Difference between revisions of "Li Lab:Publications"

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== '''Peer Reviewed Publications ''' ==
 
== '''Peer Reviewed Publications ''' ==
'''''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''''' (A <u>Li Lab member</u> is the ^(co-)first or *(co-)corresponding author); H-index = 55;  [http://scholar.google.com/citations?hl=en&user=7IUCbE4AAAAJ&view_op=list_works&pagesize=100 Citations @ Google Scholar]
 
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# <u>Feng X</u>, <u>Li L</u>, Wagner E, <u>Li W</u>: TC3A: The Cancer 3’ UTR Atlas.  <br/> '''''Nucleic Acids Research '''''(2017). Accepted <br/><br/>
# <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. [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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# Mi W^, Guan H^, <u>Lyu J^</u>, …, <u>Li W*!</u>, Li H*, Shi X*: YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. <br/>   '''''Nature Communications''''' (2017). Accepted <br/><br/>
# <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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# …, <u>Lyu J</u>, <u>Li W</u>, Kutateladze T: Covalent modifications of histone H3K9 promote binding of CHD3. <br/>     ''Cell Reports'' (2017). Accepted <br/><br/>
# <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/>
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# <u>Lin X</u>, <u>Su J</u>, <u>Chen K</u>, <u>Rodrigues B</u>, <u>Li W*</u>: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure. <br/> '''''Genome Biology''''' 18 (2017) 163 <br/><br/>
# 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''''' (2013) Accepted. <br/><br/>'''2012'''  <br/><br/>
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# Huang Y^, <u>Su J^</u>, Lei Y, Brunetti L, Gundry MC, Zhang X, Jeong M, <u>Li W*</u>, Goodell MA*: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. <br/> '''''Genome Biology''''' 18 (2017) 176. <br/><br/>
# 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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# Lei Y^, Zhang X^, <u>Su J^</u>, Jeong M, Gundry MC, Huang YH, Zhou Y, <u>Li W</u>, Goodell MA: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. <br/> '''''Nature Communications''''' 8 (2017) 16026. <br/><br/>
# 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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# Wan L, Wen H, Li Y, <u>Lyu J</u>, <u>Xi Y</u>, Hoshii T, Joseph J, Wang X, Loh Y, Erb MA, Shen L, <u>Li W</u>, Li H, Allis CD, Armstrong SA, Shi X: ENL links histone acetylation to oncogenic gene expression in AML.<br/>''Nature'' 543 (2017) 265-269. PMCID: PMC5372383 <br/><br/>
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# The Cancer Genome Atlas Research Network (include <u>Xia Z</u>, <u>Li W</u>): Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. <br/> ''Cell'' 169 1327-1341.e1323. <br/><br/>
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# Dai F, Lee H, Li Z, Yao H, <u>Xi Y</u>, Xiao Z, You MJ, <u>Li W</u>, Su X, Gan B: BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response. <br/> ''PNAS'' 114 (2017) 3192-3197. PMCID: PMC5373337 <br/><br/>
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# Brinegar AE, <u>Xia Z</u>, Loehr JA, Manning KS, <u>Li W</u>, Rodney GG, Cooper TA: Extensive alternative splicing transitions during postnatal skeletal muscle development are required for Ca2+ handling. <br/> ''eLife'' (2017) 6:e27192 <br/><br/>
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# Oegema R, Baillat D, Schot R, van Unen LM, Brooks A, Kia SK, Hoogeboom AJM, <u>Xia Z</u>, <u>Li W</u>, Cesaroni M, Lequin MH, van Slegtenhorst M, Dobyns WB, de Coo IFM, Verheijen FW, Kremer A, van der Spek PJ, Heijsman D, Wagner EJ, Fornerod M, Mancini GMS: Human Mutations in Integrator complex subunits link Transcriptome Integrity to Brain Development. <br/> ''PLOS Genetics'' 13 (2017) e1006809 <br/><br/>
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# Lee YH, Martin-Orozco N, Zheng P, Li J, Zhang P, Tan H, <u>Park HJ</u>, Jeong M, Chang SH, Kim BS, Xiong W, Zang W, Guo L, Liu Y, Dong ZJ, Overwijk WW, Hwu P, Yi Q, Kwak L, Yang Z, Mak TW, <u>Li W</u>, Radvanyi LG, Ni L, Liu D, Dong C: Inhibition of the B7-H3 immune checkpoint limits tumor growth by enhancing cytotoxic lymphocyte function. <br/> ''Cell Res'' 27 (2017) 1034-1045. PMCID <br/><br/>
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# Li J, <u>Xi Y</u>, Li W, McCarthy RL, Jain AK, Stratton S, <u>Li W</u>, Dent SY, Barton MC: TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation. <br/> ''Oncogene'' 36 (2017) 2991-3001 <br/><br/>
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# McNair C, Urbanucci A, Comstock CE, Augello MA, Goodwin JF, Launchbury R, Zhao SG, Schiewer MJ, Ertel A, Karnes J, Davicioni E, <u>Wang L</u>, Wang Q, Mills IG, Feng FY, <u>Li W</u>, Carroll JS, Knudsen KE: Cell cycle-coupled expansion of AR activity promotes cancer progression. <br/>  ''Oncogene'' 36 (2017) 1655-1668. PMCID: PMC5364060 <br/><br/>
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# Routh A, Ji P, Jaworski E, <u>Xia Z</u>, <u>Li W</u>, Wagner E: Poly(A)-ClickSeq: click-chemistry for next-generation 3’-end sequencing without RNA enrichment or fragmentation.  <br/> ''Nucleic Acids Res'' 45 (2017) e112. PMCID: PMC5499544 <br/><br/>
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# Sowalsky AG, Kissick HT, Gerrin S, Schaefer R, <u>Xia Z</u>, Russo J, Arredouani MS, Bubley GJ, Sanda MG, <u>Li W</u>, Ye H, Balk SP: Gleason Score 7 Prostate Cancers Emerge Through Branched Evolution of Clonal Gleason Pattern 3 and 4. <br/> ''Clin Cancer Res'' 23 (2017) 3823-3833. PMCID: PMC5511561 <br/><br/>
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# Koppula P, Zhang Y, <u>Shi J</u>, <u>Li W</u>, Gan B: The glutamate/cystine antiporter SLC7A11/xCT enhances cancer cell dependency on glucose by exporting glutamate. <br/> ''J Biol Chem''  292 (2017) 14240-14249. PMCID: PMC5572906 <br/><br/>
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# Gates LA, <u>Shi J</u>, Rohira AD, Feng Q, Zhu B, Bedford MT, Sagum CA, Jung SY, Qin J, Tsai MJ, Tsai SY, <u>Li W</u>, Foulds CE, O'Malley BW: Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation. <br/> ''J Biol Chem'' 292 (2017) 14456-14472. PMCID <br/><br/>
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# Watters RJ, Hartmaier RJ, Osmanbeyoglu HU, Gillihan RM, Rae J, Liao L, <u>Chen K</u>, <u>Li W</u>, Lu X, Oesterreich S: Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen.  <br/> ''Molecular and Cellular Endocrinology'' 448 (2017) 21–27 <br/><br/>
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# Hirai T, Mulpuri Y, Cheng Y, <u>Xia Z</u>, <u>Li W</u>, Ruangsri S, Spigelman I, Nishimura I: Aberrant plasticity of peripheral sensory axons in a painful neuropathy. <br/> ''Scientific Reports'' 7 (2017) 3407. PMCID: PMC5469767 <br/><br/>'''2016'''  <br/><br/>
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# Zhang X^, <u>Su J^</u>, Jeong M, Ko M, Huang Y, <u>Park HJ</u>, Guzman A, Lei Y, Huang YH, Rao A, <u>Li W*</u>!, Goodell MA*: DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. <br/> '''''Nature Genetics''''' 48 (2016) 1014-1023. PMCID: PMC4957136 <br/><br/>
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# Yang L^, <u>Rodriguez B^</u>, Mayle A^, <u>Park HJ</u>, <u>Lin X</u>, Luo M, Jeong M, Curry CV, Kim SB, Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, <u>Li W*</u>!, Goodell MA*: DNMT3A loss drives enhancer hypomethylation in FLT3-ITD-associated leukemias. <br/> '''''Cancer Cell''''' 29 (2016) 922-934. PMCID: PMC4908977 <br/><br/>
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# Li N, Li Y, Lv J, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, Wang Z, Shiekhattar R, Shi X, Lan F, <u>Chen K</u>, <u>Li W*</u>!, Li H*, Lee MG*: ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes. <br/>'''''Molecular Cell''''' 63 (2016) 470-484. PMCID: PMC4975651 <br/><br/>
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# Tasselli L, <u>Xi Y</u>, Zheng W, Tennen RI, Odrowaz Z, Simeoni F, <u>Li W*</u>!, Chua KF*: SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence.  <br/> '''''Nature Structural & Molecular Biology''''' 23 (2016) 434–440 <br/><br/>
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# Zhang X^, Peng D^, <u>Xi Y^</u>, Yuan C^, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG, <u>Li W</u>, Bedfore MT, Shi X!: G9a-mediated methylation of estrogen receptor α links the PHF20/MOF histone acetylation complex to hormonal gene expression. <br/> '''''Nature Communications''''' 7 (2016) 10810. <br/><br/>
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# Dhar S^, Lee SH^, <u>Chen K</u>^, Zhu G^, Oh W, Allton K, Gafni O, Kim YZ, Barton MC, Hanna JH, Wang Z*, <u>Li W</u>*, Lee MG*: An essential role for UTX in resolution and activation of bivalent promoters. <br/> '''''Nucleic Acids Research''''' 44 (2016) 3659-3674. PMCID: PMC4856969 <br/><br/>
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# Gabrusiewicz K^, <u>Rodriguez B</u>^, …, <u>Li W</u>, …, Gabrusiewicz AB: Glioblastoma-infiltrated innate immune cells resemble M0 macrophage phenotype. <br/> '''''Journal of Clinical Investigation Insight''''' 1 (2016) PMC4784261 <br/><br/>
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# <u>Chen K</u>, Hu Z, <u>Xia Z</u>, <u>Li W*</u>, Tyler J*: The overlooked fact: fundamental need of spike-in control for virtually all genome-wide analyses (commentary) <br/> '''''Molecular and Cellular Biology''''' 36 (2016) 662-667. PMCID: PMC4760223.<br/><br/>
