Li Lab:Publications

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== '''Peer Reviewed Publications ''' ==
== '''Peer Reviewed Publications ''' ==
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'''''Major Publications'''''; ^ (Co-)first authors; * (Co-)corresponding authors; H-index = 29;  [http://scholar.google.com/citations?hl=en&user=7IUCbE4AAAAJ&view_op=list_works&pagesize=100 Citations @ Google Scholar]
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'''''Major Publications'''''; <u>Li Lab Members</u>; ^first authors or *corresponding authors; H-index = 37;  [http://scholar.google.com/citations?hl=en&user=7IUCbE4AAAAJ&view_op=list_works&pagesize=100 Citations @ Google Scholar]
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# <u>Xia Z</u>, Donehower L, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, <u>Li W*</u>: Dynamic Analysis of Alternative Polyadenylation from RNASeq (DaPars) Reveals Global Shortening of 3′UTRs in Human Cancers. <br/> '''''Nature Communications''''' (2014) Accepted <br/><br/>
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# <u>Chen K</u>, <u>Xi Y</u>, Pan X, Dent S, He X, <u>Li W*</u>: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. <br/>'''''Genome Res.''''' (2013) Accepted. <br/><br/>
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# <u>Wang L*</u>, <u>Chen J</u>, Wang C, Zimmermann MT, Yan H, Sun Z, Zhang Y, <u>Chen K</u>, Huang H, Kocher JA*, <u>Li W*</u>: MACE: Model based Analysis of ChIP-exo.  <br/>'''''Nucleic Acids Res.''''' (2014) Accepted. <br/><br/>
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# <u>Wang L</u>, <u>Park JH</u>, Wang S, Kocher JP, <u>Li W*</u>: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model. <br/>'''''Nucleic Acids Res.''''' (2013) Accepted.<br/><br/>
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# Sowalsky AG^, <u>Xia Z^</u>, <u>Wang L</u>, <u>Zhao H</u>, Chen S, Bubley GJ, Ballk SP*, <u>Li W*</u>: Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer. <br/>'''''Molecular Cancer Research '''''  (2014) Accepted. <br/><br/>
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# <u>Chen K</u>, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, <u>Li W*</u>, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. <br/>'''''Genome Res.''''' (2013) Accepted. <br/><br/>'''2012'''  <br/><br/>
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# Challen GA^, <u>Sun D^</u>, Mayle A^, Jeong M^, Luo M^, <u>Rodrigues B</u>, Mallaney C, Celik H, Yang L, <u>Xia Z</u>, Culleng S, Berg JS, Zheng Y, Darlington GJ, <u>Li W*</u>, Goodell MA*: Dnmt3a and Dnmt3b have Overlapping and Distinct Functions in Hematopoietic Stem Cells. <br/>  '''''Cell Stem Cell''''' (2014) In press <br/><br/>
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# Barber MF^, Michishita E^, <u>Xi Y^</u>, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, <u>Chen K</u>, Struhl K, Garcia BA, Gozani O, <u>Li W*</u>, Chua KF*: SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. <br/>'''''Nature''' 487 (2012) 114-118<br/>
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# Masamha CP^, <u>Xia Z^</u>, Yang J, Albrecht TR, Li M, Shyu A*, <u>Li W*</u>, Wagner EJ*: CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression.  <br/> '''''Nature''''' 510 (2014) 412-416 <br/><br/>
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# Challen GA, <u>Sun D</u>, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, <u>Xi Y</u>, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JJ, Godley LA, <u>Li W*</u>, Goodell MA*: Dnmt3a is Essential for Hematopoietic Stem Cell Differentiation.  <br/>'''''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 <br/>
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# Jeong M^, <u>Sun D^</u>, Luo M^, Huang Y, Challen GA, <u>Rodriguez B</u>, 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, <u>Li W*</u>, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a. <br/>'''''Nature Genetics''''' 46 (2014) 17-23.<br/><br/>
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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/>
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# Wen H^, Li Y^, <u>Xi Y^</u>, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, <u>Xia Z</u>, Wu J, Li B, Barton MC, <u>Li W*</u>, Li H*, Shi X*: ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. <br/>'''''Nature''''' 508 (2014) 263-268 <br/><br/>
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# <u>Wang L</u>, Wang S, <u>Li W*</u>: RseQC: Quality Control of RNA-seq experiments. <br/>'''''Bioinformatics''''' 28 (2012) 2184-2185. <br/>
