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2024

  • Chen, R., X. Shi, X. Yao, T. Gao, G. Huang, D. Ning, Z. Cao, Y. Xu, W. Liang, S. Z. Tian, Q. Zhu, L. Fang, M. Zheng, Y. Hu, H. Cui# and W. Chen# (2024). “Specific multivalent molecules boost CRISPR-mediated transcriptional activation.” Nat Commun 15(1): 7222.
  • Fang, L.*#, L. Zhang*, M. Wang*, Y. He, J. Yang, Z. Huang, Y. Tan, K. Fang, J. Li, Z. Sun, Y. Li, Y. Tang, W. Liang, H. Cui, Q. Zhu, Z. Wu, Y. Li, Y. Hu and W. Chen# (2024). “Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition.” Cancer Res 84(5): 659-674.

2023

  • Zhu, Q.*#, X. Zhao*, Y. Zhang*, Y. Li*, S. Liu*, J. Han, Z. Sun, C. Wang, D. Deng, S. Wang, Y. Tang, Y. Huang, S. Jiang, C. Tian, X. Chen, Y. Yuan, Z. Li, T. Yang, T. Lai, Y. Liu, W. Yang, X. Zou, M. Zhang, H. Cui, C. Liu, X. Jin, Y. Hu, A. Chen, X. Xu, G. Li, Y. Hou, L. Liu#, S. Liu#, L. Fang#, W. Chen# and L. Wu# (2023). “Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines.” Nat Commun 14(1): 8170.
  • Long Y, Zhang B, Tian S, Chan JJ, Zhou J, Li Z, Li Y, An Z, Liao X, Wang Y, Sun S, Xu Y, Tay Y, Chen W*, Gao X*.Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ. Genome Res. 2023 Apr;33(4):644-657.

2022

  • Cui H*, Yi H&, Bao H, Tan Y&, Tian C&, Shi X, Gan D&, Zhang B, Liang W&, Chen R&, Zhu Q, Fang L, Gao X, Huang H, Tian R, Sperling SR, Hu Y, Chen W*.The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Nat Commun. 2022 Aug 9;13(1):4680.
  • Tian S, Zhang B, He Y, Sun Z, Li J, Li Y, Yi H, Zhao Y, Zou X, Li Y, Cui H, Fang L,Gao X, Hu Y, Chen W*. CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference. Nucleic Acids Res. 2022 Mar 21;50(5):e26.
  • Zhou J, Zhang B, Li H, Zhou L, Li Z, Long Y, Han W, Wang M, Cui H, Li J, ChenW*, Gao X*. Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):959-973. Epub 2022 Dec 15.

2021

  • Fang L*, Li G, Sun Z, Zhu Q, Cui H, Li Y, Zhang J, Liang W, Wei W, Hu Y, ChenW*. CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing. Mol Syst Biol. 2021 Apr;17(4):e10060.
  • Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W*. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance. 2021 Dec 30;5(4):e202101333.
  • Weigt M, Gao Q, Ban H, He H, Mastrobuoni G, Kempa S, Chen W*, Li F*. Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex. Epigenetics Chromatin. 2021 Jan 19;14(1):8.
  • Li Z, Li Y, Zhang B, Li Y, Long Y, Zhou J, Zou X, Zhang M, Hu Y, Chen W*, GaoX*. DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. Genomics Proteomics Bioinformatics. 2021 Mar 1:S1672-0229(21)00049-8.
  • Zohra Smaili F, Tian S, Roy A, Alazmi M, Arold ST, Mukherjee S, Scott Hefty P, Chen W*, Gao X*. QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs. Genomics Proteomics Bioinformatics. 2021 Feb 22:S1672-0229(21)00034-6.

