Selected Publications


  • Akira Imamoto, Sewon Ki, Leiming Li, Kazunari Iwamoto, Venkat Maruthamuthu, John Devany, Ocean Lu, Tomomi Kanazawa, Suxiang Zhang, Takuji Yamada, Akiyoshi Hirayama, Shinji Fukuda, Yutaka Suzuki, and Mariko Okada. Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis. Life Science Alliance. 10;3(2). pii: e201900635. doi: 10.26508/lsa.201900635, February, 2020. link [PubMed]

  • Hiroaki Imoto and Mariko Okada. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100-108. doi: 10.1016/j.coisb.2019.04.003, June, 2019. link

  • Kentaro Inoue, Hisaaki Shinohara, Marcelo Behar, Noriko Yumoto, Gouhei Tanaka, Alexander Hoffmann, Kazuyuki Aihara, and Mariko Okada-Hatakeyama. Oscillation dynamics underlie functional switching of NF-kB for B-cell activation. npj Syst. Biol. Appl. 2, 16024. doi: 10.1038/npjsba.2016.24, October, 2016. link [PubMed]

  • Hisaaki Shinohara, Marcelo Behar, Kentaro Inoue, Michio Hiroshima, Tomoharu Yasuda, Takeshi Nagashima, Shuhei Kimura, Hideki Sanjo, Shiori Maeda, Noriko Yumoto, Sewon Ki, Shizuo Akira, Yasushi Sako, Alexander Hoffmann, Tomohiro Kurosaki, Mariko Okada-Hatakeyama. Positive feedback within a kinase signaling complex functions as a switch mechanism for NFkB activation.  Science. 344(6185), 760-764, doi: 10.1126/science.1250020, PMID: 24833394, 2014. link [PubMed]

  • Takashi Nakakuki, Marc R Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A Ogunnaike, Mariko Okada-Hatakeyama, Boris N Kholodenko. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.  Cell.141(5), 884-896, doi: 10.1016/j.cell.2010.03.054, PMID: 20493519, 2010. link [PubMed]

  • Marc R Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A Ogunnaike, Jan B. Hoek, Boris N Kholodenko. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analysis.  Mol. Syst. Biol. 3:144, 2007. link [PubMed]

  • Takeshi Nagashima, Hidetoshi Shimodaira, Kaori Ide, Takashi Nakakuki, Yukitaka Tani, Kaoru Takahashi, Noriko Yumoto and Mariko Hatakeyama. Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J.Biol. Chem. 282(6), 4045-4056, doi: 10.1074/jbc.M608653200, PMID: 17142811, 2007. link [PubMed]

  • Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Noriko Yumoto, Mio Ichikawa, Jae-Hoon Kim, Kazuki Saito, Mihoro Saeki, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya. A computational model on the modulation of MAPK and Akt pathways in heregulin induced ErbB signaling.  Biochem.J. 373(Pt2), 451-463, doi:10.1042/BJ20021824, 2003. link [PubMed]

2020


  • Hiroki Michida, Hiroaki Imoto, Hisaaki Shinohara, Noriko Yumoto, Masahide Seki, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Kasukawa Takeya, Yutaka Suzuki, Mariko Okada-Hatakeyama. The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression. Cell Reports. 31, 9, 107724, 2020. link

  • Sufeng Chiang, Jia-Hsin Huang, Huai-Kuang Tsai and Mariko Okada. Computational prediction of the signal-dependent gene expression dynamics by integrating bioinformatics and modeling approaches. FEBS Letters. doi: 10.1002/1873-3468.13757, Accepted. February, 2020

  • Akira Imamoto, Sewon Ki, Leiming Li, Kazunari Iwamoto, Venkat Maruthamuthu, John Devany, Ocean Lu, Tomomi Kanazawa, Suxiang Zhang, Takuji Yamada, Akiyoshi Hirayama, Shinji Fukuda, Yutaka Suzuki, and Mariko Okada. Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis. Life Science Alliance. 10;3(2). pii: e201900635. doi: 10.26508/lsa.201900635, February, 2020. link [PubMed]

  • Mariko Okada, and Takeshi Bamba. 2SBP: overview of the trans-omics session-measure × analyze metabolic adaptation of biological systems-at the 2019 BSJ Meeting in Miyazaki. Biophys Rev. doi: 10.1007/s12551-020-00660-1, March 02, 2020. link [PubMed]

  • Keisuke Yoshida, Toshio Maekawa, Nhung Hong Ly, Shin-ichiro Fujita, Masafumi Muratani, Minami Ando, Yuki Katou, Hiromitsu Araki, Fumihito Miura, Katsuhiko Shirahige, Mariko Okada, Takashi Ito, Bruno Chatton, and Shunsuke Ishii. ATF7-Dependent Epigenetic Changes Are Required for the Intergenerational Effect of a Paternal Low-Protein Diet. Mol Cell. pii: S1097-2765(20)30148-9. doi: 10.1016/j.molcel.2020.02.028, March 7, 2020. link [PubMed]

2019


  • Takashi Mino, Noriki Iwai, Masayuki Endo, Kentaro Inoue, Kotaro Akaki, Fabian Hia, Takuya Uehata, Tomoko Emura, Kumi Hidaka, Yutaka Suzuki, Daron M. Standley, Mariko Okada-Hatakeyama, Shigeo Ohno, Hiroshi Sugiyama, Akio Yamashita, Osamu Takeuchi. Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs. Nucleic Acids Res. 47(16), 8838–8859. pii: gkz628. doi: 10.1093/nar/gkz628, July, 2019. link [PubMed]

  • Shuhei Kimura, Masato Tokuhisa, and Mariko Okada. Inference of genetic networks using random forests: Assigning different weights for gene expression data. J Bioinform Comput Biol. 17(4). doi: 10.1142/S021972001950015X, August, 2019. link [PubMed]

