応用ゲノム解析技術研究チーム

論文



創薬等先端支援技術基盤プラットフォーム(BINDS)

  1. Yasuoka Y, Matsumoto M, Yagi K, Okazaki Y, Evolutionary History of GLIS genes illuminates their Roles in Cell Reprogramming and Ciliogenesis. Mol Biol Evol. 37(1),100-109(2020) doi: 10.1093/molbev/msz205.
  2. Kanatsu-Shinohara M, Yamamoto T, Toh H., Kazuki Y, Kazuki K., Imoto J, Ikeo K, Oshima M., Shirahige K, Iwama A, Nabeshima Y, Sasaki H, Shinohara T, Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation. Proc Natl Acad Sci U S A. 116 (33), 16404-16409(2019) doi: 10.1073/pnas.1904980116.
  3. Jin J, Togo S, Kadoya K, Tulafu M, Namba Y, Iwai M, Watanabe J, Nagahama K, Okabe T, Hidayat M, Kodama Y, Kitamura H, Ogura T, Kitamura N, Ikeo K, Sasaki S, Tominaga S, Takahashi K, Pirfenidone attenuates lung fibrotic fibroblast responses to transforming growth factor-β1. Respir Res. 20(1),119 (2019) doi: 10.1186/s12931-019-1093-z.
  4. Kadoya K, Togo S, Tulafu M, Namba Y, Iwai M, Watanabe J, Okabe T, Jin J, Kodama Y, Kitamura H, Ogura T, Kitamura N, Ikeo K, Takeda T, Kondo N,Takahashi K, Specific Features of Fibrotic Lung Fibroblasts Highly Sensitive to Fibrotic Processes Mediated via TGF-β-ERK5 Interaction. Cell Physiol Biochem. 52(4),822-837 (2019) doi: 10.33594/000000057.
  5. Matsuda T, Irie T, Katsurabayashi S, Hayashi Y, Nagai T, Hamazaki N, Adefuin AMD, Miura F, Ito T, Kimura H, Shirahige K, Takeda T, Iwasaki K, Imamura T, Nakashima K, Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. Neuron 101(3),472-485.e7(2019) doi: 10.1016/j.neuron.2018.12.010.
  6. Tabuchi Y, Hirohashi Y, Hashimoto S, Mariya T, Asano T, Ikeo K, Kuroda T, Mizuuchi M, Murai A, Uno S, Kawai N, Kubo T, Nakatsugawa M, Kanaseki T, Tsukahara T, Saito T, Torigoe T, Clonal analysis revealed functional heterogeneity in cancer stem-like cell phenotypes in uterine endometrioid adenocarcinoma. Exp Mol Pathol. 106,78-88(2019) doi: 10.1016/j.yexmp.2018.11.013.
  7. Hayashi S, Khan A, Simons BC, Homan C, Matsui T, Ogawa K, Kawashima K, Murakami S, Takahashi S, Isogawa M, Ikeo K, Mizokami M, McMahon BJ, Tanaka Y, An Association Between Core Mutations in Hepatitis B Virus Genotype F1b and Hepatocellular Carcinoma in Alaskan Native People. Hepatology 69(1), 19-33(2019) doi: 10.1002/hep.30111. Epub 2018 Dec 10.

Others

  1. Ramilowski J, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy I, Mendez M, Ooi J, Ouyang J, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov I, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cannistraci C, Cardenas R, Cardon M, Chang H, Ducoli J, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada E, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly T, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon A, Leek J, Lennartsson A, Lizio M, Lopez F, Luginbuhl J, Maeda S, Makeev V, Marchionni L, Medvedeva Y, Minoda A, Muller F, Aguirre M, Murata M, Nishiyori H, Nitta K, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr C, Rackham O, Rizzu P, Sanchez D, Sandelin A, Sanjana P, Semple C, Sharma H, Shibayama Y, Sivaraman D, Suzuki T, Szumowski S, Tagami M, Taylor M, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov I, Yamamoto C, Young R, Baillie JK, Forrest A, Guigo R, Hoffman M, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, FANTOM consortium, de Hoon M, Shin J, Carninci P, Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. bioRxiv,700864(2019) doi.org/10.1101/700864
  2. Yasuoka Y, Enhancer Evolution in Chordates: Lessons from Functional Analyses of Cephalochordate Cis-Regulatory Modules. Development, Growth & Differentiation, in press, doi: 10.1111/dgd.12684 (2020)
  3. Yasuoka Y, Morphogenetic Mechanisms Forming the Notochord Rod: the Turgor Pressure-Sheath Strength Model. Development, Growth & Differentiation, in press, doi: 10.1111/dgd.12665 (2020)
  4. Yasuoka Y,Tando Y, Kubokawa K, Taira M, Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. Zoological Letters, 5,27 (2019)
  5. Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y, Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y, Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome. Neurogenetics, 20, 9-25(2019)
  6. Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin Y, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P, Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians. Proc Nat Acad Sci., 116, 24242-24251(2019)
  7. Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, Hori C, Ishida JK, Kasahara H, Kiba T, Kim MS, Koo N, Laohavisit A, Lee YH, Lumba S, McCourt P, Mortimer JC, Mutuku JM, Nomura T, Sasaki-Sekimoto Y, Seto Y, Wang Y, Wakatake T, Sakakibara H, Demura T, Yamaguchi S, Yoneyama K, Manabe RI, Nelson DC, Schulman AH, Timko MP, dePamphilis CW, Choi D, Shirasu K, Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism.Curr Biol. 29(18), 3041-3052.e4.(2019)  doi: 10.1016/j.cub.2019.07.086.
  8. Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W, Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Commun Biol.2,263(2019) doi: 10.1038/s42003-019-0515-2.
  9. Takashima M, Manabe RI, Ohkuma M, Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type Strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956. Microbiol Resour Announc.8(26) pii: e01727-18(2019) doi: 10.1128/MRA.01727-18.
  10. Takashima M, Manabe RI, Nishimura Y, Endoh R, Ohkuma M, Sriswasdi S, Sugita T, Iwasaki W, Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales. Fungal Genet Biol. 130,31-42(2019)  doi: 10.1016/j.fgb.2019.04.013.
  11. Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Cadez N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A, Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum Cell 175(6),1533-1545.e20 (2018) doi: 10.1016/j.cell.2018.10.023.
  12. Suzuki S, Endoh R, Manabe RI, Ohkuma M, Hirakawa Y, Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca. Scientific Reports 8, Article number:940 (2018) doi:10.1038/s41598-017-18378-8
  13. Takashima M, Sriswasdi S, Manabe RI, Ohkuma M, Sugita T, Iwasaki W, A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes. Yeast (2017) doi: 10.1002/yea.3284.
  14. 眞鍋理一郎 NGSで解き明かす網羅的遺伝子解析. 生物の科学 遺伝 71 486-491 (2017)
  15. Uzuhashi S, Endoh R, Manabe RI, Ohkuma M, Draft Genome Sequences of the Oomycete Pilasporangium apinafurcum Strains JCM 30513 and JCM 30514, Formerly Classified as Pythium apinafurcum. Genome Announc. 5(35) :e00899-17(2017) doi: 10.1128/genomeA.00899-17.
  16. Noguchi S, Arakawa T, Fukuda S, et al, FANTOM5 CAGE profiles of human and mouse samples. Sci. Data.4,170112 (2017)