遺伝子制御回路研究チーム

主要論文

  1. The Human Cell Atlas: Technical approaches and challenges.
    Hon CC, Shin JW, Carninci P, Stubbington MJT.
    Brief Funct Genomics., [Epub ahead of print]: (2017)
  2. SCPortalen: human and mouse single-cell centric database.
    Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A, Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C, Carninci P, Kasukawa T.
    Nucleic Acids Res., 46(D1):D781-D787. (2018)
  3. Distinct transcriptional responses of lymphatic endothelial cells to VEGFR-3 and VEGFR-2 stimulation.
    Dieterich LC, Ducoli L, Shin JW, Detmar M.
    Sci Data., 4:170106 (2017)
  4. FANTOM5 CAGE profiles of human and mouse samples.
    Noguchi S, et al.
    Sci Data., 4:170112 (2017)
  5. The essentiality of non-coding RNAs in cell reprogramming.
    Luginbühl J, Sivaraman DM, Shin JW.
    Non-coding RNA Res., 2(1):74-82 (2017)
  6. An integrated expression atlas of miRNAs and their promoters in human and mouse.
    de Rie D, et al.
    Nat Biotechnol., 35(9):872-878. (2017)
  7. DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.
    Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E; FANTOM consortium, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.
    J Cell Sci., 129(13):2573-85. (2016)
  8. A predictive computational framework for direct reprogramming between human cell types.
    Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J.
    Nat Genet., 48(3):331-5. (2016)
  9. Paradigm shifts in genomics through the FANTOM projects.
    de Hoon M, Shin JW, Carninci P.
    Mamm Genome., 26(9-10):391-402. (2015)
  10. DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.
    Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.
    Cell Rep., 13(7):1493-1504. (2015)
  11. A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.
    Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y, FANTOM consortium, Shin JW, Suzuki H. (co-corresponding author).
    Nucleic Acids Res., 42(14):8905-13. (2014)
  12. PAPD5-mediated 3’ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.
    Boele J, Persson H, Shin JW, Ishizu Y, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne P, Rovira C, Hayashizaki Y, de Hoon M.
    Proc Natl Acad Sci U S A., 111(31):11467-72. (2014)
  13. A promoter-level mammalian expression atlas.
    FANTOM Consortium.
    Nature., 507(7493):462-70. (2014)
  14. Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.
    Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H.
    J Immunol., 194(12):6035-44. (2015)
  15. Repositioning monocyte TFRN into fibroblasts.
    Suzuki T, Shin JW, Suzuki H.
    Methods Mol Biol., 1164:211-8. (2014)
  16. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
    Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P; FANTOM Consortium.
    Genome Res., 24(4):708-17. (2014)
  17. Temporal dynamics and transcriptional control using single-cell gene expression analysis.
    Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW.
    Genome Biol., 14(10):R118. (2013)
  18. Identification of ZNF395 as a novel modulator of adipogenesis.
    Hasegawa R, Tomaru Y, de Hoon M, Suzuki H, Hayashizaki Y, Shin JW.
    Exp Cell Res., 319(3):68-76. (2013)
  19. CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication.
    Kubosaki A, Tomaru Y, Furuhata E, Suzuki T, Shin JW, Simon C, Ando Y, Hasegawa R, Hayashizaki Y, Suzuki H.
    Biochem Biophys Res Commun., 426(1):141-7. (2012)
  20. Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.
    Shin JW, Suzuki T, Ninomiya N, Kishima M, Hasegawa Y, Kubosaki A, Yabukami H, Hayashizaki Y, Suzuki H.
    Nucleic Acids Res., 40(21):e165. (2012)
  21. Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.
    Suzuki T, Nakano-Ikegaya M, Yabukami-Okuda H, de Hoon M, Severin J, Saga-Hatano S, Shin JW, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H.
    PLoS One., 7(3):e33474. (2012)
  22. Analysis of a novel highly metastatic melanoma cell line identifies osteopontin as a new lymphangiogenic factor.
    Liersch R, Shin JW, Bayer M, Schwöppe C, Schliemann C, Berdel WE, Mesters R, Detmar M.
    Int J Oncol., 41(4):1455-63. (2012)
  23. CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells.
    Hasegawa Y, Takahashi N, Forrest AR, Shin JW, Kinoshita Y, Suzuki H, Hayashizaki Y.
    Stem Cells., 29(8):1196-205. (2011)
  24. Tumor lymphangiogenesis and metastasis to lymph nodes induced by cancer cell expression of podoplanin.
    Cueni LN, Hegyi I, Shin JW, Albinger-Hegyi A, Gruber S, Kunstfeld R, Moch H, Detmar M
    Am J Pathol., 177(2):1004-16. (2010)
  25. miR-31 functions as a negative regulator of lymphatic vascular lineage-specific differentiation in vitro and vascular development in vivo.
    Pedrioli DM, Karpanen T, Dabouras V, Jurisic G, van de Hoek G, Shin JW, Marino D, Kälin RE, Leidel S, Cinelli P, Schulte-Merker S, Brändli AW, Detmar M.
    Mol Cell Biol., 30(14):3620-34. (2010)
  26. An exquisite cross-control mechanism among endothelial cell fate regulators directs the plasticity and heterogeneity of lymphatic endothelial cells.
    Kang J, Yoo J, Lee S, Tang W, Aguilar B, Ramu S, Choi I, Otu HH, Shin JW, Dotto GP, Koh CJ, Detmar M, Hong YK.
    Blood., 116(1):140-50. (2010)
  27. Lymphatic-specific expression of dipeptidyl peptidase IV and its dual role in lymphatic endothelial function.
    Shin JW, Jurisic G, Detmar M.
    Exp Cell Res., 314(16):3048-56. (2008)
  28. Transcriptional profiling of VEGF-A and VEGF-C target genes in lymphatic endothelium reveals endothelial-specific molecule-1 as a novel mediator of lymphangiogenesis.
    Shin JW, Huggenberger R, Detmar M.
    Blood., 112(6):2318-26. (2008)
  29. Prox-1 promotes invasion of kaposiform hemangioendotheliomas.
    Dadras SS, Skrzypek A, Nguyen L, Shin JW, Schulz MM, Arbiser J, Mihm MC, Detmar M.
    J Invest Dermatol., 128(12):2798-806. (2008)
  30. Prox1 promotes lineage-specific expression of fibroblast growth factor (FGF) receptor-3 in lymphatic endothelium: a role for FGF signaling in lymphangiogenesis.
    Shin JW, Min M, Larrieu-Lahargue F, Canron X, Kunstfeld R, Nguyen L, Henderson JE, Bikfalvi A, Detmar M, Hong YK.
    Mol Biol Cell., 17(2):576-84. (2006)
  31. Development of the lymphatic vascular system: a mystery unravels.
    Hong YK, Shin JW, Detmar M.
    Dev Dyn., 231(3):462-73. Review. (2004)
  32. Lymphatic reprogramming of blood vascular endothelium by Kaposi sarcoma-associated herpesvirus.
    Hong YK, Foreman K, Shin JW, Hirakawa S, Curry CL, Sage DR, Libermann T, Dezube BJ, Fingeroth JD, Detmar M.
    Nat Genet., 36(7):683-5. (2004)