  • Hiroaki Imoto and Mariko Okada. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100-108. doi: 10.1016/j.coisb.2019.04.003, June, 2019. link

  • Masahiro Morita, Nadeem Siddiqui, Sakie Katsumura, Christopher Rouya, Ola Larsson, Takeshi Nagashima, Bahareh Hekmatnejad, Akinori Takahashi, Hiroshi Kiyonari, Mengwei, Zang, René St-Arnaud, Vincent Giguère, Ivan Topisirovic, Mariko Okada-Hatakeyama, Tadashi Yamamoto, and Nahum Sonenberg. Hepatic post-transcriptional network comprised of CCR4-NOT deadenylase and FGF21 maintains systemic metabolic homeostasis. PNAS. doi: 10.1073/pnas.1816023116, March 29, 2019 link [PubMed]

  • Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada and Tadashi Yamamoto. Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes. Development. 146(4). doi: 10.1242/dev.168146, February 7, 2019. link [PubMed]

  • Mariko Okada and Shinya Kuroda. Editorial overview: regulatory mechanism from multiomic data. Curr. Opin. Syst. Biol. Volume 15, Pages iv-vi. doi: 10.1016/j.coisb.2019.06.002, June, 2019. link

  • Ernesto Cortes, Dariusz Lachowski, Benjamin Robinson, Muge Sarper, Jaakko S. Teppo, Stephen D. Thorpe, Tyler J. Lieberthal, Kazunari Iwamoto, David A. Lee, Mariko Okada Hatakeyama, Markku T. Varjosalo, Armando E. del Río Hernández. Tamoxifen mechanically reprograms the tumor microenvironment via HIF‐1A and reduces cancer cell survival. EMBO Rep. 20(1), pii: e46557. doi: 10.15252/embr.201846557, January, 2019. link [PubMed]

  • Shuhei Kimura, Masato Tokuhisa, Akiyuki Uemura, Mariko Okada. Feature Selection based on ramdom forests and its application to a modeling of sewage treatment plant. Proc of the 2019 International Conference on Technologies and Applications of Artificial Intelligence (TAAI 2019). doi: 10.1109/TAAI48200.2019.8959859, January, 2020. link

2018


  • Rui Liu, Jinzeng Wang, Masao Ukai, Ki Sewon, Pei Chen, Yutaka Suzuki, Haiyun Wang, Kazuyuki Aihara, Mariko Okada-Hatakeyama, Luonan Chen. Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. Journal of Molecular Cell Biology. 11(8), 649–664. doi: 10.1093/jmcb/mjy059, November 1, 2018. link [PubMed]

  • Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2. RNA Biol. 15(7), 976-989. doi: 10.1080/15476286.2018.1486658, July, 2018. link [PubMed]

  • Shigeyuki Magi, Kazunari Iwamoto, Noriko Yumoto, Michio Hiroshima, Takeshi Nagashima, Rieko Ohki, Amaya Garcia-Munoz, Natalia Volinsky, Alexander von Kriegsheim, Yasushi Sako, Koichi Takahashi, Shuhei Kimura, Boris N Kholodenko and Mariko Okada-Hatakeyama. Transcriptionally inducible Pleckstrin homology-like domain, family A, member 1, attenuates ErbB receptor activity by inhibiting receptor oligomerization. J Biol Chem. 293(6), 2206-2218. doi: 10.1074/jbc.M117.778399, February 9, 2018. link [PubMed]

  • Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei. High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA. miRNA Biogenesis. 1823, 167-183. doi: 10.1007/978-1-4939-8624-8_13, June, 2018. link [PubMed]

  • Seiki Fujiwara, Midori Hoshizaki, Yu Ichida, Dennis Lex, Etsushi Kuroda, Ken J. Ishii, Shigeyuki Magi, Mariko Okada, Hiroyuki Takao, Masahiro Gandou, Hirotaka Imai, Ryujiro Hara, Herbert Herzog, Akihiko Yoshimura, Hitoshi Okamura, Josef M. Penninger, Arthur S. Slutsky, Stefan Uhlig, Keiji Kuba, and Yumiko Imai. Pulmonary phagocyte-derived NPY controls the pathology of severe influenza virus infection. Nature Microbiology. 4,258–268. doi: 10.1038/s41564-018-0289-1, November, 2018. link [PubMed]

  • Shuhei Kimura, Masato Tokuhisa, and Mariko Okada-Hatakeyama. Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-Series and Static Gene Expression Data. 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE). 98-103. doi: 10.1109/BIBE.2018.00026, December, 2018. link [PubMed]


2017


  • Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima, Atsutaka Kubosaki, Ri-ichiroh Manabe, Mitsuyoshi Murata, Sayaka Nagao-Sato, Kenichi Nakazato, Noriko Ninomiya, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka, Mizuho Sakai, Christophe Simon, Naoko Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard A. Axton, Magda Babina, J. Kenneth Baillie, Timothy C. Barnett, Anthony G. Beckhouse, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, Ailsa J. Carlisle, Hans C. Clevers, Carrie A. Davis, Michael Detmar, Taeko Dohi, Albert S.B. Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Mary C. Farach-Carson, Geoffrey J. Faulkner, Carmelo Ferrai, Malcolm E. Fisher, Lesley M. Forrester, Rie Fujita, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Thomas Gingeras, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Kelly J. Hitchens, David A. Hume, Tomokatsu Ikawa, Yuri Ishizu, Chieko Kai, Hiroshi Kawamoto, Yuki I. Kawamura, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, Sarah Klein, S. Peter Klinken, Alan J. Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weonju Lee, Andreas Lennartsson, Alan Mackay-sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J. Morris, Hozumi Motohashi, Christine L. Mummery, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian-Yang Qin, Michael Rehli, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Gundula G. Schulze-Tanzil, Anita Schwegmann, Guojun Sheng, Jay W. Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M. Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Andru Tomoiu, Hiroo Toyoda, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G. Zhang, Silvia Zucchelli, Imad Abugessaisa, Erik Arner, Jayson Harshbarger, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Naoto Kondo, Masayoshi Itoh, Carsten O. Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R.R. Forrest and Yoshihide Hayashizaki. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data. volume 4, Article number: 170112. doi: 10.1038/sdata.2017.112. PMID: 28850106, August, 29, 2017. link [PubMed]

  • Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Astrom, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, The FANTOM Consortium, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest and Michiel J L de Hoon. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology. 35(9), 872–878. doi: 10.1038/nbt.3947. PMID: 28829439, August 21, 2017. link [PubMed]

  • Shuhei Kimura, Koji Kitazawa, Masato Tokuhisa, and Mariko Okada-Hatakeyama. Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge. Chem-Bio Informatics Journal. Vol.17. 53-71. doi: 10.1273/cbij.17.53, June, 2017. link

  • Trisevgeni Rapakoulia, Xin Gao, Yi Huang, Michiel Jan Laurens de Hoon, Mariko Okada-Hatakeyama, Harukazu Suzuki and Erik Arner. Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. Bioinformatics. 33(23), 3696–3700. doi: 10.1093/bioinformatics/btx503, PMID: 28961713, August, 2017. link [PubMed]

  • Hiroyuki Masunaga, Yurie Sugimoto, Shigeyuki Magi, Ryunosuke Itasaki, Mariko Okada-Hatakeyama, and Hiroyuki Kurata. Robustness analysis of the detailed kinetic model of an ErbB signaling network by using dynamic sensitivity. PLoS ONE. 12(5), e0178250. doi: 10.1371/journal.pone.0178250, May, 2017. link [PubMed]

  • Shigeyuki Magi, Kazunari Iwamoto, and Mariko Okada-Hatakeyama. Current Status of Mathematical Modeling of Cancer - From the Viewpoint of Cancer Hallmarks. Curr. Opin. Syst. Biol. 2, 39-48. doi: 10.1016/j.coisb.2017.02.008, April, 2017. link

  • Shuhei Kimura, Masato Tokuhisa and Mariko Okada-Hatakeyama. Inference of genetic networks from time-series of gene expression levels using random forests. 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). doi: 10.1109/CIBCB.2017.8058522, October, 2017. link

  • Elisa Domínguez-Hüttinger, Panayiotis Christodoulides, Kosuke Miyauchi, Alan D. Irvine, Mariko Okada-Hatakeyama, Masato Kubo, and Reiko J. Tanaka. Mathematical modeling of atopic dermatitis reveals "double-switch" mechanisms underlying 4 common disease phenotypes. J Allergy Clin Immunol. 139(6),1861-1872.e7. doi: 10.1016/j.jaci.2016.10.026, PMID: 27931974, June, 2017. link [PubMed]

  • Yuji Okamoto, Jun-ichi Imura, and Mariko Okada-Hatakeyama. Positive Quadratic System Modeling Based on Singular Perturbation. Transactions of the Society of Instrument and Control Engineers. vol. 53, issue 3, 251-259. doi: 10.9746/sicetr.53.251, March, 2017. link

  • Yuji Okamoto, Jun-ichi Imura, and Mariko Okada-Hatakeyama. Observer design of positive quadratic systems. European Control Conference (ECC). 843-848. doi: 10.1109/ECC.2016.7810394, January, 2017. link


  • Japanese Review


  • 岩本一成, 岡田眞里子. シングルセルシーケンスデータを読み解くための情報解析. 実験医学(別冊)シングルセル解析プロトコール (菅野純夫編集). 326-331, 2017.

  • 岩本一成,間木重行,岡田眞里子. 数理モデル解析によるシグナル伝達制御機構の解明- ErbB受容体の負の制御機構の解析事例. 実験医学(増刊)はじめての数理モデルとシミュレーション (鈴木貴、久保田浩行編集). Vol 35, No.5, 788-793. 2017.

  • 田中玲子 , 久保允人, 岡田眞里子. 数理モデルを用いたアトピー性皮膚炎の発症および悪化メカニズムの解析Mathematical modelling and analysis to understand the pathogenesis of atopic dermatitis. 臨床免疫・アレルギー科 (Clinical immunology & allergology). 68(2), 230-235. 2017.

  • 久保允人, 岡田眞里子, 田中玲子. システムズバイオロジーを用いた皮膚恒常性制御機構の理解. 炎症免疫. 2017年1月号 Vol.25, No.1.



2016


  • Kentaro Inoue, Hisaaki Shinohara, Marcelo Behar, Noriko Yumoto, Gouhei Tanaka, Alexander Hoffmann, Kazuyuki Aihara, and Mariko Okada-Hatakeyama. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024. doi: 10.1038/npjsba.2016.24, October, 2016. link [PubMed]

  • Kosuke Miyauchi, Akiko Sugimoto-Ishige, Yasuyo Harada, Yu Adachi, Yoshiko Usami, Tomohiro Kaji, Kentaro Inoue, Hideki Hasegawa, Takashi Watanabe, Atsushi Hijikata, Satoshi Fukuyama, Tadashi Maemura, Mariko Okada-Hatakeyama, Osamu Ohara, Yoshihiro Kawaoka, Yoshimasa Takahashi, Toshitada Takemori, and Masato Kubo. Protective neutralizing influenza antibody response in the absence of T follicular helper cells. Nature Immunology. 17(12), 1447-1458. doi:10.1038/ni.3563, PMID: 27798619, October, 2016. link [PubMed]

