1,254 results on '"Imoto, Seiya"'
Search Results
102. Publisher Correction: Integrated exome and RNA sequencing of dedifferentiated liposarcoma
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Hirata, Makoto, Asano, Naofumi, Katayama, Kotoe, Yoshida, Akihiko, Tsuda, Yusuke, Sekimizu, Masaya, Mitani, Sachiyo, Kobayashi, Eisuke, Komiyama, Motokiyo, Fujimoto, Hiroyuki, Goto, Takahiro, Iwamoto, Yukihide, Naka, Norifumi, Iwata, Shintaro, Nishida, Yoshihiro, Hiruma, Toru, Hiraga, Hiroaki, Kawano, Hirotaka, Motoi, Toru, Oda, Yoshinao, Matsubara, Daisuke, Fujita, Masashi, Shibata, Tatsuhiro, Nakagawa, Hidewaki, Nakayama, Robert, Kondo, Tadashi, Imoto, Seiya, Miyano, Satoru, Kawai, Akira, Yamaguchi, Rui, Ichikawa, Hitoshi, and Matsuda, Koichi
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- 2020
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103. Integrated exome and RNA sequencing of dedifferentiated liposarcoma
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Hirata, Makoto, Asano, Naofumi, Katayama, Kotoe, Yoshida, Akihiko, Tsuda, Yusuke, Sekimizu, Masaya, Mitani, Sachiyo, Kobayashi, Eisuke, Komiyama, Motokiyo, Fujimoto, Hiroyuki, Goto, Takahiro, Iwamoto, Yukihide, Naka, Norifumi, Iwata, Shintaro, Nishida, Yoshihiro, Hiruma, Toru, Hiraga, Hiroaki, Kawano, Hirotaka, Motoi, Toru, Oda, Yoshinao, Matsubara, Daisuke, Fujita, Masashi, Shibata, Tatsuhiro, Nakagawa, Hidewaki, Nakayama, Robert, Kondo, Tadashi, Imoto, Seiya, Miyano, Satoru, Kawai, Akira, Yamaguchi, Rui, Ichikawa, Hitoshi, and Matsuda, Koichi
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- 2019
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104. Blautia genus associated with visceral fat accumulation in adults 20–76 years of age
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Ozato, Naoki, Saito, Shinichiro, Yamaguchi, Tohru, Katashima, Mitsuhiro, Tokuda, Itoyo, Sawada, Kaori, Katsuragi, Yoshihisa, Kakuta, Masanori, Imoto, Seiya, Ihara, Kazushige, and Nakaji, Shigeyuki
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- 2019
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105. ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics.
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Sato, Noriaki, Uematsu, Miho, Fujimoto, Kosuke, Uematsu, Satoshi, and Imoto, Seiya
- Subjects
BIOLOGICAL networks ,DATA visualization ,SYSTEMS biology ,DATABASES ,GRAMMAR - Abstract
Summary The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as a valuable systems biology resource and is widely utilized in diverse research fields. However, existing software does not allow flexible visualization and network analyses of the vast and complex KEGG data. We developed ggkegg , an R package that integrates KEGG information with ggplot2 and ggraph. ggkegg enables enhanced visualization and network analyses of KEGG data. We demonstrate the utility of the package by providing examples of its application in single-cell, bulk transcriptome, and microbiome analyses. ggkegg may empower researchers to analyze complex biological networks and present their results effectively. Availability and implementation The package and user documentation are available at: https://github.com/noriakis/ggkegg. [ABSTRACT FROM AUTHOR]
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- 2023
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106. Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples
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Moriyama, Takuya, primary, Imoto, Seiya, additional, Miyano, Satoru, additional, and Yamaguchi, Rui, additional
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- 2019
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107. Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome
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Ayada, Emi, Niida, Atsushi, Hasegawa, Takanori, Miyano, Satoru, Imoto, Seiya, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael, Series editor, Harrison, Robert, editor, Li, Yaohang, editor, and Măndoiu, Ion, editor
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- 2015
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108. A TCR Sequence Data Analysis Pipeline: Tcrip