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# Jain AK, <u>Xi Y</u>, McCarthy RL, Alton K, Akdemir KC, Aronow B, Lin C, <u>Li W</u>, Yang L, Barton MC!: LncPRESS1 is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6 mediated de-acetylation of histone H3K56. <br/> ''Molecular Cell'' 64 (2016) 967-981. PMCID: PMC5137794 <br/><br/>
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# Li X, Wang W, <u>Xi Y</u>, Gao M, Tran M, Aziz KE, Qin J, <u>Li W</u>, Chen J!: FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. <br/> ''Cell Reports'' 16 (2016) 487-497. PMCID: PMC4946253 <br/><br/>
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# Blair LP, Liu Z, Labitigan RLD, Wu L, Zheng D, <u>Xia Z</u>, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, <u>Li W</u>, Tian B, Tackett AJ, Yan Q!: KDM5 Lysine Demethylases Are Involved in Maintenance of 3’UTR Length. <br/>''Science Advances'' 2 (2016)  <br/><br/>
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# Rau RE, <u>Rodriguez B</u>, Luo M, Jeong M, Rosen A, Rogers JH, Campbell CT, Daigle SR, Deng L, Song Y, Sweet S, Chevassut T, Andreeff M, Kornblau SM, <u>Li W</u>, Goodell MA: DOT1L As a Therapeutic Target for the Treatment of DNMT3A-Mutant Acute Myeloid Leukemia. <br/>''Blood'' 128 (2016) 971-981. PMCID: PMC4990856. <br/><br/>
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# Masamha CP, <u>Xia Z</u>, Colllum S, Peart N, <u>Li W</u>, Wagner EJ, Shyu A: CFIm25 Regulates Glutaminase Alternative Terminal Exon Definition. <br/> ''RNA'' 22 (2016) 830-838. PMCID: PMC4878610 <br/><br/>
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# Xu J, Zhang W, Yan XJ, <u>Lin XQ</u>, <u>Li W</u>, Mi JQ, Li JM, Zhu J, Chen Z, Chen SJ: DNMT3A mutation leads to leukemic extramedullary infiltration mediated by TWIST1. <br/> ''J Hematol Oncol'' 9 (2016) 106. <br/><br/>
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# Lee SH, Chen TY, Dhar SS, Gu B, <u>Chen K</u>, Kim YZ, <u>Li W</u>, Lee MG: A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4, c-Myc to regulate stemness. <br/> ''Nucleic Acids Res'' 44 (2016) 10603-10618. PMCID: PMC5159542<br/><br/>
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# Giudice J, <u>Xia Z</u>, <u>Li W</u>, Cooper TA: Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1. <br/>''Scientific Reports'' 6 (2016) 35550.<br/><br/>'''2015'''  <br/><br/>
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#<u>Chen K^</u>, Chen Z^, Wu D, Zhang L, <u>Lin X</u>, <u>Su J</u>, <u>Rodriguez B</u>, <u>Xi Y</u>, <u>Xia Z</u>, Chen X, Shi X, Wang Q*, <u>Li W*</u>!: Broad H3K4me3 is Asscoated with Increased Transcription Elongation and Enhancer Activity at Tumor Suppressor Genes. <br/> '''''Nature Genetics''''' 47 (2015) 1149-1157.  See reports in Nature Editor’s [http://blogs.nature.com/freeassociation/2015/08/methylation-marks-tumor-suppressors.html Blog], [http://cancerdiscovery.aacrjournals.org/content/early/2015/09/01/2159-8290.CD-RW2015-166.abstract Cancer Discovery], [http://www.ebiotrade.com/newsf/2015-8/2015825165005119.htm ebiotrade.com] (in Chinese), [http://fromthelabs.bcm.edu/2015/10/15/novel-epigenetic-signature-for-tumor-suppressors-in-normal-cells-found/ BCM news] and [http://cancer.osu.edu/news-and-media/news/studies-suggest-new-ways-to-inhibit-oncogenes-enhance-tumor-suppressor-activity OSU news]; and an error we found in a [http://www.cell.com/cell/fulltext/S0092-8674(15)01407-5 Cell paper].<br/><br/>
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# Luo M^, Jeong M^, <u>Sun D^</u>, <u>Park HJ^</u>, <u>Rodrigues B^</u>, <u>Xia Z</u>, Yang L, Zhang X, Darlington GJ, <u>Li W*</u>!, Goodell MA*: Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function. <br/> '''''Cell Stem Cell''''' 16 (2015) 426–438 <br/><br/>
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# Chen L^, <u>Chen K^</u>, Lavery LA, Baker SA, Shaw C, <u>Li W*</u>, Zoghbi HY*: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome. <br/> '''''PNAS''''' 112 (2015) 5509-5514 <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 '''''  13 (2015) 98-106 <br/><br/>
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# Roadmap Epigenomics Consortium (including <u>Li W</u> as a co-PI/co-author)!: Integrative analysis of 111 reference human epigenomes.<br/> '''''Nature''''' 518 (2015) 317-330. <br/><br/>
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# <u>Yiu T</u>, <u>Li W</u>: Pediatric Cancer Epigenome and the Influence of Folate. (Invited Review)<br/> '''''Epigenomics''''' (2015) 1-13 <br/><br/>
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# Yang Y, Hadjikyriacou A, <u>Xia Z</u>, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, <u>Li W</u>, Clarke SG, Bedford MT!: PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145. <br/> ''Nature Communications'' 6 (2015) 6428  <br/><br/>
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# An J, Gonzalez-Avalos E, Chawla A, Jeong M, Lopez-Moyado LF, <u>Li W</u>, Goodell MA, Chavez L, Ko M, Rao A!: Acute loss of TET function results in aggressive myeloid cancer in mice. <br/>''Nature Communications'' 6 (2015) 10071 <br/><br/>
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# Morikawa Y, Zhang M, Heallen T, Leach J, Tao G, Xiao Y, Bai Y, <u>Li W</u>, Willerson JT, Martin JF!: Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice. <br/> ''Science Signaling'' 8 (2015) ra41 <br/><br/>
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# Gennarino VA, Alcott CE, Chen C, A. C, A. GM, A. RJ, Parikh S, W. WJ, Roeder ER, D. HD, Roney EK, Smith JL, Cheung SW, <u>Li W</u>, Neilson JR, Schaaf CP, Zoghbi HY: NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation. <br/> ''eLife''  4 (2015) PMC4586391. <br/><br/>
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# Mayle A, Yang L, <u>Rodriguez B</u>, Zhou T, Chang E, Curry CV, Challen GA, <u>Li W</u>, Wheeler D, Rebel VI, Goodell MA: Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation. <br/> ''Blood'' 125 (2015) 629-638 <br/><br/>
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#Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X,<u>Xia Z</u>, Salinger AP, Wilson M, Vizeacoumar F, Datti A, <u>Li W</u>, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. <br/> ''Genes & Development''  29 (2015) 803-816. PMCID <br/><br/>
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# Chen Z, Lan X, Thomas-Ahner JM, Wu D, Liu X, Ye Z, <u>Wang L</u>, Sunkel B, Grenade C, <u>Chen J</u>, Zynger DL, Yan PS, Huang J, Nephew KP, Huang TH, Lin S, Clinton SK, <u>Li W</u>, Jin VX, Wang Q: Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer.<br/> ''The EMBO Journal'' 34 (2015) 502-516 <br/><br/>
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# Poungvarin N, Chang B, Imamura M, <u>Chen J</u>, Moolsuwan K, Sae-Lee C, <u>Li W</u>, Chan L: Genome-Wide Analysis of ChREBP Binding Sites on Mouse Liver and White Adipose Chromatin. <br/> ''Endocrinology'' 156 (2015) 1982-1994. PMCID: PMC4430618. <br/><br/>
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# Li X, Wang W, Wang J, Malovannaya A, <u>Xi Y</u>, <u>Li W</u>, Guerra R, Hawke DH, Qin J, Chen J: Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. <br/> ''Molecular Systems Biology'' 11 (2015) 775  <br/><br/>'''2014''' <br/><br/>
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# <u>Xia Z</u>, Donehower L, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, <u>Li W*</u>!: Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape across 7 Tumor Types. <br/> '''''Nature Communications''''' 5 (2014) 5274 <br/><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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# 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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# 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''''' 15 (2014) 350-364. PMCID: PMC4163922 <br/><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>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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# 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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# Li Y, Wen H, <u>Xi Y</u>, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Li B, Dent SY, <u>Li W*</u>!, Li H*, Shi X*: AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.  <br/> '''''Cell ''''' 159 (2014) 558-571<br/><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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# <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.''''' 42 (2014) e156. PMCID <br/><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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# <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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# 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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# 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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 +
# <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/>
 +
# <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/>
 +
# <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/>
 +
# <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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 +
# 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/>
 
