RIKEN IMS Annual Report 2023

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90 152 Severin JM, Agrawal S, Ramilowski J, Deviatiiarov R, Shin JW, Carninci P, De Hoon MJ. ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data. NAR Genom Bioinform 5, lqad075 (2023) 153 Shan B, Barker CS, Theraulaz H, Zhang X, Ping Y, Gupta RK, Shao M, Wu Y. Protocol for quantitative proteomic analysis of heterogeneous adipose tissue-residing progenitor subpopulations in mice. STAR Protoc 4, 102676 (2023) 154 Sharif J, Koseki H, Parrish NF. Bridging multiple dimensions: roles of transposable elements in higher-order genome regulation. Curr Opin Genet Dev 80, 102035 (2023) 155 Sharma A, Lysenko A, Boroevich KA, Tsunoda T. DeepInsight-3D architecture for anti-cancer drug response prediction with deep-learning on multi-omics. Sci Rep 13, 2483 (2023) 156 Shi J, Shiraishi K, Choi J, Matsuo K, Chen T, Dai J, Hung RJ, Chen K, Shu X, Kim YT, Landi MT, Lin D, Zheng W, Yin Z, Zhou B, Song B, Wang J, Seow WJ, Song L, Chang I, Hu W, Chien L, Cai Q, Hong Y, Kim HN, Wu Y, Wong MP, Richardson BD, Funder-burk KM, Li S, Zhang T, Breeze C, Wang Z, Blechter B, Bassig BA, Kim JH, Albanes D, Wong JY, Shin M, Chung LP, Yang Y, An S, Zheng H, Yatabe Y, Zhang X, Kim Y, Caporaso NE, Chang J, Ho JC, Kubo M, Daigo Y, Song M, Momozawa Y, Kamatani Y, Kobayashi M, Okubo K, Honda T, Hosgood DH, Kunitoh H, Patel H, Watanabe S, Miyagi Y, Nakayama H, Matsumoto S, Horinouchi H, Tsuboi M, Hamamoto R, Goto K, Ohe Y, Takahashi A, Goto A, Minamiya Y, Hara M, Nishida Y, Takeuchi K, Wakai K, Matsuda K, Murakami Y, Shimizu K, Suzuki H, Saito M, Ohtaki Y, Tanaka K, Wu T, Wei F, Dai H, Machiela MJ, Su J, Kim YH, Oh I, Lee VH, Chang G, Tsai Y, Chen K, Huang M, Su W, Chen Y, Seow A, Park JY, Kweon S, Chen K, Gao Y, Qian B, Wu C, Lu D, Liu J, Schwartz AG, Houlston R, Spitz MR, Gorlov IP, Wu X, Yang P, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeboeller H, Ji B, Wichmann H, Christiani DC, Rennert G, Arnold S, Brennan P, McKay J, Field JK, Shete SS, Le Marchand L, Liu G, Andrew A, Kiemeney LA, Zienolddiny-Narui S, Grankvist K, Johansson M, Cox A, Taylor F, Yuan J, Lazarus P, Schabath MB, Aldrich MC, Jeon H, Jiang SS, Sung JS, Chen C, Hsiao C, Jung YJ, Guo H, Hu Z, Burdett L, Yeager M, Hutchinson A, Hicks B, Liu J, Zhu B, Berndt SI, Wu W, Wang J, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Wang W, Xu J, Guan P, Tan W, Yu C, Yang G, Sihoe AD, Chen Y, Choi YY, Kim JS, Yoon H, Park IK, Xu P, He Q, Wang C, Hung H, Vermeulen RC, Cheng I, Wu J, Lim W, Tsai F, Chan JK, Li J, Chen H, Lin H, Jin L, Liu J, Sawada N, Yamaji T, Wyatt K, Li SA, Ma H, Zhu M, Wang Z, Cheng S, Li X, Ren Y, Chao A, Iwasaki M, Zhu J, Jiang G, Fei K, Wu G, Chen C, Chen C, Yang P, Yu J, Stevens VL, Fraumeni JF, Chatterjee N, Gorlova OY, Hsiung CA, Amos CI, Shen H, Chanock SJ, Rothman N, Kohno T, Lan Q. Genome-wide association study of lung adenocar-cinoma in East Asia and comparison with a European