RIKEN IMS AnnualReport 2020
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81Brumpton B, Sandvei M, Willer C, Hveem K, Zwart J, Verschuren W, Friedrich C, Hirsch S, Schilling S, Dauvillier J, Martin O, HUNT All-In Stroke;China Kadoorie Biobank Collab-orative Group;BBJ Project Xonsortium;ICAN Study Group;CADISP Group;Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study inestigators;International Stroke Genetics Consortium (ISGC); Gregory T Jones G, Bown M, Ko N, Kim H, Coleman J, Breen G, Zaroff J, Klijn C, Malik R, Dichgans M, Sargurupremraj M, Tatlisumak T, Amouyel P, Debette S, Rinkel G, Worrall B, Pera J, Slowik A, Gaal-Paavola E, Niemela M, Jääskeläinen J, Fraunberg M, Lindgren A, Broderick J, Werring D, Woo D, Redon R, Bijlenga P, Kamatani Y, Veldink J, Ruigrok Y. Genome-wide association study of intra-cranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors. Nat Genet 52, 1303-1313 (2020) 15 Beck K, Ohno H, Satoh-Takayama N. Innate lymphoid cells: Important regulators of host-bacteria interaction for border defense. Microorganisms 8, E1342 (2020) 16 Bertuzzi M, Tang D, Calligaris R, Vlachouli C, Finaurini S, Sanges R, Goldwurm S, Catalan M, Antonutti L, Manganotti P, Pizzolato G, Pezzoli G, Persichetti F, Carninci P, Gustincich S. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner. Hum Mutat 41, 807-824 (2020) 17 Bhandari V, Li CH, Bristow RG, Boutros PC, PCAWG Consortium, Nakagawa H, Boroev-ich KA, Fujimoto A, Fujita M, Furuta M, Maejima K, Nakano K, Oku‐Sasaki A, Johnson TA, Tsunoda T, Lawrence MS. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun 11, 737 (2020) 18 Bonetti A, Agostini F, Suzuki A, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash A, Ghilotti M, Cameron C, Valentine M, Medvedeva YA, Noguchi S, Eneritz A, Kashi K, Samudyata S, Luginbühl J, Cazzoli R, Agrawal S, Luscombe N, Blanchette M, Kasukawa T, De Hoon M, Arner EA, Lenhard B, Plessy C, Plessy CG, Castelo-Branco G, Orlando V, Carninci P. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun 11, 1018 (2020) 19 Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen J, PCAWG Consortium, Nakagawa H, Boroevich KA, Fujimoto A, Fujita M, Furuta M, Maejima K, Nakano K, Oku-Sasaki A, Johnson TA, Tsunoda T, Lawrence MS, PCAWG Drivers and Functional Interpretation Group, Johnson R. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol 3, 56 (2020) 20 Chandra A, Sharma A, Dehzangi A, Tsunoda T. RAM-PGK: Prediction of lysine phospho-glycerylation based on residue adjacency matrix. Genes (Basel) 11, 1524 (2020) 21 Chen Y, Chen Y, Yin W, Han H, Miller H, Li, Herrada AA, Kubo M, Sui Z, Gong Q, Liu C. The regulation of DOCK family proteins on T and B cells. J Leukoc Biol 109, 383-394 (2020) 22 Chen Z, Yin Q, Inoue A, Zhang C, Zhang Y. Allelic H3K27me3 to allelic DNA methyla-tion switch maintains non-canonical imprinting in extraembryonic cells. Sci Adv 5, eaay7246 (2020) 23 Chua KC, Xiong C, Ho C, Mushiroda T, Jiang C, Mulkey F, Lai D, Schneider B, Rashkin SR, Witte JS, Friedman P, Ratain M, McLeod H, Rugo H, Shulman LN, Kubo, Owzar K, Kroetz D. Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy. Clin Pharmacol Ther 108, 625-634 (2020) 24 Clohisey S, Parkinson N, Wang B, Bertin N, Wise H, Tomoiu A, the FANTOM5 c, Sum-mers KM, Hendry RW, Carninci P, Forrest AR, Hayashizaki Y, Digard P, Hume DA, Baillie J. Comprehensive characterisation of transcriptional activity during influenza A virus infection reveals biases in cap-snatching of host RNA sequences. J Virol 94, e01720-19 (2020) 25 Cmero M, Yuan K, Ong C, Schröder J, PCAWG Evolution and Heterogeneity Working Group, Corcoran N, Papenfuss T, Hovens C, Markowetz F, Macintyre G, PCAWG Consor-tium, Nakagawa H, Boroevich KA, Fujimoto A, Fujita M, Furuta M, Maejima K, Nakano K, Oku-Sasaki A, Johnson TA, Tsunoda T, Lawrence MS. Inferring structural variant cancer cell fraction. Nat Commun 11, 730 (2020) 26 Cortés-Ciriano I, Lee J, Xi R, Jain D, Jung Y, Yang L, Gordenin D, Klimczak L, Zhang C, Pellman D, PCAWG