# <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''''' 28 (2012) 2184-2185. <br/><br/>
 
# <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/>
# 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/>
+
# 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/>
# 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/>
 
 
# 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/>
 
# 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/>
 
# 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/>
 
# 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/>
 
# 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/>
 
# 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/>
 
# 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/>
 
# 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/>
 
# Kannan K^, <u>Wang L^</u>, Wang J, Ittmann M, <u>Li W*</u>, Yen L*: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing. <br/>'''''PNAS''''' 108 (2011) 9172-9177. <br/><br/>
 
# Kannan K^, <u>Wang L^</u>, Wang J, Ittmann M, <u>Li W*</u>, Yen L*: Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing. <br/>'''''PNAS''''' 108 (2011) 9172-9177. <br/><br/>
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# Klisch T^, <u>Xi Y^</u>, Flora A, <u>Wang L</u>, <u>Li W*</u>, Zoghbi H*: In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. <br/>'''''PNAS''''' (2011). 108 (2011) 3288-3293.  '''''Faculty of 1000''''' [http://f1000.com/9123970  Must Read] <br/><br/>
 
# Klisch T^, <u>Xi Y^</u>, Flora A, <u>Wang L</u>, <u>Li W*</u>, Zoghbi H*: In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. <br/>'''''PNAS''''' (2011). 108 (2011) 3288-3293.  '''''Faculty of 1000''''' [http://f1000.com/9123970  Must Read] <br/><br/>
 
# Daines B^, Wang H^, <u>Wang L^</u>, Li Y, Emmert D, Gelbart W, <u>Li W</u>, Gibbs R, Chen RA: The Drosophila melanogaster Transcriptome by Paired-End RNA-Sequencing. <br/>'''''Genome Res''''' 21 (2011) 315-324. <br/><br/>
 
# Daines B^, Wang H^, <u>Wang L^</u>, Li Y, Emmert D, Gelbart W, <u>Li W</u>, Gibbs R, Chen RA: The Drosophila melanogaster Transcriptome by Paired-End RNA-Sequencing. <br/>'''''Genome Res''''' 21 (2011) 315-324. <br/><br/>
# 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, <u>Li W</u>, Wang Y, O'Malley Bert W, Qin J: Analysis of the Human Endogenous Coregulator Complexome.  <br/> '''''Cell''''' 145 (2011) 787-799. <br/><br/>
+
# 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, <u>Li W</u>, Wang Y, O'Malley Bert W, Qin J!: Analysis of the Human Endogenous Coregulator Complexome.  <br/> ''Cell'' 145 (2011) 787-799. <br/><br/>
 
