Li Lab:Publications

From OpenWetWare

Baylor Blackboard.jpg Home        People        Publications        Collaborations        Software        Positions        Contact       

Peer Reviewed Publications

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

  1. Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha CP, Baillat D, Fontes CR, Shyu AB, Neilson JR, Wagner EJ*, Li W*!: 3ʹ-UTR Shortening Represses Tumor Suppressor Genes in trans by Disrupting ceRNA Crosstalk.
    Nature Genetics (2018) Accepted

  2. Park HJ, Kim S, Li W: Model-based analysis of competing-endogenous pathways (MACPath) in human cancers.
    PLOS Computational Biology (2018) Accepted

  3. Jeong M^, Park HJ^, …, Li W, Goodell MA, Challen GA: Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo.
    Cell Reports (2018) Accepted.

  4. Xi Y^, Shi J^, Li W, Tanaka K, Allton KL, Richardson D, Li J, Franco HL, Nagari A, Malladi VS, Coletta LD, Simper MS, Keyomarsi K, Shen J, Bedford MT, Shi X, Barton MC, Lee Kraus W, Li W*, Dent SYR*: Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.
    BMC Genomics 19 (2018) 150. PMCID: PMC5819162

  5. Hsu CC^, Shi J^, Yuan C, Zhao D, Jiang S, Lyu J, Wang X, Li H, Wen H, Li W*, Shi X*: Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer.
    Genes & Development 32 (2018) 58-69

  6. Chen M, Lyu G, Han M, Nie H, Shen T, Chen W, Niu Y, Song Y, Li X, Li H, Chen X, Wang Z, Xia Z, Li W, Tian XL, Ding C, Gu J, Zheng Y, Liu X, Hu J, Wei G, Tao W, Ni T: 3' UTR lengthening as a novel mechanism in regulating cellular senescence.
    Genome Res (2018).

  7. Franco HL, Nagari A, Malladi V, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL: Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.
    Genome Res 28 (2018) 159-170. PMCID: PMC5793780


  8. 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

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

  10. 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.

  11. 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 8 (2017) 1088. PMCID: PMC5651844

  12. 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.

  13. 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

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

  15. 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

  16. Tencer AH, Cox KL, Di L, Bridgers JB, Lyu J, Wang X, Sims JK, Weaver TM, Allen HF, Zhang Y, Gatchalian J, Darcy MA, Gibson MD, Ikebe J, Li W, Wade PA, Hayes JJ, Strahl BD, Kono H, Poirier MG, Musselman CA, Kutateladze TG: Covalent modifications of histone H3K9 promote binding of CHD3.
    Cell Reports 21 (2017) 455-466

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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


  28. 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

  29. 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

  30. 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

  31. 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

  32. 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.

  33. 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

  34. 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

  35. 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.

  36. 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

  37. 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

  38. 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)

  39. 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.

  40. 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

  41. 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.

  42. 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

  43. 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.


  44. 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, (in Chinese), BCM news and OSU news; and an error we found in a Cell paper.

  45. 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

  46. 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

  47. 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

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

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

  50. 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

  51. 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

  52. 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

  53. 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.

  54. 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

  55. 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

  56. 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

  57. 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.

  58. 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


  59. 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

  60. 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

  61. 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.

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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.

  68. 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

  69. 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.

  70. 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

  71. 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

  72. 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

  73. 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.

  74. 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.

  75. 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.

  76. 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.


  77. 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

  78. 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.

  79. 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 .

  80. 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.

  81. 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.

  82. 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.

  83. 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.

  84. 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.


  85. 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;

  86. 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

  87. 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.

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

  89. 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.

  90. 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.

  91. 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

  92. 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.

  93. 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.

  94. 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.


  95. 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.

  96. 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.

  97. 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.

  98. 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

  99. 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

  100. 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.

  101. 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.

  102. 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.

  103. 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.


  104. 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

  105. 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

  106. 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.

  107. 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.

  108. 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.

  109. 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.


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

  111. 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

  112. 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)

  113. 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.


  114. 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

  115. 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

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

  117. 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

  118. 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.

  119. 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

  120. 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


  121. 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

  122. 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.

  123. 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

  124. 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

  125. 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


  126. 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

  127. 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

  128. 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

  129. 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

  130. 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

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


  132. 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

  133. 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

  134. 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


  135. 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

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

  137. 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

  138. 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


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

  140. 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

  141. 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

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

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


  144. 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

  145. 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

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

  147. 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

  148. 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


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

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