  • Hisaaki Shinohara, Kentaro Inoue, Noriko Yumoto, Takeshi Nagashima, and Mariko Okada-Hatakeyama. Stimulus-Dependent Inhibitor of Apoptosis Protein Expression Prolongs the Duration of B Cell Signalling. Scientific Reports. 6, 27706. doi:10.1038/srep27706, PMID: 27277891, June, 2016. link [PubMed]

  • Keisuke Yoshida, Claire Renard-Guillet, Kentaro Inoue, Katsuhiko Shirahige, Mariko Okada-Hatakeyama, and Shunsuke Ishii. Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages. Genomics Data. 7:90-91. doi:10.1016/j.gdata.2015.11.028, PMID: 26981372, March, 2016. link [PubMed]

  • Kenzui Taniue, Akiko Kurimoto, Hironobu Sugimasa, Emiko Nasu, Yasuko Takeda, Kei Iwasaki, Takeshi Nagashima, Mariko Okada-Hatakeyama, Masaaki Oyama, Hiroko Kozuka-Hata, Masaya Hiyoshi, Joji Kitayama, Lumi Negishi, Yoshihiro Kawasaki, and Tetsu Akiyama. Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1.  PNAS. 113(5), 1273-1278. doi: 10.1073/pnas.1500992113, PMID: 26768845, February 2, 2016. link [PubMed]

  • Shuhei Kimura, Masato Tokuhisa, and Mariko Okada-Hatakeyama. Genetic network inference using hierarchical structure. Frontiers in physiology. 7, 57. doi: 10.3389/fphys.2016.00057, PMID: 26941653, 2016. link [PubMed]

  • Kenzui Taniue, Akiko Kurimoto, Yasuko Takeda, Takeshi Nagashima, Mariko Okada-Hatakeyama, Yuki Katou, Katsuhiko Shirahige, and Tetsu Akiyama. ASBEL–TCF3 complex is required for the tumorigenicity of colorectal cancer cells. PNAS. 113 (45), 12739-12744. doi.org/10.1073/pnas.1605938113, PMID: 27791078, November, 2016. link [PubMed]

  • Shuhei Kimura, Masato Tokuhisa, and Mariko Okada-Hatakeyama. Simultaneous execution method of gene clustering and network inference. 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). doi: 10.1109/CIBCB.2016.7758123 October, 2016. link

  • Yoko Shigeno-Nakazawa, Takuma Kasai, Sewon Ki, Elina Kostyanovskaya, Jana Pawlak, Junya Yamagishi, Noriaki Okimoto, Makoto Taiji, Mariko Okada, Jody Westbrook, Yoko Satta, Takanori Kigawa, and Akira Imamoto. A pre-metazoan origin of the CRK gene family and co-opted signaling network. Scientific reports. 6: 34349. doi: 10.1038/srep34349, PMID: 27686861, September, 2016. link [PubMed]

  • Yoshihiro Kawasaki, Mimon Komiya, Kosuke Matsumura, Lumi Negishi, Sakiko Suda, Masumi Okuno, Naoko Yokota, Tomoya Osada, Takeshi Nagashima, Masaya Hiyoshi, Mariko Okada-Hatakeyama, Joji Kitayama, Katsuhiko Shirahige, and Tetsu Akiyama. MYU, a target lncRNA for Wnt/c-Myc signaling, mediates induction of CDK6 to promote cell cycle progression. Cell reports. 16 (10), 2554-2564. doi: 10.1016/j.celrep.2016.08.015, pii: S2211-1247(16)31061-0, September, 2016. link [PubMed]



Up to 2015


  • Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, the FANTOM Consortium, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS Computational Biology. 11(4), e1004217. doi: 10.1371/journal.pcbi.1004217, April 17, 2015. link [PubMed]

  • Shuhei Kimura, Mariko Okada-Hatakeyama. Improvement of Reliabilities of Regulations using a Hierarchical Structure in a Genetic Network. Proceedings of the 2015 International Joint Conference on Neural Networks (IJCNN). 485-491. doi: 10.1109/IJCNN.2015.7280362, July, 2015. link

  • Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R. R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, FANTOM consortium, Mariko Okada-Hatakeyama, and Jessica C. Mar. Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage. PLoS One. 10(12), e0144176. doi: 10.1371/journal.pone.0144176, December 14, 2015. link [PubMed]

  • Keisuke Yoshida, Toshio Maekawa, Yujuan Zhu, Claire Renard-Guillet, Bruno Chatton, Kentaro Inoue, Takeru Uchiyama, Ken-ichi Ishibashi, Takuji Yamada, Naohito Ohno, Katsuhiko Shirahige, Mariko Okada-Hatakeyama and Shunsuke Ishii. The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory. Nature Immunology. 16, 1034–1043. doi: 10.1038/ni.3257, August 31, 2015. link [PubMed]

  • Marco Mina, Shigeyuki Magi, Giuseppe Jurman, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R. R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, the FANTOM Consortium, Mariko Okada-Hatakeyama and Cesare Furlanello. Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells. Scientific Reports. 5, Article number: 11999, doi: 10.1038/srep11999, July 16, 2015. link [PubMed]

  • Tomohiro Kaji, Atsushi Hijikata, Akiko Ishige, Toshimori Kitami, Takashi Watanabe, Osamu Ohara, Noriyuki Yanaka, Mariko Okada, Michiko Shimoda, Masaru Taniguchi, Toshitada Takemori. CD4 memory T cells develop and acquire functional competence by sequential cognate interactions and stepwise gene regulation. International Immunology. 28 (6), 267–282. doi: 10.1093/intimm/dxv071, December 29, 2015. link [PubMed]

  • Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama. Positive quadratic system approximate representation of nonlinear systems. IFAC-PapersOnLine. 48 (18), 65-70. doi: 10.1016/j.ifacol.2015.11.012, 2015. link

  • Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama. Positive quadratic system representation of molecular interaction in a cell. The Proc. of the 2015 European Control Conference (ECC). 2015, 1554-1559. doi:10.9746/sicetr.52.368, 2015. link

  • Hisaaki Shinohara, Marcelo Behar, Kentaro Inoue, Michio Hiroshima, Tomoharu Yasuda, Takeshi Nagashima, Shuhei Kimura, Hideki Sanjo, Shiori Maeda, Noriko Yumoto, Sewon Ki, Shizuo Akira, Yasushi Sako, Alexander Hoffmann, Tomohiro Kurosaki, Mariko Okada-Hatakeyama. Positive feedback within a kinase signaling complex functions as a switch mechanism for NFkB activation. Science. 344(6185), 760-764, doi: 10.1126/science.1250020, PMID: 24833394, 2014. link [PubMed]

  • Naoki Iwanaga, Kaori Ide, Takeshi Nagashima, Takeo Tomita, Yoshihiro Agari, Akeo Shinkai, Seiki Kuramitsu, Mariko Okada-Hatakeyema, Tomohisa Kuzuyama and Makoto Nishiyama. Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus. Extremophiles. 18(6), 995–1008, doi: 10.1007/s00792-014-0669-2, July 29, 2014. link [PubMed]

  • Hiroko Yukinaga, Clara Shionyu, Eishu Hirata, Kumiko Ui-Tei, Takeshi Nagashima, Shinji Kondo, Mariko Okada-Hatakeyama, Honda Naoki, Michiyuki Matsuda. Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells. Journal of Cell Science, 127, 1805-1815, doi: 10.1242/jcs.139733, April 15, 2014. link [PubMed]

  • Hiromasa Morikawa, Naganari Ohkura, Alexis Vandenbon, Masayoshi Itoh, Sayaka Nagao-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Daron M. Standley, Hiroshi Date, Shimon Sakaguchi, and the FANTOM Consortium. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences. 111(14), 5289-5294, April 8, 2014. [PubMed]

  • Yuki Hasegawa, Dave Tang, Naoko Takahashi, Yoshihide Hayashizaki, Alistair R. R. Forrest, the FANTOM consortium and Harukazu Suzuki. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports. 4, Article number: 5228. doi: 10.1038/srep05228, June 24, 2014. link [PubMed]

  • Shuhei Kimura, Munehiro Furuta, Masanao Sato, Mariko Okada-Hatakeyama. A Fast Parameter Estimation Method for Inferring Reduced S-system Models of Genetic Networks. Proceeding of 2014 International Conference on Information Systems and Computing Technology. 45-50, October, 2014.

  • Takeshi Nagashima, Norihiko Inoue, Noriko Yumoto, Yuko Saeki, Shigeyuki Magi, Natalia Volinsky, Alexander Sorkin, Boris N. Kholodenko, Mariko Okada-Hatakeyama. Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity. FEBS Journal. 282(4), 613-629. doi: 10.1111/febs.13172, February, 2015. link [PubMed]

  • Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama. An Effective Method for the Inference of Reduced S-system Models of Genetic Networks. IPSJ Transactions on Bioinformatics. 7, 30-38. doi: 10.2197/ipsjtbio.7.30, December, 2014. link

  • Erik Arner, Carsten O. Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drabløs, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic, Tom C. Freeman, Ahmad M. N. Alhendi, Peter Arner, Richard Axton, J. Kenneth Baillie, Anthony Beckhouse, Beatrice Bodega, James Briggs, Frank Brombacher, Margaret Davis, Michael Detmar, Anna Ehrlund, Mitsuhiro Endoh, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Geoffrey J. Faulkner, Carmelo Ferrai, Malcolm E. Fisher, Lesley Forrester, Daniel Goldowitz, Reto Guler, Thomas Ha, Mitsuko Hara, Meenhard Herlyn, Tomokatsu Ikawa, Chieko Kai, Hiroshi Kawamoto, Levon M. Khachigian, S. Peter Klinken, Soichi Kojima, Haruhiko Koseki, Sarah Klein, Niklas Mejhert, Ken Miyaguchi, Yosuke Mizuno, Mitsuru Morimoto, Kelly J. Morris, Christine Mummery, Yutaka Nakachi, Soichi Ogishima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Xian-Yang Qin, Sugata Roy, Hiroki Sato, Suzana Savvi, Alka Saxena, Anita Schwegmann, Daisuke Sugiyama, Rolf Swoboda, Hiroshi Tanaka, Andru Tomoiu, Louise N. Winteringham, Ernst Wolvetang, Chiyo Yanagi-Mizuochi, Misako Yoneda, Susan Zabierowski, Peter Zhang, Imad Abugessaisa, Nicolas Bertin, Alexander D. Diehl, Shiro Fukuda, Masaaki Furuno, Jayson Harshbarger, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Yuri Ishizu, Masayoshi Itoh, Tsugumi Kawashima, Miki Kojima, Naoto Kondo, Marina Lizio, Terrence F. Meehan, Christopher J. Mungall, Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Serkan Sahin, Sayaka Nagao-Sato, Jessica Severin, Michiel J. L. de Hoon, Jun Kawai, Takeya Kasukawa, Timo Lassmann, Harukazu Suzuki, Hideya Kawaji, Kim M. Summers, Christine Wells, FANTOM Consortium, David A. Hume, Alistair R. R. Forrest, Albin Sandelin, Piero Carninci, Yoshihide Hayashizaki. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 347(6225), 1010-1014, doi: 10.1126/science.1259418, February, 2015. link [PubMed]