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Yamaguchi, Rui, Imoto, Seiya, Miyano, Satoru, and Nakamura, Yusuke, editor
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- 2015
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109. A novel ASXL1–OGT axis plays roles in H3K4 methylation and tumor suppression in myeloid malignancies
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Inoue, Daichi, Fujino, Takeshi, Sheridan, Paul, Zhang, Yao-zhong, Nagase, Reina, Horikawa, Sayuri, Li, Zaomin, Matsui, Hirotaka, Kanai, Akinori, Saika, Makoto, Yamaguchi, Rui, Kozuka-Hata, Hiroko, Kawabata, Kimihito Cojin, Yokoyama, Akihiko, Goyama, Susumu, Inaba, Toshiya, Imoto, Seiya, Miyano, Satoru, Xu, Mingjiang, Yang, Feng-Chun, Oyama, Masaaki, and Kitamura, Toshio
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- 2018
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110. Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy
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Kiyotani, Kazuma, Mai, Tu H, Yamaguchi, Rui, Yew, Poh Yin, Kulis, Mike, Orgel, Kelly, Imoto, Seiya, Miyano, Satoru, Burks, A Wesley, and Nakamura, Yusuke
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- 2018
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111. Supplementary Methods, Figure Legends 1-3 from Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers
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Kogo, Ryunosuke, primary, Shimamura, Teppei, primary, Mimori, Koshi, primary, Kawahara, Kohichi, primary, Imoto, Seiya, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Suzuki, Akira, primary, Komune, Shizuo, primary, Miyano, Satoru, primary, and Mori, Masaki, primary
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- 2023
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112. Supplementary Figure 1 from Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers
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Kogo, Ryunosuke, primary, Shimamura, Teppei, primary, Mimori, Koshi, primary, Kawahara, Kohichi, primary, Imoto, Seiya, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Suzuki, Akira, primary, Komune, Shizuo, primary, Miyano, Satoru, primary, and Mori, Masaki, primary
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- 2023
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113. Identifying Key Regulators of Keratinization in Lung Squamous Cell Cancer Using Integrated TCGA Analysis
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Heryanto, Yusri Dwi, primary and Imoto, Seiya, additional
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- 2023
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114. Supplementary Figure 2 from Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers
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Kogo, Ryunosuke, primary, Shimamura, Teppei, primary, Mimori, Koshi, primary, Kawahara, Kohichi, primary, Imoto, Seiya, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Suzuki, Akira, primary, Komune, Shizuo, primary, Miyano, Satoru, primary, and Mori, Masaki, primary
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- 2023
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115. Data from Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers
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Kogo, Ryunosuke, primary, Shimamura, Teppei, primary, Mimori, Koshi, primary, Kawahara, Kohichi, primary, Imoto, Seiya, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Suzuki, Akira, primary, Komune, Shizuo, primary, Miyano, Satoru, primary, and Mori, Masaki, primary
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- 2023
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116. Data from Plastin3 Is a Novel Marker for Circulating Tumor Cells Undergoing the Epithelial–Mesenchymal Transition and Is Associated with Colorectal Cancer Prognosis
