publications

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Peer Reviewed Publications

Major Publications; Li Lab Members; ^ (Co-)first authors; * (Co-)corresponding authors; H-index = 34; Citations @ Google Scholar

1. Jeong M^, Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a.
          Nature Genetics. Accepted.
   
   
2. Akdemir KC, Jain AK, Alton K, Arronow B, J. CA, ..., Li W*, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells.
          Nucleic Acids Res. Accepted.
   
   
3. Klein JB, Piao L, …, Li W, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.
          Cell Reports. Accepted.
   
   2013
   
   
4. Chen K, Xi Y, Pan X, Dent S, He X, Li W*: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
          Genome Res. 23 (2013) 341-351. BCM News; Epigenie Headline
   
   
5. Wang L, Park JH, Wang S, Kocher JP, Li W*: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model.
          Nucleic Acids Res. 41 (2013) e74.
   
   
6. Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W*: BseQC: Quality Control of bisulfite sequencing experiments.
          Bioinformatics 29 (2013) 3227-3229. PMCID: PMC3842756 .
   
   
7. Chen K^, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, Li W*, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
          Genome Res. 23 (2013) 312-322.
   
   
8. The Cancer Genome Atlas Research Network (including Xia Z, Li W as co authors): The Cancer Genome Atlas Pan-Cancer analysis project.
          Nature Genetics 45 (2013) 1113-1120.
   
   
9. Huang Z^, Chen K^, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang RS, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds.
          Cell Reports 3 (2013) 577-585.
   
   
10. Kosters A^, Sun D^, Tian F, Felix J, Wu H, Li W, Karpen S: Sexually Dimorphic Genome-Wide Binding of Retinoid X Receptor alpha (RXRα) Determines Male-Female Differences in the Expression of Hepatic Lipid Processing Genes in Mice.
           PLoS ONE 8 (2013) e71538.
    
    
11. Yao J, Liu X, T. S, Li W, Xi Y, Aravamudhan P, Joglekar A, Li W, Watanabe Y, He X: Plasticity and Epigenetic Inheritance of Centromere Specific Histone H3 (CENP-A) Containing-Nucleosome Positioning in the Fission Yeast.
           J Biol Chem 288 (2013) 19184-19196.
    
    2012
    
    
12. Barber MF^, Michishita E^, Xi Y^, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W*, Chua KF*: SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.
           Nature 487 (2012) 114-118. BCM News;
    
    
13. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JJ, Godley LA, Li W*, Goodell MA*: Dnmt3a is Essential for Hematopoietic Stem Cell Differentiation.
           Nature Genetics 44 (2012) 23-31; News and Views in Nature Genetics 44 (2012) 13-14; Faculty of 1000 Must Read; Research Highlights in Nature Reviews Genetics 13 (2012) 73
    
    
14. Xi Y, Bock C, Muller F, Sun D, Meissner A, Li W*: RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing.
           Bioinformatics 28 (2012) 430-432.
    
    
15. Wang L, Wang S, Li W*: RseQC: Quality Control of RNA-seq experiments.
           Bioinformatics 28 (2012) 2184-2185.
    
    
16. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner KH: Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation.
           Cell 151 (2012) 1608-1616.
    
    
17. Qin J, Liu X, Laffin B, Chen X, Choy G, Jeter C, Calhoun-Davis T, Li H, Palapattu GS, Pang S, Lin K, Huang J, Ivanov I, Li W, Suraneni M, Tang DG: The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration.
           Cell Stem Cell 10 (2012) 556-569.
    
    
18. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho FA, Pan X: Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy.
            PLOS Genetics 8 (2012) e1003083. PMCID: PMC3510038
    
    
19. Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS: CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.
            Bioinformatics 28 (2012) 1411-1412.
    
    
20. Xiao R, Sun D, Ayers S, Xi Y, Li W, Baxter JD, Moore DD: The Estrogen Receptor Alpha Cistrome Defined by DamIP.
            Mol Endocrinol 26 (2012) 349-357.
    
    
21. Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, Li W, Bedford MT: Loss of the methyl-lysine effector molecule PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF.
           J Biol Chem 287 (2012) 429-437.
    