  • Natalia Volinsky, Cormac J. McCarthy, Alexander von Kriegsheim, Nina Saban, Mariko Okada-Hatakeyama, Walter Kolch, Boris N. Kholodenko. Signalling mechanisms regulating phenotypic changes in breast cancer cells.  Bioscience Reports. 35(2), e00178. doi: 10.1042/BSR20140172, February 3, 2015. link [PubMed]

  • Laurence D. Hurst, Avazeh T. Ghanbarian, Alistair R. R. Forrest, FANTOM consortium , Lukasz Huminiecki. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology. 13(12), e1002315, doi: 10.1371/journal.pbio.1002315, December 2015. (Contributed as a FANTOM Consortium member) link [PubMed]

  • Masahito Yoshihara, Hiroko Ohmiya, Susumu Hara, Satoshi Kawasaki, FANTOM consortium , Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji , Motokazu Tsujikawa, Kohji Nishida. Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body. PLoS One. 10(3), e0117581, doi: 10.1371/journal.pone.0117581, March 2015. (Contributed as a FANTOM Consortium member) link [PubMed]

  • Cong Liang, the FANTOM Consortium, Alistair R.R. Forrest and Günter P. Wagner. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature Communications. 6, 6066, doi: 10.1038/ncomms7066, January 2015. (Contributed as a FANTOM Consortium member) link [PubMed]

  • Erik Arner, Alistair R. R. Forrest, Anna Ehrlund, Niklas Mejhert, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Jurga Laurencikiene, Mikael Rydén, Peter Arner, and the FANTOM consortium. Ceruloplasmin Is a Novel Adipokine Which Is Overexpressed in Adipose Tissue of Obese Subjects and in Obesity-Associated Cancer Cells. PLoS One. 9(3), e80274, doi.org/10.1371/journal.pone.0080274, 2014. (Contributed as a FANTOM Consortium member) link [PubMed]

  • FANTOM Consortium and the RIKEN PMI and CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C. Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-sim, Ri-ichiroh Manabe, Jessica C. Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine L. Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. ’t Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci and Yoshihide Hayashizaki. A promoter-level mammalian expression atlas. Nature. 507, 462–470. doi: 10.1038/nature13182, 2014. link [PubMed]

  • Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner, Eivind Valen, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin, Frederik Otzen Bagger, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin, Owen Rackham, A. Maxwell Burroughs, J. Kenneth Baillie, Yuri Ishizu, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Yutaka Negishi, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh, Hideya Kawaji, Naoto Kondo, Jun Kawai, Andreas Lennartsson, Carsten O. Daub, Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, The FANTOM Consortium, Alistair R. R. Forrest, Piero Carninci, Michael Rehli and Albin Sandelin. An atlas of active enhancers across human cell types and tissues. Nature. 507, 455–461. doi: 10.1038/nature12787, 2014. (Contributed as a FANTOM Consortium member) link [PubMed]

  • Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama. Inference of Vohradsky's models of genetic networks by solving two-dimensional function optimization problems. PLoS One. 30, 8(12), e83308. doi: 10.1371/journal.pone.0083308, December 2013. link [PubMed]

  • Masaki Nomura and Mariko Okada-Hatakeyama. Phase responses of oscillating components in a signaling pathway. Frontiers doi: 10.3389/fphys.2013.00068, April 2013. link [PubMed]

  • Kenzui Taniue, Akiko Kurimoto, Hironobu Sugimasa, Emiko Nasu, Takeshi Nagashima, Mariko Okada-Hatakeyama, Tetsu Akiyama. Functional analysis of a novel long ncRNA involved in the tumorigenicity of colorectal cancer. Proceedings: AACR 104th Annual Meeting 2013. 73 (8), Supplement 1. doi: 10.1158/1538-7445. AM2013-1831, April 15, 2013. link

  • Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama. Development of an efficient parameter estimation method for the inference of Vohradsky's neural network models of genetic networks. Proceedings of the 2013 International Joint Conference on Neural Networks. 2676-2681, August, 2013.

  • Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda, and Jun Sese. Statistical significance of combinatorial regulations. Proceedings of National Academy of Sciences of the United States of America. 110 (32), 12996-13001, doi: 10.1073/pnas.1302233110. August 6, 2013. link [PubMed]

  • Kazuhiro Kajiyama, Mariko Okada-Hatakeyama, Yoshihide Hayashizaki, Hideya Kawaji, Hirokazu Suzuki. Capturing drug responses by quantitative promoter activity profiling. CPT: Pharmacometrics and Systems Pharmacology. 2(9), e77, September 25, 2013. [PubMed]

  • Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama. Inference of Vohradský's Models of Genetic Networks by Solving Two-Dimensional Function Optimization Problems. Plos One. 8(12), e83308, doi: 10.1371/journal.pone.0083308, December 30, 2013. link [PubMed]

  • Tomohiro Kaji, Koji Furukawa, Akiko Ishige, Itsumi Toyokura, Masaki Nomura, Mariko Okada, Yoshimasa Takahashi, Michiko Shimoda, Toshitada Takemori. Both mutated and unmutated memory B cells accumulate mutations in the course of the secondary response and develop a new antibody repertoire optimally adapted to the secondary stimulus. International Immunology. 25(12):683-695, doi: 10.1093/intimm/dxt030, December, 2013. link [PubMed]

  • Junya Yamagishi, Noriaki Okimoto, Takuma Kasai, Atsushi Suenaga, Mariko Okada, Akira Imamoto, and Makoto Taiji. Computational design of small peptide inhibitors of Protein-Protein interactions in CRK-SH2 mediated intracellular signaling. Models in Bioscience and Materials Research. P155-166, ISBN: 978-1-62808-052-0, 2013.