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Yokobori, Takehiko, primary, Iinuma, Hisae, primary, Shimamura, Teppei, primary, Imoto, Seiya, primary, Sugimachi, Keishi, primary, Ishii, Hideshi, primary, Iwatsuki, Masaaki, primary, Ota, Daisuke, primary, Ohkuma, Masahisa, primary, Iwaya, Takeshi, primary, Nishida, Naohiro, primary, Kogo, Ryunosuke, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Toh, Hiroyuki, primary, Sato, Tetsuya, primary, Barnard, Graham F., primary, Fukagawa, Takeo, primary, Yamamoto, Seiichiro, primary, Nakanishi, Hayao, primary, Sasaki, Shin, primary, Miyano, Satoru, primary, Watanabe, Toshiaki, primary, Kuwano, Hiroyuki, primary, Mimori, Koshi, primary, Pantel, Klaus, primary, and Mori, Masaki, primary
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- 2023
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117. Supplementary Figures S1-S9 from Plastin3 Is a Novel Marker for Circulating Tumor Cells Undergoing the Epithelial–Mesenchymal Transition and Is Associated with Colorectal Cancer Prognosis
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Yokobori, Takehiko, primary, Iinuma, Hisae, primary, Shimamura, Teppei, primary, Imoto, Seiya, primary, Sugimachi, Keishi, primary, Ishii, Hideshi, primary, Iwatsuki, Masaaki, primary, Ota, Daisuke, primary, Ohkuma, Masahisa, primary, Iwaya, Takeshi, primary, Nishida, Naohiro, primary, Kogo, Ryunosuke, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Toh, Hiroyuki, primary, Sato, Tetsuya, primary, Barnard, Graham F., primary, Fukagawa, Takeo, primary, Yamamoto, Seiichiro, primary, Nakanishi, Hayao, primary, Sasaki, Shin, primary, Miyano, Satoru, primary, Watanabe, Toshiaki, primary, Kuwano, Hiroyuki, primary, Mimori, Koshi, primary, Pantel, Klaus, primary, and Mori, Masaki, primary
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- 2023
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118. Supplementary Tables S1-S2 from Plastin3 Is a Novel Marker for Circulating Tumor Cells Undergoing the Epithelial–Mesenchymal Transition and Is Associated with Colorectal Cancer Prognosis
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Yokobori, Takehiko, primary, Iinuma, Hisae, primary, Shimamura, Teppei, primary, Imoto, Seiya, primary, Sugimachi, Keishi, primary, Ishii, Hideshi, primary, Iwatsuki, Masaaki, primary, Ota, Daisuke, primary, Ohkuma, Masahisa, primary, Iwaya, Takeshi, primary, Nishida, Naohiro, primary, Kogo, Ryunosuke, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Toh, Hiroyuki, primary, Sato, Tetsuya, primary, Barnard, Graham F., primary, Fukagawa, Takeo, primary, Yamamoto, Seiichiro, primary, Nakanishi, Hayao, primary, Sasaki, Shin, primary, Miyano, Satoru, primary, Watanabe, Toshiaki, primary, Kuwano, Hiroyuki, primary, Mimori, Koshi, primary, Pantel, Klaus, primary, and Mori, Masaki, primary
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- 2023
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119. Supplementary Figure Legends from Plastin3 Is a Novel Marker for Circulating Tumor Cells Undergoing the Epithelial–Mesenchymal Transition and Is Associated with Colorectal Cancer Prognosis
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Yokobori, Takehiko, primary, Iinuma, Hisae, primary, Shimamura, Teppei, primary, Imoto, Seiya, primary, Sugimachi, Keishi, primary, Ishii, Hideshi, primary, Iwatsuki, Masaaki, primary, Ota, Daisuke, primary, Ohkuma, Masahisa, primary, Iwaya, Takeshi, primary, Nishida, Naohiro, primary, Kogo, Ryunosuke, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Toh, Hiroyuki, primary, Sato, Tetsuya, primary, Barnard, Graham F., primary, Fukagawa, Takeo, primary, Yamamoto, Seiichiro, primary, Nakanishi, Hayao, primary, Sasaki, Shin, primary, Miyano, Satoru, primary, Watanabe, Toshiaki, primary, Kuwano, Hiroyuki, primary, Mimori, Koshi, primary, Pantel, Klaus, primary, and Mori, Masaki, primary
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- 2023
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120. Supplementary Figure 3 from Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers
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Kogo, Ryunosuke, primary, Shimamura, Teppei, primary, Mimori, Koshi, primary, Kawahara, Kohichi, primary, Imoto, Seiya, primary, Sudo, Tomoya, primary, Tanaka, Fumiaki, primary, Shibata, Kohei, primary, Suzuki, Akira, primary, Komune, Shizuo, primary, Miyano, Satoru, primary, and Mori, Masaki, primary
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- 2023