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# <u>Sun D^</u>, Luo M^, Jeong M^, <u>Rodriguez B</u>, <u>Xia Z</u>, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Gottgens B, Darlington GJ*, <u>Li W*</u>, Goodell MA*: Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. <br/>  '''''Cell Stem Cell ''''' 14 (2014) 673-688  <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''''' 151 (2012) 1608-1616. <br/>
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# Singh RK^, <u>Xia Z^</u>, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, <u>Li W*</u>, Cooper TA: Rbfox2-Coordinated Alternative Splicing of Mef2d and Rock2 Controls Myoblast Fusion during Myogenesis. <br/>'''''Molecular Cell''''' 55 (2014) (2014) 592-603 <br/><br/>
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# 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/>
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# <u>Sun D</u>, <u>Xi Y</u>, <u>Rodriguez B</u>, <u>Park HJ</u>, Pan T, Meong M, Goodell MA, <u>Li W*</u>: MOABS: Model based Analysis of Bisulfite Sequencing data. <br/> '''''Genome Biology''''' 15 (2014) R38. <br/><br/>
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# 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/>
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# Zheng H^, <u> Chen K^</u>, <u> Xia Z</u>, Chavez M, Pal S, Seol J, Chen C, <u> Li W*</u>, Tyler JK*: Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging. <br/>'''''Genes & Development''''' 28 (2014) 396-408.<br/><br/>
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# Huang Z, Srinivasan S, Zhang J, <u>Chen K</u>, Li Y, <u>Li W</u>, Quiocho FA, Pan X: Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy. <br/> ''PLOS Genetics'' 8 (2012) e1003083. PMCID: PMC3510038 <br/>
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# <u>Akdemir KC</u>, Jain AK, Allton K, Aronow B, Xu X, Cooney AJ, <u>Li W*</u>, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells. <br/>'''''Nucleic Acids Res.''''' 42 (2014) 205-223. PMCID: PMC3874181<br/><br/>
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# Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, <u>Li W</u>, Long H, Zhang Y, Liu XS: CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. <br/> ''Bioinformatics'' 28 (2012) 1411-1412. <br/>
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# Giudice J, <u>Xia Z</u>, Wang ET, Ruddy MA, Ward AJ, Kalsotra A, Burge CB, <u>Li W</u>, Cooper TA: Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development.  <br/> '''''Nature Communications''''' 5 (2014) 3603 <br/><br/>
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# Xiao R, <u>Sun D</u>, Ayers S, <u>Xi Y</u>, <u>Li W</u>, Baxter JD, Moore DD: The Estrogen Receptor Alpha Cistrome Defined by DamIP. <br/> ''Mol Endocrinol'' 26 (2012) 349-357. <br/>
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# Pathiraja TN, Nayak S, <u>Xi Y</u>, Jiang S, …, Schiff R, <u>Li W</u>, Oesterreich S: Epigenetic Reprogramming of HOXC10 in Endocrine-Resistant Breast Cancer. <br/>'''''Science Translational Medicine'''''  6 (2014) 229ra241 <br/><br/>
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# Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, <u>Chen K</u>, Kusewitt D, Richie E, <u>Li W</u>, Bedford MT: Loss of the methyl-lysine effector molecule PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. <br/>''J Biol Chem'' 287 (2012) 429-437.<br/>'''2011'''  <br/><br/>
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# Klein BJ, Piao L, <u>Xi Y</u>, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, <u>Xia Z</u>, Cortazar MA, Pena PV, Mangan A, Bentley DL, Strahl BD, Groudine M, <u>Li W</u>, Shi X, Kutateladze TG: The Histone-H3K4-Specific Demethylase KDM5B Binds to Its Substrate and Product through Distinct PHD Fingers.<br/>'''''Cell Reports''''' 6 (2014) 325-335. <br/><br/>
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# The Cancer Genome Atlas Research Network (including <u>Xia Z</u>,<u>Li W</u> as co authors): Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin. <br/>'''''Cell''''' 158 (2014) 929-944.<br/><br/>
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# Blackmore JK, Karmakar S, Gu G, Chaubal V, <u>Wang L</u>, Fuqua S, <u>Li W</u>, Smith CL: The SMRT Coregulator Enhances Growth of Estrogen Receptor-α-Positive Breast Cancer Cells by Promotion of Cell Cycle Progression and Inhibition of Apoptosis.<br/>''Endocrinology'' 155 (2014) 3251-3261.<br/><br/>
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# Adikesavan AK, Karmakar S, Pardo P, <u>Wang L</u>, Liu S, <u>Li W</u>, Smith CL: Activation of p53 Transcriptional Activity by SMRT: an HDAC3-Independent Function of a Transcriptional Corepressor.<br/>''Molecular and Cellular Biology'' 34 (2014) 1246-1261.<br/><br/>'''2013''' <br/><br/>