# Huang Z, <u>Chen K</u>, Xu T, Zhang J, Li Y, <u>Li W</u>, Agarwal AK, Clark AM, Phillips JD, Pan X: Sampangine inhibits heme biosynthesis in both yeast and human.  <br/> ''Eukaryotic Cell''  (2011) Accepted. <br/><br/>
 
# Huang Z, <u>Chen K</u>, Xu T, Zhang J, Li Y, <u>Li W</u>, Agarwal AK, Clark AM, Phillips JD, Pan X: Sampangine inhibits heme biosynthesis in both yeast and human.  <br/> ''Eukaryotic Cell''  (2011) Accepted. <br/><br/>
 
# Chen Y, Meyer CA, Liu T, Taing L, <u>Li W</u>, Liu JS, Liu XS: MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip/seq data. <br/> ''Genome Biology'' 12 (2011) R11.<br/><br/> '''2010'''  <br/><br/>
 
# Chen Y, Meyer CA, Liu T, Taing L, <u>Li W</u>, Liu JS, Liu XS: MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip/seq data. <br/> ''Genome Biology'' 12 (2011) R11.<br/><br/> '''2010'''  <br/><br/>
 
# <u>Wang L</u>, <u>Xi Y</u>, Yu J, Dong L, Yen L, <u>Li W*</u>: A Statistical Method for the Detection of Alternative Splicing using RNA-seq. <br/>'''''PLoS ONE''''' 5 (2010) e8529.[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008529 Full Article];  Highlighted in This Week in PLoS in [http://www.genomeweb.com/blog/week-plos-67 '''''GenomeWeb.com''''']<br/><br/>
 
# <u>Wang L</u>, <u>Xi Y</u>, Yu J, Dong L, Yen L, <u>Li W*</u>: A Statistical Method for the Detection of Alternative Splicing using RNA-seq. <br/>'''''PLoS ONE''''' 5 (2010) e8529.[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008529 Full Article];  Highlighted in This Week in PLoS in [http://www.genomeweb.com/blog/week-plos-67 '''''GenomeWeb.com''''']<br/><br/>
 
# Chen Z^, <u>Wang L^</u>, Wang Q*, <u>Li W*</u>: Histone modifications and chromatin organization in prostate cancer (Invited Review). <br/>'''''Epigenomics''''' 2 (2010) 551-560. [http://openwetware.org/images/e/e9/Li.pdf  Full Article] <br/><br/>
 
# Chen Z^, <u>Wang L^</u>, Wang Q*, <u>Li W*</u>: Histone modifications and chromatin organization in prostate cancer (Invited Review). <br/>'''''Epigenomics''''' 2 (2010) 551-560. [http://openwetware.org/images/e/e9/Li.pdf  Full Article] <br/><br/>
# 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, <u>Xi Y</u>, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, <u>Li W</u>, 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. <br/>'''''Nature Biotechnology'''''  28 (2010) 1097-1105. <br/><br/>
+
# 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, <u>Xi Y</u>, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, <u>Li W</u>, 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. <br/>''Nature Biotechnology''  28 (2010) 1097-1105. <br/><br/>
 
# Lanz RB, Bulynko Y, Malovannaya A, Labhart P, <u>Wang L</u>, <u>Li W</u>, Qin J, Harper M, O'Malley BW:  Global Characterization of Transcriptional Impact of the SRC-3 Coregulator. <br/> ''Mol Endocrinol'' 24 (2010) 859-872.<br/><br/>
 
# Lanz RB, Bulynko Y, Malovannaya A, Labhart P, <u>Wang L</u>, <u>Li W</u>, Qin J, Harper M, O'Malley BW:  Global Characterization of Transcriptional Impact of the SRC-3 Coregulator. <br/> ''Mol Endocrinol'' 24 (2010) 859-872.<br/><br/>
 
# Kim BJ, Li Y, Zhang J, <u>Xi Y</u>, Yang T, Jung SY, Pan X, Chen R, <u>Li W</u>, Wang Y, Qin J: Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells. <br/> ''J Biol Chem'' 285 (2010) 22784-22792.<br/><br/>
 
# Kim BJ, Li Y, Zhang J, <u>Xi Y</u>, Yang T, Jung SY, Pan X, Chen R, <u>Li W</u>, Wang Y, Qin J: Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells. <br/> ''J Biol Chem'' 285 (2010) 22784-22792.<br/><br/>
 
# Wang M, Song X, Han P, <u>Li W</u>, Jiang B: Couplet- syntax: an improved syntax to represent pre-miRNA’s local continuous structure-sequence information. <br/>''Journal of Theoretical Biology''. 264 (2010) 578-584. <br/><br/> '''2009''' <br/><br/>
 
# Wang M, Song X, Han P, <u>Li W</u>, Jiang B: Couplet- syntax: an improved syntax to represent pre-miRNA’s local continuous structure-sequence information. <br/>''Journal of Theoretical Biology''. 264 (2010) 578-584. <br/><br/> '''2009''' <br/><br/>
 
# <u>Xi Y</u>, <u>Li W*</u>: BSMAP: whole genome Bisulfite Sequence MAPping program.  <br/>''''' BMC Bioinformatics''''' (2009) 10:232.[http://www.biomedcentral.com/1471-2105/10/232 Full Article];  '''''BioMed Central Highly Accessed'''''<br/><br/>
 
# <u>Xi Y</u>, <u>Li W*</u>: BSMAP: whole genome Bisulfite Sequence MAPping program.  <br/>''''' BMC Bioinformatics''''' (2009) 10:232.[http://www.biomedcentral.com/1471-2105/10/232 Full Article];  '''''BioMed Central Highly Accessed'''''<br/><br/>
# Wang Q^, <u>Li W^</u>, Zhang Y, Yuan X, ..., Kantoff PW, Liu XS*, Brown M*: Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer.  <br/>'''''Cell''''' 138 (2009) 245-256  [http://www.cell.com/fulltext/S0092-8674(09)00517-0?large_figure=true Full Article];      '''''Faculty of 1000''''' [http://f1000biology.com/article/id/1162908/evaluation/sections  Must Read];    [http://www.nature.com/nrc/journal/v9/n9/full/nrc2727.html Prostate-cancer Research Highlights] in  ''''' Nature Review Cancer ''''';    [http://pubs.acs.org/doi/abs/10.1021/cb9002046 Spotlight] in  '''''ACS Chem. Biol'''''<br/><br/>
+
# Wang Q^, <u>Li W^</u>, Zhang Y, Yuan X, ..., Kantoff PW, Liu XS*, Brown M*!: Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer.  <br/>'''''Cell''''' 138 (2009) 245-256  [http://www.cell.com/fulltext/S0092-8674(09)00517-0?large_figure=true Full Article];      '''''Faculty of 1000''''' [http://f1000biology.com/article/id/1162908/evaluation/sections  Must Read];    [http://www.nature.com/nrc/journal/v9/n9/full/nrc2727.html Prostate-cancer Research Highlights] in  ''''' Nature Review Cancer ''''';    [http://pubs.acs.org/doi/abs/10.1021/cb9002046 Spotlight] in  '''''ACS Chem. Biol'''''<br/><br/>
 