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121. Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification
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Wang, Zhikang, primary, Bi, Yue, additional, Pan, Tong, additional, Wang, Xiaoyu, additional, Bain, Chris, additional, Bassed, Richard, additional, Imoto, Seiya, additional, Yao, Jianhua, additional, Daly, Roger J, additional, and Song, Jiangning, additional
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- 2023
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122. COVID-19 infection risk assessment and management at the Tokyo 2020 Olympic and Paralympic Games: A scoping review
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Murakami, Michio, primary, Fujii, Kenkichi, additional, Naito, Wataru, additional, Kamo, Masashi, additional, Kitajima, Masaaki, additional, Yasutaka, Tetsuo, additional, and Imoto, Seiya, additional
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- 2023
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123. PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships
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Pan, Tong, primary, Li, Chen, additional, Bi, Yue, additional, Wang, Zhikang, additional, Gasser, Robin B, additional, Purcell, Anthony W, additional, Akutsu, Tatsuya, additional, Webb, Geoffrey I, additional, Imoto, Seiya, additional, and Song, Jiangning, additional
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- 2023
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124. Explainable AI for Estimating Pathogenicity of Genetic Variants Using Large-Scale Knowledge Graphs
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Abe, Shuya, primary, Tago, Shinichiro, additional, Yokoyama, Kazuaki, additional, Ogawa, Miho, additional, Takei, Tomomi, additional, Imoto, Seiya, additional, and Fuji, Masaru, additional
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- 2023
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125. Characteristics of patients with COVID-19 who have deteriorating chest X-ray findings within 48 hours: a retrospective cohort study
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Kusumoto, Tatsuya, primary, Chubachi, Shotaro, additional, Namkoong, Ho, additional, Tanaka, Hiromu, additional, Lee, Ho, additional, Otake, Shiro, additional, Nakagawara, Kensuke, additional, Fukushima, Takahiro, additional, Morita, Atsuho, additional, Watase, Mayuko, additional, Asakura, Takanori, additional, Masaki, Katunori, additional, Kamata, Hirofumi, additional, Ishii, Makoto, additional, Hasegawa, Naoki, additional, Harada, Norihiro, additional, Ueda, Tetsuya, additional, Ueda, Soichiro, additional, Ishiguro, Takashi, additional, Arimura, Ken, additional, Saito, Fukuki, additional, Yoshiyama, Takashi, additional, Nakano, Yasushi, additional, Mutoh, Yoshikazu, additional, Suzuki, Yusuke, additional, Edahiro, Ryuya, additional, Murakami, Koji, additional, Sato, Yasunori, additional, Okada, Yukinori, additional, Koike, Ryuji, additional, Kitagawa, Yuko, additional, Tokunaga, Katsushi, additional, Kimura, Akinori, additional, Imoto, Seiya, additional, Miyano, Satoru, additional, Ogawa, Seishi, additional, Kanai, Takanori, additional, and Fukunaga, Koichi, additional
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- 2023
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126. Sensitivity of rapid antigen tests for COVID-19 during the Omicron variant outbreak among players and staff members of the Japan Professional Football League and clubs: a retrospective observational study
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Murakami, Michio, primary, Sato, Hitoshi, additional, Irie, Tomoko, additional, Kamo, Masashi, additional, Naito, Wataru, additional, Yasutaka, Tetsuo, additional, and Imoto, Seiya, additional
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- 2023
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127. Diagnostic significance of secondary bacteremia in patients with COVID-19