Structural Variation Working Group, Park P, PCAWG Consortium, Nakagawa H, Boroevich KA, Fujimoto A, Fujita M, Furuta M, Maejima K, Nakano K, Oku-Sasaki A, Johnson TA, Tsunoda T, Lawrence MS. Comprehensive analysis of chro-mothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 52, 331-341 (2020) 27 Danoy M, Poulain S, Lereau Bernier M, Kato S, Scheidecker B, Kido T, Miyajima A, Sakai Y, Plessy C, Leclerc E. Characterization of liver zonation-like transcriptomic patterns in HLCs derived from hiPSCs in a microfluidic biochip environment. Biotechnol Prog 36, e3013 (2020) 28 Danoy M, Poulain SG, Jellali R, Gilard F, Kato S, Plessy CG, Kido T, Miyajima A, Sakai Y, Leclerc E. Integration of metabolomic and transcriptomic profiles of hiPSCs- derived hepatocytes in a microfluidic environment. Biochem Eng J 155, (2020) 29 Danoy M, Poulain SG, Koui Y, Tauran Y, Scheidecker B, Kido T, Miyajima A, Sakai Y, Plessy CG, Leclerc E. Transcriptome profiling of hiPSCs-derived LSECs with nanoCAGE. Mol Biosyst 16, 138-146 (2020) 30 Danoy M, Tauran Y, Poulain S, Arakawa H, Mori D, Araya K, Kato S, Kido T, Kusuhara H, Kato Y, Miyajima A, Plessy C, Sakai Y, Leclerc E. Analysis of hiPSCs differentiation to-ward hepatocyte-like cells upon extended exposition to oncostatin. Differentiation 114, 36-48 (2020) 31 de Groot A, Saito Y, Kawakami E, Hashimoto M, Aoki Y, Ono R, Ogahara I, Fujiki S, Kaneko A, Watanabe T, Takagi M, Tomizawa D, Koh K, Eguchi M, Ishii E, Ohara O, Shultz LD, Mizutani S, Ishikawa F. Targeting critical kinases and anti-apoptotic molecules overcomes steroid resistance in MLL-rearranged leukemia. EBioMedicine (Epub 2020) 32 de la Fuente L, Arzalluz-Luque Á, Tardáguila M, del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JR, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 21, 119 (2020) 33 El‐Boraie A, Chenoweth M, Pouget J, Benowitz N, Fukunaga K, Mushiroda T, Kubo, Nollen N, Cox LS, Lerman C, Knight J, Tyndale RF. Transferability Of Ancestry‐Specific And Cross‐Ancestry CYP2A6 Activity Genetic Risk Scores In African And European Populations. Clin Pharmacol Ther (Epub 2020) 34 Eto H, Kishi, Yakushiji-Kaminatsui, Sugishita, Utsunomiya S, Koseki, Gotoh Y. The Polycomb group protein Ring1 regulates dorsoventral patterning of the mouse telen-cephalon. Nat Commun 11, 5709 (2020) 35 Finlay B, Goldszmid R, Honda K, Trinchieri G, Wargo J, Zitvogel L. Can we harness the microbiota to enhance the efficacy of cancer immunotherapy? Nat Rev Immunol 20, 522-528 (2020) 36 Fujii K, Tanaka S, Hasegawa T, Narazaki M, Kumanogoh A, Koseki H, Kurosaki T, Ise W. Tet DNA demethylase is required for plasma cell differentiation by controlling expres-sion levels of IRF4. Int Immunol 32, 683-690 (2020) 37 Fujimoto A, Fujita M, Maejima K, Hasegawa T, Nakano K, Sasaki‐Oku A, Hao J, Shirai-shi Y, Miyano S, Imoto S, Nakagawa H. Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. Genome Res 30, 334-346 (2020) 38 Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, Takata S, Inai C, Aoi T, Mizukoshi M, Hirata M, Murakami Y, Kamatani Y, Kubo M, Akagi K, Matsuda K, Nak-agawa H, Momozawa Y. Population-based Screening for Hereditary Colorectal Cancer Variants in Japan. J Clin Gastroenterol Hepatol S1542-3565, 31664-5 (2020) 39 Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi s, Maejima K, Na-kano K, Fujimoto A, Ono A, Aikata H, Ueno, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H. Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic altera-tions. EBioMedicine 53, (2020) 40 Fukui T, Fukaya T, Uto T, Takagi H, Nasu J, Miyanaga N, Nishikawa Y, Koseki H, Choi-jookhuu N, Hishikawa Y, Yamashita Y, Sato K. Pivotal role of CD103 in the development of psoriasiform dermatitis. Sci Rep 10, 16375 (2020) 41 Fukunaga K, Hishinuma E, Hiratsuka M, Kato K, Okusaka T, Saito T, Ikeda M, Yoshida T, Zembutsu H, Iwata N, Mushiroda T. Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population. J Hum Genet 66, 139-149 (2020)

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