  • Yuko Saeki, Takeshi Nagashima, Shuhei Kimura, Mariko Okada. An ErbB receptor-mediated AP-1 regulatory network is modulated by STAT3 and c-MYC during calcium-dependent keratinocyte differentiation. Experimental Dermatology. 21(4), 293-298. doi: 10.1111/j.1600-0625.2012.01453.x, April, 2012. link [PubMed]

  • Frank D. Till, Alex Cheong, Mariko Okada, Boris N. Kholodenko. Catching transcriptional regulation by thermostatistical modeling. Physical Biology. 9(4), 1-11. doi: 10.1088/1478-3975/9/4/045007, August 7, 2012. link . doi: 10.1111/j.1600-0625.2012.01453.x, April, 2012. link [PubMed]

  • Tomohiro Kaji, Akiko Ishige, Masaki Hikida, Junko Taka, Atsushi Hijikata, Masato Kubo, Takeshi Nagashima, Yoshimasa Takahashi, Tomohiro Kurosaki, Mariko Okada, Osamu Ohara, Klaus Rajewsky, Toshitada Takemori. Distinct cellular pathways select germline-encoded and somatically mutated antibodies into immunological memory. Journal of Experimental Medicine. 209 (11), 2079–2097. doi: 10.1084/jem.20120127, October 22, 2012. link [PubMed]

  • Hiromi Nishida, Shinji Kondo, Takashi Matsumoto, Yutaka Suzuki, Hirofumi Yoshikawa, Todd. D. Taylor, Junta Sugiyama. Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping. Open Biology. 2(4), 120043. doi: 10.1098/rsob.120043. April 2, 2012. link [PubMed]

  • Takamasa Katagiri, Hiroshi Kawamoto, Takashi Nakakuki, Ken Ishiyama, Mariko Okada, Sigeki Ohtake, Yu Seiki, Kohei Hosokawa, Nakao Shinji. Individual hematopoietic stem cells in human bone marrow of patients with aplastic anemia or myelodysplastic syndrome stably give rise to limited cell lineages. Stem Cells. 31(3), 536-546. doi: 10.1002/stem.1301, March, 2013. link

  • Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama. Inference of S-system models of genetic networks by solving linear programming problems and sets of linear algebraic equations. The 2012 International Joint Conference on Neural Networks (IJCNN). 1-8. doi: 10.1109/IJCNN.2012.6252644, June, 2012. link

  • Michio Hiroshima, Yuko Saeki, Mariko Okada-Hatakeyama, and Yasushi Sako. Dynamically varying interactions between heregulin and ErbB proteins detected by single-molecule analysis in living cells. Proceedings of the National Academy of Sciences of the United States of America. 109 (35), 13984-13989. doi: 10.1073/pnas.1200464109, August 28, 2012. link [PubMed]

  • Shuhei Kimura, Daisuke Araki, Koki Matsumura, Mariko Okada-Hatakeyama. Inference of S-system models of genetic networks by solving one-dimensional function optimization problems. Mathematical Biosciences. 235(2), 161-170. doi: 10.1016/j.mbs.2011.11.008, February 2012. link [PubMed]

  • Masahiro Morita, Yuichi Oike, Takeshi Nagashima, Tsuyoshi Kadomatsu, Mistuhisa Tabata, Toru Suzuki, Takahisa Nakamura, Nobuaki Yoshida, Mariko Okada, Tadashi Yamamoto. Obesity resistance and increased hepatic expression of catabolism-related mRNAs in Cnot3+/- mice. The EMBO Journal. 30(22), 4678-4691. doi: 10.1038/emboj.2011.320, September 2011. link [PubMed]

  • Yuichi Shiraishi, Mariko Okada-Hatakeyama and Satoru Miyano.  A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics. 27(17), 2399-2405. doi: 10.1093/bioinformatics/btr382, 2011. link [PubMed]

  • Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai and Mariko Okada-Hatakeyama. Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity. BMC Systems Biology. 5(1): 29. doi: 10.1186/1752-0509-5-29, 2011. link [PubMed]

  • Masaaki Oyama, Takeshi Nagashima, Takashi Suzuki, Hiroko Kozuka-Hata, Noriko Yumoto, Yuichi Shiraishi, Kazuhiro Ikeda, Yoko Kuroki, Noriko Gotoh, Takanori Ishida, Satoshi Inoue, Hiroaki Kitano & Mariko Okada-Hatakeyama. Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer. The Journal of Biological Chemistry. 286(1), 818-829. doi: 10.1074/jbc.M110.156877, 2011. link [PubMed]

  • Saswati Dana, Takashi Nakakuki, Mariko Okada-Hatakeyama, Shuhei Kimura and Soumyendu Raha. Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway. Computer Methods and Programs in Biomedicine. 101(1), 1-22. doi: 10.1016/j.cmpb.2010.04.001, 2011. link [PubMed]

  • Shuhei Kimura, Koki Matsumura and Mriko Okada-Hatakeyama.  Efficient Parameter Estimation for the Inference of S-system Models of Genetic Networks: Proposition of Further Problem Decomposition and Alternate Function Optimization. Chem-Bio Informatics Journal. 11, 24-40. doi: 10.1273/cbij.11.24, 2011. link

  • Shuhei Kimura, Takashi Nakakuki, Seiji Kirita and Mariko Okada. AGLSDC: a genetic local search suitable for parallel computation. SICE Journal of Control, Measurement, and System Integration. 4, 105-113. org/10.9746/sicetr.52.368, 2011. link

