Li Lab:Publications

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(Peer Reviewed Publications)
(Peer Reviewed Publications)
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# <u>Xi Y</u>, Bock C, Muller F, <u>Sun D</u>, Meissner A, <u>Li W*</u>: RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing. <br/>'''''Bioinformatics''''' 28 (2012) 430-432. <br/><br/>
# <u>Xi Y</u>, Bock C, Muller F, <u>Sun D</u>, Meissner A, <u>Li W*</u>: RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing. <br/>'''''Bioinformatics''''' 28 (2012) 430-432. <br/><br/>
# <u>Wang L</u>, Wang S, <u>Li W*</u>: RseQC: Quality Control of RNA-seq experiments. <br/>'''''Bioinformatics''''' (2012) Accepted. <br/><br/>
# <u>Wang L</u>, Wang S, <u>Li W*</u>: RseQC: Quality Control of RNA-seq experiments. <br/>'''''Bioinformatics''''' (2012) Accepted. <br/><br/>
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# Li Z, Gadue P, <u>Chen K<u>, Tuteja G, Schug J, <u>Li W<u>, Kaestner KH: Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation. <br/>'''''Cell''''' (2012) Accepted. <br/><br/>
+
# Li Z, Gadue P, <u>Chen K</u>, Tuteja G, Schug J, <u>Li W</u>, Kaestner KH: Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation. <br/>'''''Cell''''' (2012) Accepted. <br/><br/>
# 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, <u>Li W</u>, Suraneni M, Tang DG: The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration.<br/> '''''Cell Stem Cell''''' 10 (2012) 556-569. <br/><br/>
# 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, <u>Li W</u>, Suraneni M, Tang DG: The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration.<br/> '''''Cell Stem Cell''''' 10 (2012) 556-569. <br/><br/>
# Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, <u>Chen K</u>, Pan X, Ira G: The Fun30 nucleosome remodeler promotes resection of DNA double-strand break ends.<br/> '''''Nature''''' (2012) Accepted. <br/><br/>
# Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, <u>Chen K</u>, Pan X, Ira G: The Fun30 nucleosome remodeler promotes resection of DNA double-strand break ends.<br/> '''''Nature''''' (2012) Accepted. <br/><br/>

Revision as of 17:41, 28 August 2012

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Peer Reviewed Publications

Major Publications; ^ (Co-)first authors; * (Co-)corresponding authors; H-index = 28; Citations @ Google Scholar

  1. 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

  2. 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

  3. 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.

  4. Wang L, Wang S, Li W*: RseQC: Quality Control of RNA-seq experiments.
    Bioinformatics (2012) Accepted.

  5. 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 (2012) Accepted.

  6. 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.

  7. Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, Chen K, Pan X, Ira G: The Fun30 nucleosome remodeler promotes resection of DNA double-strand break ends.
    Nature (2012) Accepted.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  21. 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

  22. 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.

  23. 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.

  24. 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.

  25. 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

  26. Xi Y, Li W*: BSMAP: whole genome Bisulfite Sequence MAPping program.
    BMC Bioinformatics (2009) 10:232.Full Article; BioMed Central Highly Accessed

  27. 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

  28. 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)

  29. 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

  30. 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

  31. 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

  32. Li W, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides.
    BMC Genomics (2008). Abstract Full Article; News in Bioinform

  33. 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

  34. 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.

  35. 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

  36. 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

  37. 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

  38. 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.

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. The DNA sequence, annotation and analysis of human chromosome 3. (list author)
    Nature 440 (2006) 1194-1198. Abstract

    2005

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. (list author)
    Nature 431 (2004) 931-945. Abstract

  55. 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

  56. 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

  57. 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

  58. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). (joint first author)
    Chin. Sci. Bull. 48 (2003) 941-948. Abstract

  59. 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

  60. 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

  61. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).(joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 180-192. Abstract

  62. Evolution and Variation of the SARS-CoV Genome. (joint first author)
    Genomics Proteomics Bioinformatics 1 (2003) 216-225. Abstract

  63. 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

  64. 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

  65. 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

  66. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). (list author)
    Science 296 (2002) 79-92. Abstract

  67. 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

  68. 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

  69. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. (list author)
    Nature 409 (2001) 860-921. Abstract

  70. A draft sequence of the rice (Oryza sativa ssp. indica) genome. (list author)
    Chin. Sci. Bull. 46 (2001) 1937-1942.
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