    2011
    
    
22. Kuo AJ^, Cheung P^, Chen K^, Zee BM, Lauring J, Xi Y, Park BH, Shi X, Kioi M, Garcia BA, Li W*, Gozani O*: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming.
           Molecular Cell 44 (2011) 609-620.
    
    
23. Zhang C^, Wang L^, Wu D, Chen H, Chen Z, Thomas-Ahner JM, Zynger DL, Eeckhoute J, Yu J, Luo J, Brown M, Clinton SK, Nephew KP, Huang TH, Li W*, Wang Q*: Definition of a FoxA1 cistrome that is crucial for G1-S phase cell cycle transit in castration resistant prostate cancer.
           Cancer Res 71 (2011) 6738-6748.
    
    
24. Kannan K^, Wang L^, Wang J, Ittmann M, Li W*, Yen L*: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing.
           PNAS 108 (2011) 9172-9177.
    
    
25. Xi Y, Yao J, Chen R*, Li W*, He X*: Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.
           Genome Res 21 (2011) 718-724. Faculty of 1000 Recommended
    
    
26. Klisch T^, Xi Y^, Flora A, Wang L, Li W*, Zoghbi H*: In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development.
           PNAS (2011). 108 (2011) 3288-3293. Faculty of 1000 Must Read
    
    
27. 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 21 (2011) 315-324.
    
    
28. Malovannaya A, Lanz Rainer B, Jung Sung Y, Bulynko Y, Le Nguyen T, Chan Doug W, Ding C, Shi Y, Yucer N, Krenciute G, Kim B-J, Li C, Chen R, Li W, Wang Y, O'Malley Bert W, Qin J: Analysis of the Human Endogenous Coregulator Complexome.
            Cell 145 (2011) 787-799.
    
    
29. Huang Z, Chen K, Xu T, Zhang J, Li Y, Li W, Agarwal AK, Clark AM, Phillips JD, Pan X: Sampangine inhibits heme biosynthesis in both yeast and human.
            Eukaryotic Cell (2011) Accepted.
    
    
30. 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 12 (2011) R11.
    
    2010
    
    
31. 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
    
    
32. 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
    
    
33. 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.
    
    
34. 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.
    
    
35. 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.
    
    
36. 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
    
    
37. Xi Y, Li W*: BSMAP: whole genome Bisulfite Sequence MAPping program.
            BMC Bioinformatics (2009) 10:232.Full Article; BioMed Central Highly Accessed
    
    
38. 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
    
    
39. 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)
    
    
40. 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.
           PNAS 106 (2009) 4260-4265.
    
    2008
    
    
41. 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
    
    
42. 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
    
    
43. Li W, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides.
            BMC Genomics (2008). Abstract Full Article; News in Bioinform
    
    
44. 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
    
    
45. 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.
    
    
46. 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
    
    
47. 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
    
    
48. 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
    
    
49. 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.
    
    
50. 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
    
    
51. 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
    
    
52. 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
    
    
53. Johnson WE^, Li W^, Meyer CA^, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip.
    PNAS. U S A 103 (2006) 12457-12462. Abstract Full Article
    
    
54. 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
    
    
55. 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
    
    
56. 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
    
    
57. 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
    
    
58. The DNA sequence, annotation and analysis of human chromosome 3. (list author)
    Nature 440 (2006) 1194-1198. Abstract
    
    2005
    
    
59. 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
    
    
60. 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
    
    
61. 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
    
    2004
    
    
62. 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
    
    
63. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. (list author)
    Nature 431 (2004) 931-945. Abstract
    
    
64. 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
    
    
65. 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
    
    
66. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). (joint first author)
    Chin. Sci. Bull. 48 (2003) 941-948. Abstract
    
    
67. 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
    
    
68. 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
    
    
69. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).(joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 180-192. Abstract
    
    
70. Evolution and Variation of the SARS-CoV Genome. (joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 216-225. Abstract
    
    2002
    
    
71. 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
    
    
72. 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
    
    
73. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). (list author)
    Science 296 (2002) 79-92. Abstract
    
    
74. 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
    
    
75. 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
    
    2001
    
    
76. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. (list author)
    Nature 409 (2001) 860-921. Abstract
    
    
77. A draft sequence of the rice (Oryza sativa ssp. indica) genome. (list author)
    Chin. Sci. Bull. 46 (2001) 1937-1942.