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Nakagawara, Kensuke, primary, Kamata, Hirofumi, additional, Chubachi, Shotaro, additional, Namkoong, Ho, additional, Tanaka, Hiromu, additional, Lee, Ho, additional, Otake, Shiro, additional, Fukushima, Takahiro, additional, Kusumoto, Tatsuya, additional, Morita, Atsuho, additional, Azekawa, Shuhei, additional, Watase, Mayuko, additional, Asakura, Takanori, additional, Masaki, Katsunori, additional, Ishii, Makoto, additional, Endo, Akifumi, additional, Koike, Ryuji, additional, Ishikura, Hiroyasu, additional, Takata, Tohru, additional, Matsushita, Yasushi, additional, Harada, Norihiro, additional, Kokutou, Hiroyuki, additional, Yoshiyama, Takashi, additional, Kataoka, Kensuke, additional, Mutoh, Yoshikazu, additional, Miyawaki, Masayoshi, additional, Ueda, Soichiro, additional, Ono, Hiroshi, additional, Ono, Takuya, additional, Shoko, Tomohisa, additional, Muranaka, Hiroyuki, additional, Kawamura, Kodai, additional, Mori, Nobuaki, additional, Mochimaru, Takao, additional, Fukui, Mototaka, additional, Chihara, Yusuke, additional, Nagasaki, Yoji, additional, Okamoto, Masaki, additional, Amishima, Masaru, additional, Odani, Toshio, additional, Tani, Mayuko, additional, Nishi, Koichi, additional, Shirai, Yuya, additional, Edahiro, Ryuya, additional, Ando, Akira, additional, Hashimoto, Naozumi, additional, Ogura, Shinji, additional, Kitagawa, Yuichiro, additional, Kita, Toshiyuki, additional, Kagaya, Takashi, additional, Kimura, Yasuhiro, additional, Miyazawa, Naoki, additional, Tsuchida, Tomoya, additional, Fujitani, Shigeki, additional, Murakami, Koji, additional, Sano, Hirohito, additional, Sato, Yuki, additional, Tanino, Yoshinori, additional, Otsuki, Ryo, additional, Mashimo, Shuko, additional, Kuramochi, Mizuki, additional, Hosoda, Yasuo, additional, Hasegawa, Yoshinori, additional, Ueda, Tetsuya, additional, Takaku, Yotaro, additional, Ishiguro, Takashi, additional, Fujiwara, Akiko, additional, Kuwahara, Naota, additional, Kitamura, Hideya, additional, Hagiwara, Eri, additional, Nakamori, Yasushi, additional, Saito, Fukuki, additional, Kono, Yuta, additional, Abe, Shinji, additional, Ishii, Tomoo, additional, Ohba, Takehiko, additional, Kusaka, Yu, additional, Watanabe, Hiroko, additional, Masuda, Makoto, additional, Watanabe, Hiroki, additional, Kimizuka, Yoshifumi, additional, Kawana, Akihiko, additional, Kasamatsu, Yu, additional, Hashimoto, Satoru, additional, Okada, Yukinori, additional, Takano, Tomomi, additional, Katayama, Kazuhiko, additional, Ai, Masumi, additional, Kumanogoh, Atsushi, additional, Sato, Toshiro, additional, Tokunaga, Katsushi, additional, Imoto, Seiya, additional, Kitagawa, Yuko, additional, Kimura, Akinori, additional, Miyano, Satoru, additional, Hasegawa, Naoki, additional, Ogawa, Seishi, additional, Kanai, Takanori, additional, and Fukunaga, Koichi, additional
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- 2023
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128. Surformer: An Interpretable Pattern-Perceptive Survival Transformer for Cancer Survival Prediction from Histopathology Whole Slide Images
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Wang, Zhikang, primary, Gao, Qian, additional, Yi, Xiao-Ping, additional, Zhang, Xinyu, additional, Zhang, Yiwen, additional, Zhang, Daokun, additional, Liò, Pietro, additional, Bain, Christopher, additional, Bassed, Richard, additional, Li, Shanshan, additional, Guo, Yuming, additional, Imoto, Seiya, additional, Yao, Jianhua, additional, Daly, Roger J., additional, and Song, Jiangning, additional
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- 2023
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129. A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models
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Hasegawa, Takanori, Niida, Atsushi, Mori, Tomoya, Shimamura, Teppei, Yamaguchi, Rui, Miyano, Satoru, Akutsu, Tatsuya, and Imoto, Seiya
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- 2016
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130. Additional file 8 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
- Abstract
Additional file 8. Proportion of thrombosis and myocardial injury in bacterial respiratory co-infection and secondary infection with coronavirus disease 2019.