# Huang J, Chen T, Liu X, Jiang J, Li J, Li D, Liu XS, <u>Li W</u>, Kang J, Pei G: More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells. <br/>''Cell Res'' (2009) <br/><br/>
 
# Huang J, Chen T, Liu X, Jiang J, Li J, Li D, Liu XS, <u>Li W</u>, Kang J, Pei G: More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells. <br/>''Cell Res'' (2009) <br/><br/>
 
# Xia X, Lemieux M, <u>Li W</u>, Carroll JS, Brown M, Liu XS and Kung A: Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. <br/>''PNAS'' 106 (2009) 4260-4265.<br/><br/> '''2008''' <br/><br/>
 
# Xia X, Lemieux M, <u>Li W</u>, Carroll JS, Brown M, Liu XS and Kung A: Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. <br/>''PNAS'' 106 (2009) 4260-4265.<br/><br/> '''2008''' <br/><br/>
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# Johnson D^, <u>Li W^</u>, 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.  <br/>'''''Genome Res'''''. 18 (2008) 393-403.  [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Systematic+evaluation+of+variability+in+ChIP-chip+experiments+using+predefined+DNA+targets Abstract] [http://www.genome.org/cgi/content/full/18/3/393 Full Article];        [http://www.nature.com/nmeth/journal/v5/n4/abs/nmeth0408-288.html Highlights] in '''''Nature Method'''''<br/><br/>
 
# Johnson D^, <u>Li W^</u>, 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.  <br/>'''''Genome Res'''''. 18 (2008) 393-403.  [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Systematic+evaluation+of+variability+in+ChIP-chip+experiments+using+predefined+DNA+targets Abstract] [http://www.genome.org/cgi/content/full/18/3/393 Full Article];        [http://www.nature.com/nmeth/journal/v5/n4/abs/nmeth0408-288.html Highlights] in '''''Nature Method'''''<br/><br/>
 
# <u>Li W</u>, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides. <br/> '''''BMC Genomics''''' (2008). [http://www.ncbi.nlm.nih.gov/pubmed/18366610?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18366610 Full Article];  [http://www.bioinform.com/issues/12_20/in_print/146975-1.html News] in '''''Bioinform''''' <br/><br/>
 
# <u>Li W</u>, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides. <br/> '''''BMC Genomics''''' (2008). [http://www.ncbi.nlm.nih.gov/pubmed/18366610?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18366610 Full Article];  [http://www.bioinform.com/issues/12_20/in_print/146975-1.html News] in '''''Bioinform''''' <br/><br/>
# Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, <u>Li W</u>, Carroll JS, Liu XS and Brown M: FoxA1 translates epigenetic signatures into lineage-specific transcription. <br/>'''''Cell''''' 132 (2008) 958-970 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=FoxA1+translates+epigenetic+signatures+into+lineage-specific+transcription Abstract]<br/><br/>
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# Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, <u>Li W</u>, Carroll JS, Liu XS and Brown M!: FoxA1 translates epigenetic signatures into lineage-specific transcription. <br/>''Cell'' 132 (2008) 958-970 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=FoxA1+translates+epigenetic+signatures+into+lineage-specific+transcription Abstract]<br/><br/>
 
# Agoulnik IU, Bingman WE, Nakka M, <u>Li W</u>, Wang Q, Brown M, Liu XS, Weigel NL: Target Gene Specific Regulation of Androgen Receptor Activity by p42/p44 MAPK. <br/>''Mol Endocrinol'' 22 (2008) 2420-2432.<br/><br/>
 
# Agoulnik IU, Bingman WE, Nakka M, <u>Li W</u>, Wang Q, Brown M, Liu XS, Weigel NL: Target Gene Specific Regulation of Androgen Receptor Activity by p42/p44 MAPK. <br/>''Mol Endocrinol'' 22 (2008) 2420-2432.<br/><br/>
 
# Yagi S, Hirabayashi K, Sato S, <u>Li W</u>, 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. <br/>''Genome Res'' 18 (2008) 1969-1978<br/><br/>
 
# Yagi S, Hirabayashi K, Sato S, <u>Li W</u>, 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. <br/>''Genome Res'' 18 (2008) 1969-1978<br/><br/>
 
# Gottardo R, <u>Li W</u>, Liu XS and Johnson WE: A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. <br/>''Biometrics'' 64 (2008) 468-478. [http://www.ncbi.nlm.nih.gov/pubmed/17888037?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] <br/><br/> '''2007'''  <br/><br/>
 
# Gottardo R, <u>Li W</u>, Liu XS and Johnson WE: A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. <br/>''Biometrics'' 64 (2008) 468-478. [http://www.ncbi.nlm.nih.gov/pubmed/17888037?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] <br/><br/> '''2007'''  <br/><br/>
# Wang Q, <u>Li W</u>, 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)  <br/>'''''Mol Cell''''' 27 (2007) 380-392.  [http://www.ncbi.nlm.nih.gov/pubmed/17679089?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract];    '''''Faculty of 1000''''' [http://www.f1000biology.com/article/id/1089669 Recommended]<br/><br/>
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# Wang Q, <u>Li W</u>, 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)  <br/>''Mol Cell'' 27 (2007) 380-392.  [http://www.ncbi.nlm.nih.gov/pubmed/17679089?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract];    '''''Faculty of 1000''''' [http://www.f1000biology.com/article/id/1089669 Recommended]<br/><br/>
 
# O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser R, Wong KK, <u>Li W</u>, 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. <br/>''J Exp Med'' 204 (2007) 3059-3066.<br/><br/>
 
# O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser R, Wong KK, <u>Li W</u>, 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. <br/>''J Exp Med'' 204 (2007) 3059-3066.<br/><br/>
 
# Song JS, Johnson WE, Zhu X, Zhang X, <u>Li W</u>, Manrai AK, Liu JS, Chen R and Liu XS: Model-based analysis of two-color arrays (MA2C). <br/>''Genome Biol'' 8 (2007) R178. [http://www.ncbi.nlm.nih.gov/pubmed/17727723?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
 
# Song JS, Johnson WE, Zhu X, Zhang X, <u>Li W</u>, Manrai AK, Liu JS, Chen R and Liu XS: Model-based analysis of two-color arrays (MA2C). <br/>''Genome Biol'' 8 (2007) R178. [http://www.ncbi.nlm.nih.gov/pubmed/17727723?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
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# Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.(<u>list author</u>) <br/>''Genome Biol'' 8 (2007) R45.  [http://www.ncbi.nlm.nih.gov/pubmed/17407547?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17407547 Full Article]<br/><br/> '''2006'''  <br/><br/>
 
# Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.(<u>list author</u>) <br/>''Genome Biol'' 8 (2007) R45.  [http://www.ncbi.nlm.nih.gov/pubmed/17407547?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17407547 Full Article]<br/><br/> '''2006'''  <br/><br/>
 
