Li Lab:Publications

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Peer Reviewed Publications)
Current revision (09:52, 8 December 2014) (view source)
(Peer Reviewed Publications)
 
(27 intermediate revisions not shown.)
Line 4: Line 4:
== '''Peer Reviewed Publications ''' ==
== '''Peer Reviewed Publications ''' ==
-
'''''Major Publications'''''; <u>Li Lab Members</u>; ^ (Co-)first authors; * (Co-)corresponding authors; H-index = 35;  [http://scholar.google.com/citations?hl=en&user=7IUCbE4AAAAJ&view_op=list_works&pagesize=100 Citations @ Google Scholar]
+
'''''Major Publications'''''; <u>Li Lab Members</u>; ^first authors or *corresponding authors; H-index = 38;  [http://scholar.google.com/citations?hl=en&user=7IUCbE4AAAAJ&view_op=list_works&pagesize=100 Citations @ Google Scholar]
-
# 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''''' (2014) In press <br/><br/>
+
# Roadmap Epigenomics Consortium (including <u>Li W</u> as a co-author): Integrative analysis of 111 reference human epigenomes.<br/> '''''Nature''''' (2014). In Revision <br/><br/>
 +
# Li X, Wang W, Wang J, Malovannaya A, <u>Xi Y</u>, <u>Li W</u>, Qin J, Chen J: Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. <br/> ''Molecular Systems Biology'' (2014) Accepted  <br/><br/>
 +
# Chen Z, …, <u>Li W</u>, Jin VX, Wang Q: Agonist and Antagonist Switch DNA Motifs Recognized by Human Androgen Receptor in Prostate Cancer.<br/> ''EMBO Journal'' (2014) Accepted <br/><br/>
 +
# Poungvarin N, Chang B, Imamura M, <u>Chen J</u>, <u>Li W</u>, Chan L: Genome-Wide Analysis of ChREBP Binding Sites on Mouse Liver and White Adipose Chromatin. <br/> ''Endocrinology'' (2014) Accepted <br/><br/>
 +
# Mayle A, Yang L, <u>Rodriguez B</u>, ..., <u>Li W</u>, Wheeler D, Rebel VI, Goodell MA: Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation. <br/> ''Blood'' (2014) In press <br/><br/>
 +
# Sowalsky AG^, <u>Xia Z^</u>, <u>Wang L</u>, <u>Zhao H</u>, Chen S, Bubley GJ, Ballk SP*, <u>Li W*</u>: Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer. <br/>'''''Molecular Cancer Research '''''  (2014) In press. <br/><br/>
 +
# <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/>
 +
# 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/>
# 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/>
# 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/>
 +
# 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/>
# 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/>
# 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/>
# <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/>
# <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/>
-
# 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''''' Accepted <br/><br/>
+
# 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/>
-
# Singh RK^, <u>Xia Z^</u>, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, <u>Li W*</u>, Cooper TA: The splicing regulator Rbfox2 is required for myoblast fusion during a late stage of muscle differentiation. <br/>'''''Molecular Cell''''' (2014) Accepted <br/><br/>
+
# 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/>
# <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/>
# <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/>
 +
# <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/>
# 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/>
# 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/>
# <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/>
# <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/>
Line 17: Line 26:
# 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/>
# 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/>
# 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/>
-
# 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'' Accepted.
+
# 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/>
# 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>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/>

Current revision

Home        People        Publications        Collaborations        Software        Positions        Contact       


Peer Reviewed Publications

Major Publications; Li Lab Members; ^first authors or *corresponding authors; H-index = 38; Citations @ Google Scholar

  1. Roadmap Epigenomics Consortium (including Li W as a co-author): Integrative analysis of 111 reference human epigenomes.
    Nature (2014). In Revision

  2. Li X, Wang W, Wang J, Malovannaya A, Xi Y, Li W, Qin J, Chen J: Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes.
    Molecular Systems Biology (2014) Accepted

  3. Chen Z, …, Li W, Jin VX, Wang Q: Agonist and Antagonist Switch DNA Motifs Recognized by Human Androgen Receptor in Prostate Cancer.
    EMBO Journal (2014) Accepted

  4. Poungvarin N, Chang B, Imamura M, Chen J, Li W, Chan L: Genome-Wide Analysis of ChREBP Binding Sites on Mouse Liver and White Adipose Chromatin.
    Endocrinology (2014) Accepted

  5. Mayle A, Yang L, Rodriguez B, ..., Li W, Wheeler D, Rebel VI, Goodell MA: Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation.
    Blood (2014) In press

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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  21. 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.

  22. 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.

  23. 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.

  24. 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

  25. 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

  26. 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.

  27. 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 .

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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

  33. 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;

  34. 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

  35. 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.

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

  37. 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.

  38. 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.

  39. 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

  40. 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.

  41. 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.

  42. 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

  43. 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.

  44. 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.

  45. 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.

  46. 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

  47. 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

  48. 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.

  49. 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.

  50. 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.

  51. 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

  52. 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

  53. 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

  54. 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.

  55. 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.

  56. 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.

  57. 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

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

  59. 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

  60. 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)

  61. 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

  62. 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

  63. 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

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

  65. 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

  66. 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.

  67. 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

  68. 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

  69. 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

  70. 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.

  71. 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

  72. 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

  73. 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

  74. 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

  75. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS and Brown M: Genome-wide analysis of estrogen receptor binding sites.
    Nat. Genet. 38 (2006) 1289-1297. Abstract

  76. 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

  77. 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

  78. 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

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

    2005

  80. 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

  81. 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

  82. 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

  83. 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

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

  85. 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

  86. 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

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

  88. 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

  89. 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

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

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

    2002

  92. 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

  93. 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

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

  95. 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

  96. 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

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

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