2020

  • Fang L, Wang W, Li G, Zhang L, Li J, Gan D, Yang J, Tang Y, Ding Z, Zhang M, Zhang W, Deng D, Song Z, Zhu Q, Cui H, Hu Y, Chen W. CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators. Mol Syst Biol. 2020. Nov;16(11):e10025. doi:10.15252/msb.202010025.
  • Li Y, Schaefke B* , Zou X, Zhang M, Heyd F, Sun W, Zhang B, Li G, Liang W, He Y, Zhou J, Li Y, Fang L, Hu Y, and Chen W*. Pan-tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation. Mol Syst Biol. 2020 Apr; 16(4): e9367. doi: 10.15252/msb.20199367
  • Preussner M, Gao Q, Morrison E, Herdt O, Finkernagel F, Schumann M, Krause E, Freund C, Chen W*, Heyd F*. Splicing-accessible coding 3’UTRs control protein stability and interaction networks. Genome Biol. 2020 Jul 29;21(1):186. doi: 10.1186/s13059-020-02102-3.
  • Hu J, Liang H, Zhang H, Yang M, Sun W, Zhang P, Luo L, Feng J, Bai H, Liu F, Zhang T, Yang J, Gao Q, Long Y, Ma Y, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng M, Cao N, Wang J, Chen W*, Yang H*, and Gao S*. FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells. Nucleic Acids Res. 2020 Mar 18; 48(5): 2733–2748, doi: 10.1093/nar/gkaa049
  • Yi, HY; Li, GP; Long, YK; Liang, WZ; Cui, HN; Zhang, B; Tan, Y; Li, YF; Shen, LC; Deng, DQ; Tang, YS; Mao, CY; Tian, SY; Cai, YT; Zhu, QH; Hu, YH*; Chen, W*; Fang, L*. Integrative multi-omics analysis of a colon cancer cell line with heterogeneous Wnt activity revealed RUNX2 as an epigenetic regulator of EMT, Oncogene, 2020 Jul;39(28):5152-5164. doi: 10.1038/s41388-020-1351-z

2019

  • Lam J, Li Y, Zhu L*, Umarov R, Jiang H, Héliou A, Sheong FK, Liu T, Long Y, Li Y, Fang L, Altman RB, Chen W*, Huang X*, and Gao X*. A deep learning framework to predict binding preference of RNA constituents on protein surface. Nat Commun. 2019; 10: 4941. doi: 10.1038/s41467-019-12920-0
  • Chen, T; Zhang, B; Ziegenhals, T; Prusty, AB; Frohler, S; Grimm, C; Hu, YH; Schaefke, B; Fang, L; Zhang, M; Kraemer, N; Kaindl, AM*; Fischer, U*; Chen, W*. A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing, PLoS Genet. 2019 Oct; 15(10): e1008460. doi: 10.1371/journal.pgen.1008460
  • Zou X, Gao X* and Chen W*. Deep Learning Deepens the Analysis of Alternative Splicing, Genomics Proteomics Bioinformatics. 2019 Apr; 17(2): 219–221. doi: 10.1016/j.gpb.2019.05.001
  • Wang X, You X, Langer JD, Hou J, Rupprecht F, Vlatkovic I, Quedenau C, Tushev G, Epstein I, Schaefke B, Sun W, Fang L, Li G, Hu Y, Schuman EM, Chen W. Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus, Nat Commun. 2019; 10: 5009. doi: 10.1038/s41467-019-13037-0

2018

  • Xia Z, Li Y, Zhang B, Li Z, Hu Y, Chen W*, Gao X* DeeReCT-PolyA: a robust and generic deep learning method for PAS identification. Bioinformatics. 2018 Nov 30. doi: 10.1093/bioinformatics/bty991. [Epub ahead of print] PMID:30500881
  • Sun W, Gao Q, Schaefke B, Hu YH, Chen W. Pervasive allele-specific regulation on RNA decay in hybrid mice. Life Science Alliance 2018 May 16. DOI: 10.26508/lsa.201800052
  • Schaefke B, Sun W, Li YS, Fang L, Chen W. The evolution of posttranscriptional regulation. Wiley Interdiscip Rev RNA. 2018 May 31:e1485. doi: 0.1002/wrna.1485. [Epub ahead of print] Review.

2016

  • Xiao MS, Zhang B, Li YS, Gao Q, Sun W, Chen W. Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation. Mol Syst Biol. 2016 Dec 8;12(12):890. doi: 10.15252/msb.20167375.
  • Chen W, Schuman E. Circular RNAs in Brain and Other Tissues: A Functional Enigma. Trends Neurosci. 2016 Jul 18. pii: S0166-2236(16)30069-8. doi: 10.1016/j.tins.2016.06.006. [Epub ahead of print]
  • Wang X, Hou J, Quedenau C, Chen W. Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals. (Cover story) Mol Syst Biol. 2016 Jul 18;12(7):875. doi: 10.15252/msb.20166941.