population. Nat Commun 14, 3043 (2023) 157 Shibata R, Itoh N, Nakanishi Y, Kato T, Suda W, Nagao M, Iwata T, Yoshida H, Hat-tori M, Fujisawa T, Shimojo N, Ohno H. Gut microbiota and fecal metabolites in sustained unresponsiveness by oral immunotherapy in school-age children with cow’s milk allergy. Allergol Int 73, 126-136 (2023) 158 Shibutani S, Endo M, Mizukami K, Hosoi E, Sakai Y, Taniguchi M, Harada H, Mo-mozawa Y, Iwata H. Development of a high-throughput screening method for the detection of 188 pathogenic variants and its application in Mishima cattle. Anim Genet 54, 416-417 (2023) 159 Shima Y, Sasagawa S, Ota N, Oyama R, Tanaka M, Kubota-Sakashita M, Sun X, Kim Y, Kamatani Y, Matsuda K, Nagane M, Shibahara J, Tanaka T, Rikitake Y, Mataga N, Takahashi S, Kosaki K, Okano H, Furihata T, Nakaki R, Akimitsu N, Wada Y, Otsuka T, Kurihara H, Kamiguchi H, Okabe S, Nakafuku M, Kato T, Nakagawa H, Saito N, Nakatomi H. Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms. Sci Transl Med 15, eabq7721 (2023) 160 Shimizu K, Ueda S, Kawamura M, Aoshima H, Satoh M, Fujii S, Nakabayashi J. Combination of cancer vaccine with CD122-biased IL-2/anti-IL-2 Ab complex shapes the stem-like effector NK and CD8+ T cells against tumor. J Immunother Cancer 11, e006409 (2023) 161 Shimomura Y, Sugi Y, Kume A, Tanaka W, Yoshihara T, Matsuura T, Komiya Y, Ogata Y, Suda W, Hattori M, Higurashi T, Nakajima A, Matsumoto M. Strain-level detec-tion of Fusobacterium nucleatum in colorectal cancer specimens by targeting the CRISPR–Cas region. Microbiol Spectr 11, e05123-22 (2023) 162 Shiota M, Akamatsu S, Sekine Y, Kimura H, Narita S, Fujimoto N, Terada N, Blas L, Habuchi T, Kamoto T, Momozawa Y, Eto M. Genetic variations predicting progres-sion with docetaxel and novel androgen‐receptor pathway inhibitors. Cancer Sci 114, 1625-1634 (2023) 163 Shiota M, Tatarano S, Kamoto T, Matsuyama H, Sakai H, Igawa T, Kamba T, Fuji-moto N, Sekine Y, Kimura H, Narita S, Terada N, Momozawa Y, Akamatsu S, Habu-chi T, Yokomizo A, Naito S, Eto M. Genome-wide association studies in advanced prostate cancer: KYUCOG-1401-A study. Endocr Relat Cancer 30, e230044 (2023) 164 Shiraishi K, Takahashi A, Momozawa Y, Daigo Y, Kaneko S, Kawaguchi T, Kunitoh H, Matsumoto S, Horinouchi H, Goto A, Honda T, Shimizu K, Torasawa M, Takayanagi D, Saito M, Saito A, Ohe Y, Watanabe S, Goto K, Tsuboi M, Tsuchihara K, Takata S, Aoi T, Takano A, Kobayashi M, Miyagi Y, Tanaka K, Suzuki H, Maeda D, Yamaura T, Matsuda M, Shimada Y, Mizuno T, Sakamoto H, Yoshida T, Goto Y, Yoshida T, Yamaji T, Sonobe M, Toyooka S, Yoneda K, Masago K, Tanaka F, Hara M, Fuse N, Nishizuka SS, Motoi N, Sawada N, Nishida Y, Kumada K, Takeuchi K, Tanno K, Ya-tabe Y, Sunami K, Hishida T, Miyazaki Y, Ito H, Amemiya M, Totsuka H, Nakayama H, Yokose T, Ishigaki K, Nagashima T, Ohtaki Y, Imai K, Takasawa K, Minamiya Y, Kobayashi K, Okubo K, Wakai K, Shimizu A, Yamamoto M, Iwasaki M, Matsuda K, Inazawa J, Shiraishi Y, Nishikawa