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- 2023
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131. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, 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Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Waddell, Nicola, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wala, Jeremiah A, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weischenfeldt, Joachim, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Mark H, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
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- 2023
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132. Additional file 6 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
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Additional file 6. Admission to intensive care unitand use of invasive mechanical ventilationof bacterial respiratory infection with coronavirus disease 2019.
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- 2023
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133. Additional file 4 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
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Additional file 4. Details of respiratory secondary infection.
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- 2023
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134. Additional file 5 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
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Additional file 5. Association of anti-IL-6 receptor antibody use with incidence of secondary infection and death.
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- 2023
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135. Additional file 2 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
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Additional file 2. Evaluation of white blood cells, neutrophils, lymphocytes, neutrophil-lymphocyte ratio, C-reactive protein, and procalcitonin on admission as predictors of respiratory bacterial co-infection based on the area under the curve
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- 2023
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136. Additional file 1 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
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Additional file 1. Identification of organisms in ventilator-associated pneumoniacases
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- 2023
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137. Combined burden and functional impact tests for cancer driver discovery using DriverPower
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Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Gallinger, Steven, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Boutros, Paul C, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
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- 2023
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138. Additional file 7 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
- Abstract
Additional file 7. Forest plot of adjusted oddsratios by multivariate logistic regression analysis of risk factors of death in patients of coronavirus disease 2019with secondary infection except ventilator-associated pneumoniaand VAP.
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- 2023
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139. Integrative pathway enrichment analysis of multivariate omics data
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Reimand, Jüri, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
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- 2023
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140. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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141. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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142. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowski, Julia, 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Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, 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Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, 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Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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143. Additional file 3 of Impact of respiratory bacterial infections on mortality in Japanese patients with COVID-19: a retrospective cohort study
- Author