2015 and earlier

  • Etlioglu HE, Sun W, Huang Z, Chen W*, Schmucker D*. Characterization of a Single Genomic Locus Encoding the Clustered Protocadherin Receptor Diversity in Xenopus tropicalis.G3 (Bethesda). 2016 Jun 3. pii: g3.116.027995. doi: 10.1534/g3.116.027995. [Epub ahead of print] 29. Hou J, Wang X, McShane E, Zauber H, Sun W, Selbach M, Chen W. Extensive allele-specific translational regulation in hybrid mice. Mol Syst Biol.2015 Aug 7;11(8):825. doi: 10.15252/msb.156240.
  • Gao Q, Sun W, Ballegeer M, Libert C, Chen W.Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing. Mol Syst Biol. 2015 Jul 1;11(7):816. doi: 10.15252/msb.20145970.
  • You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C, Wang X, Hou J, Liu H, Sun W, Sambandan S, Chen T, Schuman EM, Chen W. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci. 2015 Feb 25. doi: 10.1038/nn.3975. [Epub ahead of print]
  • von Bernuth H*, Ravindran E, Du H, Fröhler S, Strehl K, Krämer N, Issa-Jahns L, Amulic B, Ninnemann O, Xiao MS, Eirich K, Kölsch U, Hauptmann K, John R, Schindler D, Wahn V, Chen W*, Kaindl AM*. : Combined immunodeficiency develops with age in Immunodeficiency-centromeric instability-facial anomalies syndrome 2 (ICF2) Orphanet J Rare Dis. 2014 Oct 21;9(1):116.
  • Armitage SA, Sun W, You X, Kurtz J, Schmucker D, Chen W.: Quantitative Profiling of Drosophila melanogaster Dscam1 Isoforms Reveals No Changes in Splicing after Bacterial Exposure. PLoS One. 2014 Oct 13;9(10):e108660. doi: 10.1371/journal.pone.0108660. eCollection 2014
  • Fröhler S, Kieslich M, Langnick C, Feldkamp M, Opgen-Rhein B, Berger F, Will JC and Chen W: Exome sequencing helped the fine diagnosis of two siblings afflicted with atypical Timothy syndrome (TS2). BMC Medical Genetics.2014, 15:48 DOI: 10.1186/1471-2350-15-48
  • Farag HG, Froehler S, Oexle K, Ravindran E, Schindler D, Staab T, Huebner A, Kraemer N, Chen W*, Kaindl AM*. (2013) Abnormal centrosome and spindle morphology in a patient with autosomal recessive primary microcephaly type 2 due to compound heterozygous WDR62 gene mutations. Orphanet J Rare Dis. 2013 Nov 14;8(1):178. [Epub ahead of print]
  • Wang, Y., Gogol-Döring, A., Hu, H., Fröhler, S., Ma, Y., Jens, M., Maaskola, J., Murakawa, Y., Quedenau, C., Landthaler, M., Kalscheuer, V., Wieczorek, D., Wang, Y., Hu, Y. and Chen, W (2013) Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation. EMBO Mol Med. 2013 doi: 10.1002/emmm.201302663.
  • Gao Q, Sun W, You X, Fröhler S, Chen W (2013) A systematic evaluation of hybridization-based mouse exome capture system. BMC Genomics 2013, 14:492
  • Sun W, You X, Gogol-Döring A, He H, Kise Y, Sohn M, Chen T, Klebes A, Schmucker D, Chen W (2013) Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing. EMBO J. 2013 Jun 21. doi: 10.1038/emboj.2013.144. [Epub ahead of print]
  • Li N, You X, Chen T, Mackowiak SD, Friedländer MR, Weigt M, Du H, Gogol-Döring A, Chang Z, Dieterich C, Hu Y, Chen W (2013) Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery. Nucleic Acids Res. 2013 Apr 1;41(6):3619-34. doi: 10.1093/nar/gkt072.
  • Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Phoebe Chen YP, Li N, Hu Y, Fu N, Ning Z, Zeng R, Yang H, Chen W*, Gelfand M*, Khaitovich P*.(2013) Widespread splicing changes in human brain development and aging. Mol Syst Biol. 2013 Jan 22;9:633.
  • Dudziec E, Gogol-Döring A, Cookson V, Chen W*, Catto J* (2012) Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells. PLoS One. 7(3):e32750.
  • Doering A & Chen W (2012) An overview of the analysis of next generation sequencing data. Methods Mol Biol. 802:249-57
