Cui Y, Arnold FJ, Li JS, Wu J, Wang D, Philippe J, Colwin MR, Michels S, Chen C,
Sallam T, Thompson LM , La Spada AR, Li W: Multi-omic quantitative trait loci link tandem repeat size variation to gene regulation in human brain
Nature Genetics (2025)

Cui Y, Ye W, Li JS, Li JJ, Vilain E, Sallam T, Li W: A genome-wide spectrum of tandem repeat expansions in 338,963 humans
Cell 187 (2024), 2336-2341

Chen H, Wang Z, Gong L, Wang Q, Chen W, Wang J, Ma X, Ding R, Li X, Zou X, Plass M, Lian C, Ni T, Wei G, Li W, Deng L, Li L: A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study
Nature Communications 15 (2024), 1729

Li Y, Xu J, Chen C, Lu Z, Wan D, Li D, Li JS, Sorg AJ, Roberts CC, Mahajan S, Gallant MA, Pinkoviezky I, Cui Y, Taggart DJ, Li W: Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection.
Genome Medicine (2024), 16:9

Li L, Ma X, Cui Y, Rotival M, Chen W, Chen W, Zou X, Ding R, Qin Y, Wang Y, Wang Q, Quintana-Murci L, Li W: Immune-response 3′UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases.
Nature Communications 14 (2023), 8347

Cui Y, Arnold FJ, Peng F, Wang D, Li JS, Michels S, Wagner EJ, La Spada AR, Li W: Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders.
Nature Communications 14 (2023), 583

Gu T^, Hao D^, Woo J, Huang T, Guo L, Lin X, Guzman AG, Tovy A, Rosas C, Jeong M, Yubin Zhou Y, Deneen B, Huang Y, Li W, Goodell MA: DNA methyltransferase 3a (DNMT3A) plays a crucial role during mammalian disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development.
Nature Genetics 54 (2022), 625-636

Li Y^, Ge X^, Peng F, Li W* and Li JJ*: Exaggerated false positives by popular differential expression methods when analyzing human population samples.
Genome Biology 23,79 (2022)

Lin N, Lin Y, Xu J, Liu D, Li D, Meng H, Gallant MA, Kubota N, Roy D, Li JS, Gorospe, EC, Sherman M, Gish RG, Abou-Alfa GK, Nguyen MH, Taggart DJ, Van Etten RA, Hoshida Y, Li W: A multi-analyte cell-free DNA–based blood test for early detection of hepatocellular carcinoma.
Hepatology Communications 6 (3) (2022), 1–11

Xu J, Shi J, Cui X, Cui Y, Li JJ, Goel A, Chen X, Issa JP, Su J, Li W: Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression.
Nature Communications 12 (2021), 1-9 
New study points to better diagnostics for cancer

Shi J, Xu J, YE Chen, Li JS, Cui Y,Shen L, Li JJ, Li W: The concurrence of DNA methylation and demethylation is associated with transcription regulation.
Nature Communications 12 (2021), 1-12

Gao Y, Li L, Amos CI, Li W: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.
Genome Research 10 (2021), 31, 1856-1866
Highlighted in GenomeWeb.com

Cui Y, Peng F, Wang D, Li Y, Li JS, Li L, Li W: 3′ aQTL-atlas: an atlas of 3′ UTR alternative polyadenylation quantitative trait loci across human normal tissues.
Nucleic Acids Research 8 (2021), 1-7

Sengupta D^, Zeng L^, Li Y^, Hausmann S, Ghosh D, Yuan G, Nguyen TN, Lyu R, Caporicci M, Benitez AM, Coles GL, Kharchenko V, Czaban I, Azhibek D, Fischle W, Jaremko M, Wistuba II, Sage J, Jaremko L, Li W*, Mazur PK*, Gozani O*: NSD2 dimethylation at H3K36 promotes lung adenocarcinoma pathogenesis.
Molecular Cell 9 (2021)

Kandimalla R^, Xu J^, Link A, Matsuyama T, Yamamura K, Parker MI, Uetake H, Balaguer F, Borazanci E, Tsai S, Evans D, Meltzer SJ, Baba H, Brand R, Hoff DV, Li W*, Goel A*: EpiPanGI Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers.
Clinical Cancer Research 10 (2021), 1-10

Cui Y, Cui Z, Xu J, Hao D, Shi J, Wang D, Xiao H, Duan X, Chen R, Li W: NG-Circos: next-generation Circos for data visualization and interpretation. 
NAR Genomics and Bioinformatics 2 (2020)

Lyu J, Li JJ, Su J, Peng F, Chen YE, Ge X, Li W: DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features.
Science Advances 6 (2020), eaba6784 
New prediction algorithm identifies previously undetected cancer driver genes

Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha CP, Baillat D, Fontes-Garfias CR, Shyu AB, Neilson JR, Wagner EJ, Li W: 3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk.
Nature Genetics 50 (2018) 783-789. PMCID 

Zhang Y, Shi J, Liu X, Feng L, Gong Z, Koppula P, Sirohi K, Li X, Wei Y, Lee H, Zhuang L, Chen G, Xiao Z, Hung M, Chen J, Huang P, Li W, Gan B: BAP1 links metabolic regulation of ferroptosis to tumour suppression.
Nature Cell Biology 20 (2018) 1181–1192

Gu T^, Lin X^, Cullen SM^, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi LS, Chen JJ, Kyba M, Huang Y, Chen T, Li W*, Goodell MA*: DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells.
 Genome Biol 19 (2018) 88. PMCID.

Su J^, Huang YH^, Cui X, Wang X, Zhang X, Lei Y, Xu J, Lin X, Chen K, Lv J, Goodell MA*, Li W*: Homeobox oncogene activation by pan-cancer DNA hypermethylation.
Genome Biol 19 (2018) 108. PMCID 

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 

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

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 

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

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 

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 Biol 15 (2014) R38. PMCID

Wang L*, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP*, Li W*: MACE: Model based Analysis of ChIP-exo.  
Nucleic Acids Res. 42 (2014) e156.

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

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

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

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.

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 

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.

Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W*, Dent S*: Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor.    
Genome Res. 23 (2013) 312-322. PMCID: PMC3561872

Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W*: DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.
Genome Res. 23 (2013) 341-351 

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 

34. 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. 

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

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. 

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. 

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. 

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.

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 

Xi Y, Li W*: BSMAP: whole genome Bisulfite Sequence MAPping program.
BMC Bioinformatics 10 (2009) 232. PMCID: PMC2724425 

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