Selected Publications

(† co-first author; * co-corresponding author)

2018

  1. Kandimalla R†, Gao F†, Matsuyama T, Ishikawa T, Uetake H, Takahashi N, Yamada Y, Becerra C, Kopetz S, Wang X* and Goel A*. Genome-wide discovery and identification of a novel miRNA signature for recurrence prediction in stage II and III colorectal cancer. Clin Cancer Research 2018, doi:10.1158/1078-0432.CCR-17-3236
  2. Xu Z, Wang W, Ren Y, Zhang W, Fang P, Huang L, Wang X, Shi P. Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A. Biomaterials 2018;157: 125–135.
  3. Qi L, Wang W, Xing X, Wang K and Wang X, Complete canonical correlation analysis for multi-omic molecular subtyping of colorectal cancer, International Conference on Biological Information and Biomedical Engineering (BIBE 2018), in press
  4. Linnekamp JF†, van Hooff SR†, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, van Bochove GGW, de Jong JH, Cameron K, van Leersum R, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G and Medema JP, Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models, Cell Death and Differentiation 2018, doi:10.1038/s41418-017-0011-5

2017

  1. Sonohara F†, Gao F†, Iwata N, Kanda M, Koike M, Takahashi N, Yamada Y, Kodera Y, Wang X*, Goel A*, Genome-wide Discovery of a Novel Gene-expression Signature for the Identification of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma, Annals of Surgery 2017, doi:10.1097/SLA.0000000000002622
  2. Ozawa T†, Kandimalla R†, Gao F†, Nozawa H, Hata K, Nagata H, Okada S, Izumi D, Baba H, Fleshman J, Wang X, Watanabe T, Goel A, A microRNA Signature Associated With Metastasis of T1 Colorectal Tumors to Lymph Nodes, Gastroenterology 2017, doi: 10.1053/j.gastro.2017.11.275
  3. Wang Y, Lin X, Chen X, Chen X, Xu Z, Zhang W, Liao Q, Duan X, Wang X, Liu M, Wang F, He J & Shi P, Tetherless near-infrared control of brain activity in behaving animals using fully implantable upconversion microdevices, Biomaterials 2017, 142, 136-148

2016

  1. Yu VWC, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT, Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells, Cell, 167(5):1310 - 1322
  2. Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJK, Reimers MS, Swets M, Koopman M, Nagtegaal I, Jansen M, Hooijer GKJ, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L, Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry, Clinical Cancer Research 2016, doi: 10.1158/1078-0432.CCR-16-0680
  3. Fessler E, Drost J, van Hooff SR, Linnekamp JF, Wang X, Jansen M, De Sousa E Melo F, Prasetyanti PR, IJspeert JEG, Franitza M, Nürnberg P, van Noesel CJM, Dekker E, Vermeulen L, Clevers H, and Medem JP, TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype, EMBO Molecular Medicine 2016, 8(7): 745–760, doi: 10.15252/emmm.201606184
  4. Fessler E, Jansen M, De Sousa E Melo F, Zhao L, Prasetyanti PR, Rodermond H, Kandimalla R, Linnekamp JF, Franitza M, van Hooff SR, de Jong JH, Oppeneer SC, van Noesel CJM, Dekker E, Stassi G, Wang X*, Medema JP*, and Vermeulen L*, A multidimensional network approach reveals microRNAs as determinants of the mesenchymal colorectal cancer subtype, Oncogene 2016, doi: 10.1038/onc.2016.134 (co-corresponding author)
  5. Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell APW, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T, Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin, Science 2016, 351(6270):285-289

2015

  1. Guinney J†, Dienstmann R†, Wang X†, de Reyniès A†, Schlicker A†, Soneson C†, Marisa L†, Roepman P†, Nyamundanda G†, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L & Sabine Tejpar, The consensus molecular subtypes of colorectal cancer, Nature Medicine 2015, 10.1038/nm.3967
  2. Alekseyenko AA†, Walsh EM†, Wang X†, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, and French CA, The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains, Genes Dev 2015, 29: 1507-1523
  3. Wang X and Markowetz F, “Joining the dots–network analysis of gene perturbation data”, book chapter, In Systems Genetics: linking phenotype and genotype, Markowetz F and Boutros M, Cambridge University Press, 2015

2014

  1. Sadanandam A†, Wang X†, Felipe de Sousa E, Gray JW, Vermeulen L, Hanahan D, & Medema JP, Reconciliation of classification systems defining molecular subtypes of colorectal cancer, Cell Cycle 2014, 13(3): 353-357
  2. Wang X, Yuan K, Hellmayr C, Liu W and Markowetz F, Reconstructing evolving signaling networks by hidden Markov nested effects models, Annals of Applied Statistics 2014, 8(1): 448-480

2013

  1. De Sousa E Mello, F†, Wang X†, Jansen M, Fessler E, Trinh A, et al., Poor prognosis colon cancer is defined by a distinct molecular subtype and develops from serrated precursor lesions, Nature Medicine 2013, 19(5): 614-618

~2012

  1. Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, et al., Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology 2012, 14(7):753-763
  2. Wang X, Castro MA, Mulder KW and Markowetz F, Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS Computational Biology 2012, 8(6):e1002566
  3. Castro MA, Wang X, Fletcher M, Ponder BAJ, Meyer KB, Markowetz F, RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations, Genome Biology 2012, 13:R29
  4. Wang X†, Terfve C†, Rose JC, Markowetz F, HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics 2011, 27(6):879

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