# Johnson WE^, <u>Li W^</u>, Meyer CA^, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. <br/>'''''PNAS'''''. U S A 103 (2006) 12457-12462. [http://www.ncbi.nlm.nih.gov/pubmed/16895995?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16895995 Full Article] <br/><br/>
 
# Johnson WE^, <u>Li W^</u>, Meyer CA^, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. <br/>'''''PNAS'''''. U S A 103 (2006) 12457-12462. [http://www.ncbi.nlm.nih.gov/pubmed/16895995?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16895995 Full Article] <br/><br/>
# Carroll JS, Meyer CA, Song J, <u>Li W</u>, 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. <br/> '''''Nat. Genet'''''. 38 (2006) 1289-1297. [http://www.ncbi.nlm.nih.gov/pubmed/17013392?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
 
 
# Ji X^, <u>Li W^</u>, Song J, Wei L and Liu XS: CEAS: cis-regulatory element annotation system.  <br/> '''''Nucleic Acids Res.''''' 34 (2006) W551-554.  [http://www.ncbi.nlm.nih.gov/pubmed/16845068?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16845068 Full Article]<br/><br/>
 
# Ji X^, <u>Li W^</u>, Song J, Wei L and Liu XS: CEAS: cis-regulatory element annotation system.  <br/> '''''Nucleic Acids Res.''''' 34 (2006) W551-554.  [http://www.ncbi.nlm.nih.gov/pubmed/16845068?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16845068 Full Article]<br/><br/>
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# Carroll JS, Meyer CA, Song J, <u>Li W</u>, 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. <br/> ''Nature Genetics''. 38 (2006) 1289-1297. [http://www.ncbi.nlm.nih.gov/pubmed/17013392?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
 
# Nelson EA, Walker SR, <u>Li W</u>, Liu XS and Frank DA: Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology. <br/>''J. Biol. Chem''. 281 (2006) 26216-26224. [http://www.ncbi.nlm.nih.gov/pubmed/16840779?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.jbc.org/cgi/content/full/281/36/26216 Full Article]<br/><br/>
 
# Nelson EA, Walker SR, <u>Li W</u>, Liu XS and Frank DA: Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology. <br/>''J. Biol. Chem''. 281 (2006) 26216-26224. [http://www.ncbi.nlm.nih.gov/pubmed/16840779?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.jbc.org/cgi/content/full/281/36/26216 Full Article]<br/><br/>
 
# Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, <u>Li W</u>, Liu XS, Young RA and Look AT: Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. <br/>''Blood'' 108 (2006) 986-992. [http://www.ncbi.nlm.nih.gov/pubmed/16621969?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16621969 Full Article]<br/><br/>
 
# Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, <u>Li W</u>, Liu XS, Young RA and Look AT: Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. <br/>''Blood'' 108 (2006) 986-992. [http://www.ncbi.nlm.nih.gov/pubmed/16621969?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16621969 Full Article]<br/><br/>
# The DNA sequence, annotation and analysis of human chromosome 3. (<u>list author</u>) <br/>'''''Nature''''' 440 (2006) 1194-1198. [http://www.ncbi.nlm.nih.gov/pubmed/16641997?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/> '''2005'''  <br/><br/>
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# The DNA sequence, annotation and analysis of human chromosome 3. (<u>list author</u>) <br/>''Nature'' 440 (2006) 1194-1198. [http://www.ncbi.nlm.nih.gov/pubmed/16641997?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/> '''2005'''  <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/>
 
# <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/>
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# 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/>
# 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/>
# 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/>
 
# 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/>
 
 
# <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/>
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# 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/>
# 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/>
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# 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/>
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# 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/>
# A draft sequence of the rice genome (Oryza sativa L. ssp. indica). (<u>list author</u>) <br/>'''''Science''''' 296 (2002) 79-92.  [http://www.ncbi.nlm.nih.gov/pubmed/11935017?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] <br/><br/>  
+
# A draft sequence of the rice genome (Oryza sativa L. ssp. indica). (<u>list author</u>) <br/>''Science'' 296 (2002) 79-92.  [http://www.ncbi.nlm.nih.gov/pubmed/11935017?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] <br/><br/>  
 
# Ling L, Wang J, Cui Y, <u>Li W</u> 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. <br/>[http://www.ncbi.nlm.nih.gov/pubmed/12383754?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNH-46WNYGM-6&_user=5674961&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000003838&_version=1&_urlVersion=0&_userid=5674961&md5=c12dc08952da2b5a9545bf27a4017384 Full Article]<br/><br/>
 
# Ling L, Wang J, Cui Y, <u>Li W</u> 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. <br/>[http://www.ncbi.nlm.nih.gov/pubmed/12383754?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNH-46WNYGM-6&_user=5674961&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000003838&_version=1&_urlVersion=0&_userid=5674961&md5=c12dc08952da2b5a9545bf27a4017384 Full Article]<br/><br/>
 
# Zhong L, Wang K, Tan J, <u>Li W</u> and Li S: Putative cytochrome P450 genes in rice genome (Oryza sativa L. ssp. indica) and their EST evidence. <br/>''Sci. China C Life Sci''. 45 (2002) 512-517.  [http://scholar.ilib.cn/A-zgkx-ec200205007.html Abstract]<br/><br/> '''2001'''  <br/><br/>
 
# Zhong L, Wang K, Tan J, <u>Li W</u> and Li S: Putative cytochrome P450 genes in rice genome (Oryza sativa L. ssp. indica) and their EST evidence. <br/>''Sci. China C Life Sci''. 45 (2002) 512-517.  [http://scholar.ilib.cn/A-zgkx-ec200205007.html Abstract]<br/><br/> '''2001'''  <br/><br/>
# International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. (<u>list author</u>) <br/>'''''Nature''''' 409 (2001) 860-921.  [http://www.ncbi.nlm.nih.gov/pubmed/11237011?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
+
# International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. (<u>list author</u>) <br/>''Nature'' 409 (2001) 860-921.  [http://www.ncbi.nlm.nih.gov/pubmed/11237011?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]<br/><br/>
 
# A draft sequence of the rice (Oryza sativa ssp. indica) genome. (<u>list author</u>) <br/>''Chin. Sci. Bull''. 46 (2001) 1937-1942.
 
# A draft sequence of the rice (Oryza sativa ssp. indica) genome. (<u>list author</u>) <br/>''Chin. Sci. Bull''. 46 (2001) 1937-1942.

Latest revision as of 11:31, 26 September 2017

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Peer Reviewed Publications

Major Publications (A Li Lab member is the ^(co-)first or *(co-)corresponding author); H-index = 55; Citations @ Google Scholar

  1. Feng X, Li L, Wagner E, Li W: TC3A: The Cancer 3’ UTR Atlas.
    Nucleic Acids Research (2017). Accepted

  2. Mi W^, Guan H^, Lyu J^, …, Li W*!, Li H*, Shi X*: YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer.
    Nature Communications (2017). Accepted

  3. …, Lyu J, Li W, Kutateladze T: Covalent modifications of histone H3K9 promote binding of CHD3.
    Cell Reports (2017). Accepted

  4. Lin X, Su J, Chen K, Rodrigues B, Li W*: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.
    Genome Biology 18 (2017) 163

  5. Huang Y^, Su J^, Lei Y, Brunetti L, Gundry MC, Zhang X, Jeong M, Li W*, Goodell MA*: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A.
    Genome Biology 18 (2017) 176.