  • Chen W (2011) Impact of novel sequencing technology on transcriptome analysis European Pharmaceutical Review. Volume 16 Issue4 61-63
  • Yan Z, Hu HY, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W*, Khaitovich P* (2011) Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Res. 2011 Aug;39(15):6596-607
  • Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J*, Chen W*, Selbach M*. (2011) Global quantification of mammalian gene expression control Nature. 2011 May 19;473(7347):337-42
  • Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Alvarado AS, Kempa S*, Dieterich C*, Rajewsky N*, Chen W * (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 21(7):1193-200
  • Jensen LR*, Chen W*, Moser B, Lipkowitz B, Schroeder C, Musante L, Tzschach A, Kalscheuer VM, Meloni I, Raynaud M, van Esch H, Chelly J, de Brouwer AP, Hackett A, van der Haar S, Henn W, Gecz J, Riess O, Bonin M, Reinhardt R, Ropers HH, Kuss AW. (2011) Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1. Eur J Hum Genet. 19(6):717-20
  • Somel M*, Guo S, Fu N, Yan Z, Hu HY, Xu Y, Yuan Y, Ning Z, Hu Y, Menzel C, Hu H, Lachmann M, Zeng R, Chen W*, Khaitovich P*. (2010) MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res. 20(9):1207-18
  • Xu AG, He L, Li Z, Xu Y, Li M, Fu X, Yan Z, Yuan Y, Menzel C, Li N, Somel M, Hu H, Chen W*, Pääbo S*, Khaitovich P*. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol. 6:e1000843.
  • Shao NY, Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Li N, Chen W*, Khaitovich P*. (2010) Comprehensive survey of human brain microRNA by deep sequencing. BMC Genomics. 11(1):409.
  • Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Van Bokhoven H, Chelly J, Ropers H, Chen W. (2010) Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. The HUGO Journal: Volume 3, Issue 1, Page 41.
  • Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H, Döring A, Hu Y, Kang H, Tzschach A, Hoeltzenbein M, Neitzel H, Markus S, Wiedersberg E, Kistner G, van Ravenswaaij-Arts CM, Kleefstra T, Kalscheuer VM, Ropers HH. (2009) Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Eur J Hum Genet. 18(5):539-43
  • Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Zhou YH, Chen W*, Khaitovich P*. (2009) Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics. 10(1):413.
  • Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W*, Li Y, Zeng R*, Khaitovich P*.(2009) Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics.10:161.
  • Kuss AW, Chen W (2008) MicorRNAs in brain function and disease. Curr Neurol Neurosci Rep. 8(3):190-7.
  • Chen W, Kalscheu V, Tzschach A, Menzel C, Ullmann R, Schulz M, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser BG, Vingron M, Ropers HH. (2008) Mapping translocation breakpoints by next-generation sequencing. Genome Res. 18(7):1143-9
  • Tzschach A*, Chen W*, Erdogan F, Hoeller A, Ropers HH, Castellan C, Ullmann R, Schinzel A. (2008) Characterization of interstitial Xp duplications in two families by tiling path array CGH. Am J Med Genet A. 146(2):197-203.
  • Chen W*, Jensen LR*, Gecz J, Fryns JP, Moraine C, de Brouwer A, Chelly J, Moser B, Ropers HH, Kuss AW: Mutation screening of brain-expressed X-chromosomal miRNA genes in 464 patients with nonsyndromic X-linked mental retardation (2007) Eur J Hum Genet. 15(3):375-8
  • Erdogan F*, Chen W*, Kirchhoff M, Kalscheuer VM, Hultschig C, Muller I, Schulz R, Menzel C, Bryndorf T, Ropers HH, Ullmann R. (2006) Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation. Cytogenetic and genome research. 115(3-4):247-53
  • Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R (2005) CGHPRO – A comprehensive data analysis tool for array CGH. BMC Bioinformatics, 6:85