H, Murakami Y, Kubo M, Matsuda F, Kamatani Y, Hamamoto R, Matsuo K, Kohno T. Identification of telomere maintenance gene variations related to lung adenocarcinoma risk by genome-wide association and whole genome sequencing analyses. Cancer Commun (Lond) 44, 287-293 (2023) 165 Shiratori H, Oguchi H, Isobe Y, Han K, Sen A, Yakebe K, Takahashi D, Fukushima M, Arita M, Hase K. Gut microbiota-derived lipid metabolites facilitate regulatory T cell differentiation. Sci Rep 13, 8903 (2023) 166 Shoji K, Hikino K, Saito J, Matsui T, Utano T, Takebayashi A, Tomizawa D, Kato M, Matsumoto K, Ishikawa T, Kawai T, Nakamura H, Miyairi I, Terao C, Mushiroda T. Effect of CYP2C19 on Voriconazole Pharmacokinetics in Children with Malignancy or Inborn Errors in Immunity. Open Forum Infect Dis 10, S2 (2023) 167 Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol mjad081 (2023) 168 Sonobe S, Kitabatake M, Hara A, Konda M, Ouji-Sageshima N, Terada-Ikeda C, Fu-rukawa R, Imakita N, Oda A, Takeda M, Takamura S, Inoue S, Kunkel SL, Kawagu-chi M, Ito T. THE CRITICAL ROLE OF THE HISTONE MODIFICATION ENZYME SETDB2 IN THE PATHOGENESIS OF ACUTE RESPIRATORY DISTRESS SYNDROME. Shock 60, 137-145 (2023) 169 Stolarova L, Kleiblova P, Zemankova P, Stastna B, Janatova M, Soukupova J, Achatz MI, Ambrosone C, Apostolou P, Arun BK, Auer P, Barnard M, Bertelsen B, Japan B, Blok MJ, Boddicker N, Brunet J, Burnside ES, Calvello M, Campbell I, Chan SH, Chen F, Chiang JB, Coppa A, Cortesi L, Crujeiras-Gonzalez A, Czecanca C, De Leeneer K, De Putter R, DePersia A, Devereux L, Domchek S, Efremidis A, Engel C, Ernst C, Evans DG, Feliubadalo L, Fostira F, Fuentes-Rios O, Gomez-Garcia EB, Gonzalez S, Haiman C, Hansen Tv, Hauke J, Hodge J, Hu C, Huang H, Ishak ND, Iwasaki Y, Konstantopoulou I, Kraft P, Lacey J, Lazaro C, Li N, Lim WK, Lindstrom S, Lori A, Martinez E, Martins A, Matsuda K, Matullo G, McInerny S, Michailidou K, Montagna M, Monteiro AN, Mori L, Nathanson K, Neuhausen SL, Nevanlinna H, Olson JE, Palmer J, Pasini B, Patel A, Piane M, Poppe B, Radice P, Renieri A, Resta N, Richardson ME, Rosseel T, Ruddy KJ, Santamarina M, Santos ES, Teras L, Toland AE, Trentham-Dietz A, Vachon CM, Volk AE, Weber-Lassalle N, Weitzel JN, Wiesmuller L, Winham S, Yadav S, Yannoukakos D, Yao S, Zampiga V, Zethoven M, Zhang ZW, Zima T, Spurdle AB, Ana V, Rossing M, Del Valle J, De Nicolo A, Hahnen E, Claes KB, Ngeow J, Momozawa Y, James PA, Couch FJ, Macurek L, Kleibl Z. ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. Clin Cancer Res 29, 3037-3050 (2023) 170 Sugihara R, Taneike M, Murakawa T, Tamai T, Ueda H, Kitazume-Taneike R, Oka T, Akazawa Y, Nishida H, Mine K, Hioki A, Omi J, Omiya S, Aoki J, Ikeda K, Nishida K, Arita M, Yamaguchi O, Sakata Y, Otsu K. Lysophosphatidylserine induces necrosis in pressure overloaded male mouse hearts via G protein coupled receptor 34. Nat Commun 14, 4494 (2023) 171 Suzuki T. Overview of single‐cell RNA sequencing analysis and its application to