  6. Lei Y^, Zhang X^, Su J^, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W, Goodell MA: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein.
    Nature Communications 8 (2017) 16026.

  7. Wan L, Wen H, Li Y, Lyu J, Xi Y, Hoshii T, Joseph J, Wang X, Loh Y, Erb MA, Shen L, Li W, Li H, Allis CD, Armstrong SA, Shi X: ENL links histone acetylation to oncogenic gene expression in AML.
    Nature 543 (2017) 265-269. PMCID: PMC5372383

  8. The Cancer Genome Atlas Research Network (include Xia Z, Li W): Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma.
    Cell 169 1327-1341.e1323.

  9. Dai F, Lee H, Li Z, Yao H, Xi Y, Xiao Z, You MJ, Li W, Su X, Gan B: BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response.
    PNAS 114 (2017) 3192-3197. PMCID: PMC5373337

  10. Brinegar AE, Xia Z, Loehr JA, Manning KS, Li W, Rodney GG, Cooper TA: Extensive alternative splicing transitions during postnatal skeletal muscle development are required for Ca2+ handling.
    eLife (2017) 6:e27192

  11. Oegema R, Baillat D, Schot R, van Unen LM, Brooks A, Kia SK, Hoogeboom AJM, Xia Z, Li W, Cesaroni M, Lequin MH, van Slegtenhorst M, Dobyns WB, de Coo IFM, Verheijen FW, Kremer A, van der Spek PJ, Heijsman D, Wagner EJ, Fornerod M, Mancini GMS: Human Mutations in Integrator complex subunits link Transcriptome Integrity to Brain Development.
    PLOS Genetics 13 (2017) e1006809

  12. Lee YH, Martin-Orozco N, Zheng P, Li J, Zhang P, Tan H, Park HJ, Jeong M, Chang SH, Kim BS, Xiong W, Zang W, Guo L, Liu Y, Dong ZJ, Overwijk WW, Hwu P, Yi Q, Kwak L, Yang Z, Mak TW, Li W, Radvanyi LG, Ni L, Liu D, Dong C: Inhibition of the B7-H3 immune checkpoint limits tumor growth by enhancing cytotoxic lymphocyte function.
    Cell Res 27 (2017) 1034-1045. PMCID

  13. Li J, Xi Y, Li W, McCarthy RL, Jain AK, Stratton S, Li W, Dent SY, Barton MC: TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation.
    Oncogene 36 (2017) 2991-3001

  14. McNair C, Urbanucci A, Comstock CE, Augello MA, Goodwin JF, Launchbury R, Zhao SG, Schiewer MJ, Ertel A, Karnes J, Davicioni E, Wang L, Wang Q, Mills IG, Feng FY, Li W, Carroll JS, Knudsen KE: Cell cycle-coupled expansion of AR activity promotes cancer progression.
    Oncogene 36 (2017) 1655-1668. PMCID: PMC5364060

  15. Routh A, Ji P, Jaworski E, Xia Z, Li W, Wagner E: Poly(A)-ClickSeq: click-chemistry for next-generation 3’-end sequencing without RNA enrichment or fragmentation.
    Nucleic Acids Res 45 (2017) e112. PMCID: PMC5499544

  16. Sowalsky AG, Kissick HT, Gerrin S, Schaefer R, Xia Z, Russo J, Arredouani MS, Bubley GJ, Sanda MG, Li W, Ye H, Balk SP: Gleason Score 7 Prostate Cancers Emerge Through Branched Evolution of Clonal Gleason Pattern 3 and 4.
    Clin Cancer Res 23 (2017) 3823-3833. PMCID: PMC5511561

  17. Koppula P, Zhang Y, Shi J, Li W, Gan B: The glutamate/cystine antiporter SLC7A11/xCT enhances cancer cell dependency on glucose by exporting glutamate.
    J Biol Chem 292 (2017) 14240-14249. PMCID: PMC5572906

  18. Gates LA, Shi J, Rohira AD, Feng Q, Zhu B, Bedford MT, Sagum CA, Jung SY, Qin J, Tsai MJ, Tsai SY, Li W, Foulds CE, O'Malley BW: Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation.
    J Biol Chem 292 (2017) 14456-14472. PMCID

  19. Watters RJ, Hartmaier RJ, Osmanbeyoglu HU, Gillihan RM, Rae J, Liao L, Chen K, Li W, Lu X, Oesterreich S: Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen.
    Molecular and Cellular Endocrinology 448 (2017) 21–27

  20. Hirai T, Mulpuri Y, Cheng Y, Xia Z, Li W, Ruangsri S, Spigelman I, Nishimura I: Aberrant plasticity of peripheral sensory axons in a painful neuropathy.
    Scientific Reports 7 (2017) 3407. PMCID: PMC5469767

    2016

  21. Zhang X^, Su J^, Jeong M, Ko M, Huang Y, Park HJ, Guzman A, Lei Y, Huang YH, Rao A, Li W*!, Goodell MA*: DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells.
    Nature Genetics 48 (2016) 1014-1023. PMCID: PMC4957136

  22. Yang L^, Rodriguez B^, Mayle A^, Park HJ, Lin X, Luo M, Jeong M, Curry CV, Kim SB, Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, Li W*!, Goodell MA*: DNMT3A loss drives enhancer hypomethylation in FLT3-ITD-associated leukemias.
    Cancer Cell 29 (2016) 922-934. PMCID: PMC4908977

  23. Li N, Li Y, Lv J, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, Wang Z, Shiekhattar R, Shi X, Lan F, Chen K, Li W*!, Li H*, Lee MG*: ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes.
    Molecular Cell 63 (2016) 470-484. PMCID: PMC4975651

  24. Tasselli L, Xi Y, Zheng W, Tennen RI, Odrowaz Z, Simeoni F, Li W*!, Chua KF*: SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence.
    Nature Structural & Molecular Biology 23 (2016) 434–440

  25. Zhang X^, Peng D^, Xi Y^, Yuan C^, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG, Li W, Bedfore MT, Shi X!: G9a-mediated methylation of estrogen receptor α links the PHF20/MOF histone acetylation complex to hormonal gene expression.
    Nature Communications 7 (2016) 10810.

  26. Dhar S^, Lee SH^, Chen K^, Zhu G^, Oh W, Allton K, Gafni O, Kim YZ, Barton MC, Hanna JH, Wang Z*, Li W*, Lee MG*: An essential role for UTX in resolution and activation of bivalent promoters.
    Nucleic Acids Research 44 (2016) 3659-3674. PMCID: PMC4856969

  27. Gabrusiewicz K^, Rodriguez B^, …, Li W, …, Gabrusiewicz AB: Glioblastoma-infiltrated innate immune cells resemble M0 macrophage phenotype.
    Journal of Clinical Investigation Insight 1 (2016) PMC4784261

  28. Chen K, Hu Z, Xia Z, Li W*, Tyler J*: The overlooked fact: fundamental need of spike-in control for virtually all genome-wide analyses (commentary)
    Molecular and Cellular Biology 36 (2016) 662-667. PMCID: PMC4760223.