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# <u>Chen K</u>, <u>Xi Y</u>, Pan X, Dent S, He X, <u>Li W*</u>: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. <br/>'''''Genome Res.''''' 23 (2013) 341-351. [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News];  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline]  <br/><br/>
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# <u>Wang L</u>, <u>Park JH</u>, Wang S, Kocher JP, <u>Li W*</u>: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model. <br/>'''''Nucleic Acids Res.''''' 41 (2013) e74.<br/><br/>
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# <u>Lin X</u>, <u>Sun D</u>, <u>Rodriguez B</u>, Zhao Q, Sun H, Zhang Y, <u>Li W*</u>: BseQC: Quality Control of bisulfite sequencing experiments. <br/>'''''Bioinformatics''''' 29 (2013) 3227-3229. PMCID: PMC3842756 .<br/><br/>
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# <u>Chen K^</u>, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, <u>Li W*</u>, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. <br/>'''''Genome Res.''''' 23 (2013) 312-322. <br/><br/>
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# The Cancer Genome Atlas Research Network (including <u>Xia Z</u>, <u>Li W</u> as co authors): The Cancer Genome Atlas Pan-Cancer analysis project. <br/>'''''Nature Genetics'''''  45 (2013) 1113-1120. <br/><br/>
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# Huang Z^, <u>Chen K^</u>, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, <u>Li W</u>, Chen R, Sucgang RS, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds. <br/>'''''Cell Reports''''' 3 (2013) 577-585. <br/><br/>
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# Kosters A^, <u>Sun D^</u>, Tian F, Felix J, Wu H, <u>Li W</u>, 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. <br/>''PLoS ONE''  8 (2013) e71538. <br/><br/>
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# Yao J, Liu X, T. S, Li W, <u>Xi Y</u>, Aravamudhan P, Joglekar A, <u>Li W</u>, Watanabe Y, He X: Plasticity and Epigenetic Inheritance of Centromere Specific Histone H3 (CENP-A) Containing-Nucleosome Positioning in the Fission Yeast.<br/> ''J Biol Chem'' 288 (2013) 19184-19196. <br/><br/>'''2012'''  <br/><br/>
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# Barber MF^, Michishita E^, <u>Xi Y^</u>, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, <u>Chen K</u>, Struhl K, Garcia BA, Gozani O, <u>Li W*</u>, Chua KF*: SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. <br/>'''''Nature''''' 487 (2012) 114-118. [http://www.bcm.edu/news/item.cfm?newsID=5634 BCM News];<br/><br/>
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# Challen GA, <u>Sun D</u>, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, <u>Xi Y</u>, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JJ, Godley LA, <u>Li W*</u>, Goodell MA*: Dnmt3a is Essential for Hematopoietic Stem Cell Differentiation.  <br/>'''''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 <br/><br/>
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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/>
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# <u>Wang L</u>, Wang S, <u>Li W*</u>: RseQC: Quality Control of RNA-seq experiments. <br/>'''''Bioinformatics''''' 28 (2012) 2184-2185. <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''''' 151 (2012) 1608-1616. <br/><br/>
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# 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/>
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# Huang Z, Srinivasan S, Zhang J, <u>Chen K</u>, Li Y, <u>Li W</u>, Quiocho FA, Pan X: Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy. <br/> ''PLOS Genetics'' 8 (2012) e1003083. PMCID: PMC3510038 <br/><br/>
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# Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, <u>Li W</u>, Long H, Zhang Y, Liu XS: CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. <br/> ''Bioinformatics'' 28 (2012) 1411-1412. <br/><br/>
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# Xiao R, <u>Sun D</u>, Ayers S, <u>Xi Y</u>, <u>Li W</u>, Baxter JD, Moore DD: The Estrogen Receptor Alpha Cistrome Defined by DamIP. <br/> ''Mol Endocrinol'' 26 (2012) 349-357. <br/><br/>
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# Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, <u>Chen K</u>, Kusewitt D, Richie E, <u>Li W</u>, Bedford MT: Loss of the methyl-lysine effector molecule PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. <br/>''J Biol Chem'' 287 (2012) 429-437.<br/><br/>'''2011'''  <br/><br/>