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Nakagawara, Kensuke, Kamata, Hirofumi, Chubachi, Shotaro, Namkoong, Ho, Tanaka, Hiromu, Lee, Ho, Otake, Shiro, Fukushima, Takahiro, Kusumoto, Tatsuya, Morita, Atsuho, Azekawa, Shuhei, Watase, Mayuko, Asakura, Takanori, Masaki, Katsunori, Ishii, Makoto, Endo, Akifumi, Koike, Ryuji, Ishikura, Hiroyasu, Takata, Tohru, Matsushita, Yasushi, Harada, Norihiro, Kokutou, Hiroyuki, Yoshiyama, Takashi, Kataoka, Kensuke, Mutoh, Yoshikazu, Miyawaki, Masayoshi, Ueda, Soichiro, Ono, Hiroshi, Ono, Takuya, Shoko, Tomohisa, Muranaka, Hiroyuki, Kawamura, Kodai, Mori, Nobuaki, Mochimaru, Takao, Fukui, Mototaka, Chihara, Yusuke, Nagasaki, Yoji, Okamoto, Masaki, Amishima, Masaru, Odani, Toshio, Tani, Mayuko, Nishi, Koichi, Shirai, Yuya, Edahiro, Ryuya, Ando, Akira, Hashimoto, Naozumi, Ogura, Shinji, Kitagawa, Yuichiro, Kita, Toshiyuki, Kagaya, Takashi, Kimura, Yasuhiro, Miyazawa, Naoki, Tsuchida, Tomoya, Fujitani, Shigeki, Murakami, Koji, Sano, Hirohito, Sato, Yuki, Tanino, Yoshinori, Otsuki, Ryo, Mashimo, Shuko, Kuramochi, Mizuki, Hosoda, Yasuo, Hasegawa, Yoshinori, Ueda, Tetsuya, Takaku, Yotaro, Ishiguro, Takashi, Fujiwara, Akiko, Kuwahara, Naota, Kitamura, Hideya, Hagiwara, Eri, Nakamori, Yasushi, Saito, Fukuki, Kono, Yuta, Abe, Shinji, Ishii, Tomoo, Ohba, Takehiko, Kusaka, Yu, Watanabe, Hiroko, Masuda, Makoto, Watanabe, Hiroki, Kimizuka, Yoshifumi, Kawana, Akihiko, Kasamatsu, Yu, Hashimoto, Satoru, Okada, Yukinori, Takano, Tomomi, Katayama, Kazuhiko, Ai, Masumi, Kumanogoh, Atsushi, Sato, Toshiro, Tokunaga, Katsushi, Imoto, Seiya, Kitagawa, Yuko, Kimura, Akinori, Miyano, Satoru, Hasegawa, Naoki, Ogawa, Seishi, Kanai, Takanori, and Fukunaga, Koichi
- Abstract
Additional file 3. Neutrophil-lymphocyte ratioas a predictor of co-infection in steroid and non-steroid users
- Published
- 2023
- Full Text
- View/download PDF
144. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning
- Author
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Konishi, Hiroki, Komura, Daisuke, Katoh, Hiroto, Atsumi, Shinichiro, Koda, Hirotomo, Yamamoto, Asami, Seto, Yasuyuki, Fukayama, Masashi, Yamaguchi, Rui, Imoto, Seiya, and Ishikawa, Shumpei
- Published
- 2019
- Full Text
- View/download PDF
145. ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data
- Author
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Hayashi, Shuto, Yamaguchi, Rui, Mizuno, Shinichi, Komura, Mitsuhiro, Miyano, Satoru, Nakagawa, Hidewaki, and Imoto, Seiya
- Published
- 2018
- Full Text
- View/download PDF
146. Tumor-promoting function and regulatory landscape of PD-L2 in B-cell lymphoma
- Author
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Shingaki, Sumito, primary, Koya, Junji, additional, Yuasa, Mitsuhiro, additional, Saito, Yuki, additional, Tabata, Mariko, additional, McClure, Marni B., additional, Ogawa, Seishi, additional, Katayama, Kotoe, additional, Togashi, Yosuke, additional, Imoto, Seiya, additional, Kogure, Yasunori, additional, and Kataoka, Keisuke, additional
- Published
- 2022
- Full Text
- View/download PDF
147. Dysfunctional analysis of the pre-training model on nucleotide sequences and the evaluation of different k-mer embeddings
- Author
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Zhang, Yao-zhong, primary, Bai, Zeheng, additional, and Imoto, Seiya, additional
- Published
- 2022
- Full Text
- View/download PDF
148. Loss of Dok-3 in Non-tumor Cells Induces Malignant Transformation of Benign Epithelial Tumor Cells of the Intestine
- Author
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Arimura, Sumimasa, primary, Inoue-Yamauchi, Akane, additional, Katayama, Kotoe, additional, Kanno, Tatsuo, additional, Jozawa, Hiroki, additional, Imoto, Seiya, additional, and Yamanashi, Yuji, additional
- Published
- 2022
- Full Text
- View/download PDF
149. Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification
- Author
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Park, Heewon, primary, Imoto, Seiya, additional, and Miyano, Satoru, additional
- Published
- 2022
- Full Text
- View/download PDF
150. Detailed Analysis of the Impact of Clonal Hematopoiesis on the Risk of Severe COVID-19 Infection
- Author
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Saiki, Ryunosuke, primary, Namkoong, Ho, additional, Edahiro, Ryuya, additional, Sonehara, Kyuto, additional, Wang, Qingbo S, additional, Hasegawa, Takanori, additional, Momozawa, Yukihide, additional, Makishima, Hideki, additional, Nannya, Yasuhito, additional, Kakiuchi, Nobuyuki, additional, Terao, Chikashi, additional, Shiraishi, Yuichi, additional, Chiba, Kenichi, additional, Tanaka, Hiroko, additional, Matsuda, Koichi, additional, Morisaki, Takayuki, additional, Murakami, Yoshinori, additional, Kamatani, Yoichiro, additional, Kubo, Michiaki, additional, Kimura, Akinori, additional, Imoto, Seiya, additional, Miyano, Satoru, additional, Kanai, Takanori, additional, Fukunaga, Koich, additional, Okada, Yukinori, additional, and Ogawa, Seishi, additional
- Published
- 2022
- Full Text
- View/download PDF
Catalog
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