  29. Jain AK, Xi Y, McCarthy RL, Alton K, Akdemir KC, Aronow B, Lin C, Li W, Yang L, Barton MC!: LncPRESS1 is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6 mediated de-acetylation of histone H3K56.
    Molecular Cell 64 (2016) 967-981. PMCID: PMC5137794

  30. Li X, Wang W, Xi Y, Gao M, Tran M, Aziz KE, Qin J, Li W, Chen J!: FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis.
    Cell Reports 16 (2016) 487-497. PMCID: PMC4946253

  31. Blair LP, Liu Z, Labitigan RLD, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q!: KDM5 Lysine Demethylases Are Involved in Maintenance of 3’UTR Length.
    Science Advances 2 (2016)

  32. Rau RE, Rodriguez B, Luo M, Jeong M, Rosen A, Rogers JH, Campbell CT, Daigle SR, Deng L, Song Y, Sweet S, Chevassut T, Andreeff M, Kornblau SM, Li W, Goodell MA: DOT1L As a Therapeutic Target for the Treatment of DNMT3A-Mutant Acute Myeloid Leukemia.
    Blood 128 (2016) 971-981. PMCID: PMC4990856.

  33. Masamha CP, Xia Z, Colllum S, Peart N, Li W, Wagner EJ, Shyu A: CFIm25 Regulates Glutaminase Alternative Terminal Exon Definition.
    RNA 22 (2016) 830-838. PMCID: PMC4878610

  34. Xu J, Zhang W, Yan XJ, Lin XQ, Li W, Mi JQ, Li JM, Zhu J, Chen Z, Chen SJ: DNMT3A mutation leads to leukemic extramedullary infiltration mediated by TWIST1.
    J Hematol Oncol 9 (2016) 106.

  35. Lee SH, Chen TY, Dhar SS, Gu B, Chen K, Kim YZ, Li W, Lee MG: A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4, c-Myc to regulate stemness.
    Nucleic Acids Res 44 (2016) 10603-10618. PMCID: PMC5159542

  36. Giudice J, Xia Z, Li W, Cooper TA: Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1.
    Scientific Reports 6 (2016) 35550.

    2015

  37. Chen K^, Chen Z^, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q*, Li W*!: Broad H3K4me3 is Asscoated with Increased Transcription Elongation and Enhancer Activity at Tumor Suppressor Genes.
    Nature Genetics 47 (2015) 1149-1157. See reports in Nature Editor’s Blog, Cancer Discovery, ebiotrade.com (in Chinese), BCM news and OSU news; and an error we found in a Cell paper.

  38. Luo M^, Jeong M^, Sun D^, Park HJ^, Rodrigues B^, Xia Z, Yang L, Zhang X, Darlington GJ, Li W*!, Goodell MA*: Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function.
    Cell Stem Cell 16 (2015) 426–438

  39. Chen L^, Chen K^, Lavery LA, Baker SA, Shaw C, Li W*, Zoghbi HY*: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome.
    PNAS 112 (2015) 5509-5514

  40. 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 13 (2015) 98-106

  41. Roadmap Epigenomics Consortium (including Li W as a co-PI/co-author)!: Integrative analysis of 111 reference human epigenomes.
    Nature 518 (2015) 317-330.

  42. Yiu T, Li W: Pediatric Cancer Epigenome and the Influence of Folate. (Invited Review)
    Epigenomics (2015) 1-13

  43. Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT!: PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145.
    Nature Communications 6 (2015) 6428

  44. An J, Gonzalez-Avalos E, Chawla A, Jeong M, Lopez-Moyado LF, Li W, Goodell MA, Chavez L, Ko M, Rao A!: Acute loss of TET function results in aggressive myeloid cancer in mice.
    Nature Communications 6 (2015) 10071

  45. Morikawa Y, Zhang M, Heallen T, Leach J, Tao G, Xiao Y, Bai Y, Li W, Willerson JT, Martin JF!: Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice.
    Science Signaling 8 (2015) ra41

  46. Gennarino VA, Alcott CE, Chen C, A. C, A. GM, A. RJ, Parikh S, W. WJ, Roeder ER, D. HD, Roney EK, Smith JL, Cheung SW, Li W, Neilson JR, Schaaf CP, Zoghbi HY: NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation.
    eLife 4 (2015) PMC4586391.

  47. Mayle A, Yang L, Rodriguez B, Zhou T, Chang E, Curry CV, Challen GA, Li W, Wheeler D, Rebel VI, Goodell MA: Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation.
    Blood 125 (2015) 629-638

  48. Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X,Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming.
    Genes & Development 29 (2015) 803-816. PMCID

  49. Chen Z, Lan X, Thomas-Ahner JM, Wu D, Liu X, Ye Z, Wang L, Sunkel B, Grenade C, Chen J, Zynger DL, Yan PS, Huang J, Nephew KP, Huang TH, Lin S, Clinton SK, Li W, Jin VX, Wang Q: Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer.
    The EMBO Journal 34 (2015) 502-516

  50. Poungvarin N, Chang B, Imamura M, Chen J, Moolsuwan K, Sae-Lee C, Li W, Chan L: Genome-Wide Analysis of ChREBP Binding Sites on Mouse Liver and White Adipose Chromatin.
    Endocrinology 156 (2015) 1982-1994. PMCID: PMC4430618.

  51. Li X, Wang W, Wang J, Malovannaya A, Xi Y, Li W, Guerra R, Hawke DH, Qin J, Chen J: Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes.
    Molecular Systems Biology 11 (2015) 775

    2014

  52. Xia Z, Donehower L, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W*!: Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape across 7 Tumor Types.
    Nature Communications 5 (2014) 5274

  53. 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

  54. 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.

  55. 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 15 (2014) 350-364. PMCID: PMC4163922

  56. 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

  57. 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

  58. 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

  59. Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Li B, Dent SY, Li W*!, Li H*, Shi X*: AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.
    Cell 159 (2014) 558-571

  60. 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.

  61. 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. 42 (2014) e156. PMCID

  62. 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.

  63. 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

  64. 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

  65. 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

  66. 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.

  67. 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.

  68. 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.

  69. 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

  70. 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

  71. 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.

  72. 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 .

  73. 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.

  74. 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.

  75. 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.

  76. 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.

  77. 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

  78. 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;

  79. 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

  80. 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.

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

  82. 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.

  83. 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.

  84. 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

  85. 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.

  86. 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.

  87. 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

  88. 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.

  89. 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.

  90. 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.

  91. 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

  92. 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

  93. 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.

  94. 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.

  95. 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.

  96. 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

  97. 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

  98. 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

  99. 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.

  100. 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.

  101. 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.

  102. 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

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

  104. 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

  105. 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)

  106. 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

  107. 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

  108. 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

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

  110. 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

  111. 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.

  112. 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

  113. 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

  114. 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

  115. 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.

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

  121. 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.
    Nature Genetics. 38 (2006) 1289-1297. Abstract

  122. 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

  123. 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

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

    2005

  125. 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

  126. 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

  127. 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

  128. 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

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

  130. 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

  131. 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

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

  133. 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

  134. 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

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

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

    2002

  137. 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

  138. 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

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

  140. 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

  141. 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

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

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