# Kuo AJ^, Cheung P^, <u>Chen K^</u>, Zee BM, Lauring J, <u>Xi Y</u>, Park BH, Shi X, Kioi M, Garcia BA, <u>Li W*</u>, Gozani O*: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. <br/>'''''Molecular Cell''''' 44 (2011) 609-620. <br/><br/>
# Kuo AJ^, Cheung P^, <u>Chen K^</u>, Zee BM, Lauring J, <u>Xi Y</u>, Park BH, Shi X, Kioi M, Garcia BA, <u>Li W*</u>, Gozani O*: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. <br/>'''''Molecular Cell''''' 44 (2011) 609-620. <br/><br/>
# Zhang C^, <u>Wang L^</u>, 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, <u>Li W*</u>, Wang Q*: Definition of a FoxA1 cistrome that is crucial for G1-S phase cell cycle transit in castration resistant prostate cancer. <br/>'''''Cancer Res''''' 71 (2011) 6738-6748. <br/><br/>
# Zhang C^, <u>Wang L^</u>, 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, <u>Li W*</u>, Wang Q*: Definition of a FoxA1 cistrome that is crucial for G1-S phase cell cycle transit in castration resistant prostate cancer. <br/>'''''Cancer Res''''' 71 (2011) 6738-6748. <br/><br/>
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# <u>Li W</u>, 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. <br/> '''''Bioinformatics''''' 21 Suppl 1 (ISMB2005) i274-i282. [http://www.ncbi.nlm.nih.gov/pubmed/15961467?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# <u>Li W</u>, 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. <br/> '''''Bioinformatics''''' 21 Suppl 1 (ISMB2005) i274-i282. [http://www.ncbi.nlm.nih.gov/pubmed/15961467?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# Carroll JS, Liu XS, Brodsky AS, <u>Li W</u>, 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. <br/> '''''Cell''''' 122 (2005) 33-43. [http://www.ncbi.nlm.nih.gov/pubmed/16009131?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# Carroll JS, Liu XS, Brodsky AS, <u>Li W</u>, 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. <br/> '''''Cell''''' 122 (2005) 33-43. [http://www.ncbi.nlm.nih.gov/pubmed/16009131?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
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# Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. (<u>list author</u>) <br/>''BMC Genomics'' 6 (2005) 70.  [http://www.ncbi.nlm.nih.gov/pubmed/15885146?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15885146 Full Article]<br/><br/>
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# Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. (<u>list author</u>) <br/>''BMC Genomics'' 6 (2005) 70.  [http://www.ncbi.nlm.nih.gov/pubmed/15885146?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15885146 Full Article]<br/><br/>'''2004'''  <br/><br/>
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# Yu Z, Li Y, Meng Q, Yuan J, Zhao Z, <u>Li W</u>, 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. <br/> ''China C Life Sci''. 48 (2005) 168-180. [http://www.ncbi.nlm.nih.gov/pubmed/15986890?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
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# The Chinese Human Genome Sequencing Consortium: #Beijing Region# (3pter-D3S3397) of the human genome: Complete sequence and analysis. Sci.(<u>list author</u>) <br/>''China C Life Sci''. 48 (2005) 311-329.  [http://www.ncbi.nlm.nih.gov/pubmed/16248425?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] <br/> <br/>'''2004'''  <br/><br/>
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# <u>Li W</u>, 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. <br/> '''''Gene''''' 336 (2004) 231-240. [http://www.ncbi.nlm.nih.gov/pubmed/15246534?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# <u>Li W</u>, 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. <br/> '''''Gene''''' 336 (2004) 231-240. [http://www.ncbi.nlm.nih.gov/pubmed/15246534?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. (<u>list author</u>) <br/>'''''Nature''''' 431 (2004) 931-945.  [http://www.ncbi.nlm.nih.gov/pubmed/15496913?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. (<u>list author</u>) <br/>'''''Nature''''' 431 (2004) 931-945.  [http://www.ncbi.nlm.nih.gov/pubmed/15496913?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
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# Li Y, Luo C, <u>Li W</u>, Xu Z, Zeng C, Bi S, Yu J, Wu J and Yang H: Structure-based preliminary analysis of immunity and virulence of SARS coronavirus. <br/>''Viral Immunol''. 17 (2004) 528-534. [http://www.ncbi.nlm.nih.gov/pubmed/15671749?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
 
# Wang J, Xue Y, Feng X, Li X, Wang H, <u>Li W</u>, 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. <br/>''Proteomics'' 4 (2004) 136-150. [http://www.ncbi.nlm.nih.gov/pubmed/14730678?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# Wang J, Xue Y, Feng X, Li X, Wang H, <u>Li W</u>, 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. <br/>''Proteomics'' 4 (2004) 136-150. [http://www.ncbi.nlm.nih.gov/pubmed/14730678?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# Lu H, Zhao Y, Zhang J, Wang Y, <u>Li W</u>, Zhu X, Sun S, Xu J, Ling L, Cai L, Bu D and Chen R: Date of origin of the SARS coronavirus strains. <br/>''BMC Infect. Dis''. 4 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15028113?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15028113 Full Article] <br/> <br/> '''2003'''  <br/><br/>
# Lu H, Zhao Y, Zhang J, Wang Y, <u>Li W</u>, Zhu X, Sun S, Xu J, Ling L, Cai L, Bu D and Chen R: Date of origin of the SARS coronavirus strains. <br/>''BMC Infect. Dis''. 4 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15028113?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15028113 Full Article] <br/> <br/> '''2003'''  <br/><br/>
Line 71: Line 89:
# A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China.(<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 101-107.  [http://www.ncbi.nlm.nih.gov/pubmed/15626340?dopt=Abstract Abstract]<br/><br/>
# A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China.(<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 101-107.  [http://www.ncbi.nlm.nih.gov/pubmed/15626340?dopt=Abstract Abstract]<br/><br/>
# Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).(<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 180-192. [http://www.ncbi.nlm.nih.gov/pubmed/15629030?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
# Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).(<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 180-192. [http://www.ncbi.nlm.nih.gov/pubmed/15629030?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
-
# Evolution and Variation of the SARS-CoV Genome. (<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 216-225.  [http://www.ncbi.nlm.nih.gov/pubmed/15629034?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
+
# Evolution and Variation of the SARS-CoV Genome. (<u>joint first author</u>) <br/>''Genomics Proteomics Bioinformatics'' 1 (2003) 216-225.  [http://www.ncbi.nlm.nih.gov/pubmed/15629034?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/> '''2002'''  <br/><br/>
-
# Qi Z, Hu Y, <u>Li W</u>, 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. <br/>''Chin. Sci. Bull'' 48 (2003) 1175-1178. [http://scholar.ilib.cn/A-kxtb-e200312003.html Abstract] <br/><br/> '''2002'''  <br/><br/>
+
# Bao Q^, Tian Y^, <u>Li W^</u>, 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.  <br/> '''''Genome Res'''''. 12 (2002) 689-700.  [http://www.ncbi.nlm.nih.gov/pubmed/11997336 Abstract] [http://www.genome.org/cgi/content/full/12/5/689 Full Article]<br/><br/>
# Bao Q^, Tian Y^, <u>Li W^</u>, 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.  <br/> '''''Genome Res'''''. 12 (2002) 689-700.  [http://www.ncbi.nlm.nih.gov/pubmed/11997336 Abstract] [http://www.genome.org/cgi/content/full/12/5/689 Full Article]<br/><br/>
# <u>Li W</u>, Fang W, Ling L, Wang J, Xuan Z and Chen R: Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis.  <br/> ''''' J. Biol. Phys.''''' 28 (2002) 439-447. [http://www.springerlink.com/content/pru88138220482x6 Abstract]<br/><br/>
# <u>Li W</u>, Fang W, Ling L, Wang J, Xuan Z and Chen R: Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis.  <br/> ''''' J. Biol. Phys.''''' 28 (2002) 439-447. [http://www.springerlink.com/content/pru88138220482x6 Abstract]<br/><br/>

Current revision

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Peer Reviewed Publications

Major Publications; Li Lab Members; ^first authors or *corresponding authors; H-index = 37; Citations @ Google Scholar

  1. Xia Z, Donehower L, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W*: Dynamic Analysis of Alternative Polyadenylation from RNASeq (DaPars) Reveals Global Shortening of 3′UTRs in Human Cancers.
    Nature Communications (2014) Accepted

  2. Wang L*, Chen J, Wang C, Zimmermann MT, Yan H, Sun Z, Zhang Y, Chen K, Huang H, Kocher JA*, Li W*: MACE: Model based Analysis of ChIP-exo.
    Nucleic Acids Res. (2014) Accepted.

  3. Sowalsky AG^, Xia Z^, Wang L, Zhao H, Chen S, Bubley GJ, Ballk SP*, Li W*: Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer.
    Molecular Cancer Research (2014) Accepted.

  4. Challen GA^, Sun D^, Mayle A^, Jeong M^, Luo M^, Rodrigues B, Mallaney C, Celik H, Yang L, Xia Z, Culleng S, Berg JS, Zheng Y, Darlington GJ, Li W*, Goodell MA*: Dnmt3a and Dnmt3b have Overlapping and Distinct Functions in Hematopoietic Stem Cells.
    Cell Stem Cell (2014) In press

  5. Masamha CP^, Xia Z^, Yang J, Albrecht TR, Li M, Shyu A*, Li W*, Wagner EJ*: CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression.
    Nature 510 (2014) 412-416

  6. 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 46 (2014) 17-23.

  7. Wen H^, Li Y^, Xi Y^, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W*, Li H*, Shi X*: ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression.
    Nature 508 (2014) 263-268

  8. Sun D^, Luo M^, Jeong M^, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Gottgens B, Darlington GJ*, Li W*, Goodell MA*: Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal.
    Cell Stem Cell 14 (2014) 673-688

  9. Singh RK^, Xia Z^, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, Li W*, Cooper TA: Rbfox2-Coordinated Alternative Splicing of Mef2d and Rock2 Controls Myoblast Fusion during Myogenesis.
    Molecular Cell 55 (2014) (2014) 592-603

  10. Sun D, Xi Y, Rodriguez B, Park HJ, Pan T, Meong M, Goodell MA, Li W*: MOABS: Model based Analysis of Bisulfite Sequencing data.
    Genome Biology 15 (2014) R38.

  11. Zheng H^, Chen K^, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W*, Tyler JK*: Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging.
    Genes & Development 28 (2014) 396-408.

  12. Akdemir KC, Jain AK, Allton K, Aronow B, Xu X, Cooney AJ, 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. 42 (2014) 205-223. PMCID: PMC3874181

  13. Giudice J, Xia Z, Wang ET, Ruddy MA, Ward AJ, Kalsotra A, Burge CB, Li W, Cooper TA: Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development.
    Nature Communications 5 (2014) 3603

  14. Pathiraja TN, Nayak S, Xi Y, Jiang S, …, Schiff R, Li W, Oesterreich S: Epigenetic Reprogramming of HOXC10 in Endocrine-Resistant Breast Cancer.
    Science Translational Medicine 6 (2014) 229ra241

  15. Klein BJ, Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Xia Z, Cortazar MA, Pena PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG: The Histone-H3K4-Specific Demethylase KDM5B Binds to Its Substrate and Product through Distinct PHD Fingers.
    Cell Reports 6 (2014) 325-335.

  16. The Cancer Genome Atlas Research Network (including Xia Z,Li W as co authors): Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin.
    Cell 158 (2014) 929-944.

  17. Blackmore JK, Karmakar S, Gu G, Chaubal V, Wang L, Fuqua S, Li W, Smith CL: The SMRT Coregulator Enhances Growth of Estrogen Receptor-α-Positive Breast Cancer Cells by Promotion of Cell Cycle Progression and Inhibition of Apoptosis.
    Endocrinology 155 (2014) 3251-3261.

  18. Adikesavan AK, Karmakar S, Pardo P, Wang L, Liu S, Li W, Smith CL: Activation of p53 Transcriptional Activity by SMRT: an HDAC3-Independent Function of a Transcriptional Corepressor.
    Molecular and Cellular Biology 34 (2014) 1246-1261.

    2013

  19. 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

  20. 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.

  21. 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 .

  22. 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.

  23. 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.

  24. 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.

  25. 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.

  26. 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

  27. 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;

  28. 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

  29. 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.

  30. Wang L, Wang S, Li W*: RseQC: Quality Control of RNA-seq experiments.
    Bioinformatics 28 (2012) 2184-2185.

  31. 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.

  32. 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.

  33. 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

  34. 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.

  35. 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.

  36. 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

  37. 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.

  38. 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.

  39. 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.

  40. 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

  41. 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

  42. 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.

  43. 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.

  44. 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.

  45. 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

  46. 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

  47. 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

  48. 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.

  49. 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.

  50. 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.

  51. 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

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

  53. 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

  54. 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)

  55. 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

  56. 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

  57. 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

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

  59. 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

  60. 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.

  61. 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

  62. 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

  63. 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

  64. 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.

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

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

    2005

  74. 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

  75. 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

  76. 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

  77. 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

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

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