  • Shuhei Kimura, Yusuke Amano, Koki Matsumura, Mariko Okada-Hatakeyama. Effective parameter estimation for S-system models using LPMs and evolutionary algorithms. Proceedings of the 2010 IEEE Congress on Evolutionary Computation. 2034-2041. doi: 10.1109/CEC.2010.5586248, 2010. link

  • Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama. Bootstrap analysis of genetic networks inferred by the method using LPMs. International Conference on on Computational Science and Its Applications (ICCSA). 296-299. org/10.1109/ICCSA.2010.69, 2010. link

  • Shuhei Kimura, Yuichi Shiraishi, Mariko Okada. Inference of genetic networks using linear programming machines: application of a priori knowledge. Proceedings of the IJCNN (the International Joint Conferences on Neural Networks). 1617-1624. doi: 1109/IJCNN.2009.5178679, 2009. link

  • Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Kotaro Yoshida, Koki Matsumura , Mariko Hatakeyama. Inference of genetic networks using a reduced NGnet model. Proceedings of the IJCNN (the International Joint Conferences on Neural Networks). 932-937, 2007. link

  • Shuhei Kimura, Yuichi Shiraishi and Mariko Okada.  Inference of genetic networks using LPMS: Assessments of confidence values of regulations. Journal of Bioinformatics and Computational Biology. 8(4), 661-677. doi: 10.1142/S0219720010004859, 2010. link

  • Yuichi Shiraishi, Shuhei Kimura and Mariko Okada. Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics . 26(8), 1073-1081. doi: 10.1093/bioinformatics/btq094, 2010. link [PubMed]

  • Takashi Nakakuki, Marc R Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A Ogunnaike, Mariko Okada-Hatakeyama, Boris N Kholodenko. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.  Cell .141(5), 884-896, doi: 10.1016/j.cell.2010.03.054, PMID: 20493519, 2010. link [PubMed]

  • Yuko Saeki, Takaho Endo, Kaori Ide, Takeshi Nagashima, Noriko Yumoto, Tetsuro Toyoda, Harukazu Suzuki, Yoshihide Hayashizaki, Yoshiyuki Sakaki and Mariko Okada-Hatakeyama. Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells. BMC Genomics. 10,54. doi: 10.1186/1471-2164-10-545, 2009. link [PubMed]

  • Takeshi Nagashima, Ryoko Nakayama, Atsushi Suenaga, Kaori Ide, Noriko Yumoto, Yoshimi Naruo, Kaoru Takahashi, Yuko Saeki, Makoto Taiji, Hiroshi Tanaka, Tsai Shih-Feng and Mariko Hatakeyama. Mutation of epidermal growth factor receptor is associated with MIG6 expression. The FEBS Journal. 276(18), 5239-5251. doi: 10.1111/j.1742-4658.2009.07220.x, 2009. link [PubMed]

  • The FANTOM Consortium, Harukazu Suzuki, Alistair R R Forrest, Erik van Nimwegen, Carsten O Daub, Piotr J Balwierz, Katharine M Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel J L de Hoon, Shintaro Katayama, Kate Schroder, Piero Carninci, Yasuhiro Tomaru, Mutsumi Kanamori-Katayama, Atsutaka Kubosaki, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara, Timothy Bailey, Vladimir B Bajic, Denis Bauer, Anthony G Beckhouse, Nicolas Bertin, Johan Björkegren, Frank Brombacher, Erika Bulger, Alistair M Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Pär G Engström, Magbubah Essack, Geoffrey J Faulkner, J Lynn Fink, David Fredman, Ko Fujimori, Masaaki Furuno, Takashi Gojobori, Julian Gough, Sean M Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hörnquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus C Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga, Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron MacPherson, Norihiro Maeda, Christopher A Maher, Monique Maqungo, Jessica Mar, Nicholas A Matigian, Hideo Matsuda, John S Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Mika Nakano, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Jun Otomo, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saito, Albin Sandelin, Sebastian Schmeier, Christian Schönbach, Ariel S Schwartz, Colin A Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St. Laurent, Masanori Suzuki, Takahiro Suzuki, Matthew J Sweet, Ryan J Taft, Shizu Takeda, Yoichi Takenaka, Kai Tan, Martin S Taylor, Rohan D Teasdale, Jesper Tegnér, Sarah Teichmann, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine A Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan and David A Hume, Takahiro Arakawa, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ai Kaiho, Tsugumi Kawashima, Chika Kawazu, Yayoi Kitazume, Miki Kojima, Hisashi Miura, Kayoko Murakami, Mitsuyoshi Murata, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Chihiro Ogawa, Takuma Sano, Christophe Simon, Michihira Tagami, Yukari Takahashi, Jun Kawai & Yoshihide Hayashizaki. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41(5), 553-562. doi: 10.1038/ng.375, 2009. link [PubMed]

  • Ji-Heui Seo, Atsushi Suenaga, Mariko Hatakeyama, Makoto Taiji, Akira Imamoto. Structural and Functional Basis of a Role for CRKL in a Fibroblast Growth Factor 8-Induced Feed-Forward Loop. Molecular and Cellular Biology. 29(11), 3076-3087. doi:1128/MCB.01686-08, 2009. link [PubMed]

  • Atsushi Suenaga, Mariko Hatakeyama, Anatoly B. Kiyatkin, Ravi Radhakrishnan, Makoto Taiji and Boris N. Kholodenko. Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor. Biophysical journal. 96(6): 2278-2288. doi: 10.1016/j.bpj.2008.11.018, 2009. link [PubMed]

  • Shuhei Kimura, Satoshi Nakayama, Mariko Hatakeyama. Genetic network inference as a series of discrimination task. Bioinformatics. 25(7): 918-925. doi: 1093/bioinformatics/btp072, 2009. link

  • Takeshi Nagashima, Mariko Oyama, Hiroko Kozuka-Hata, Noriko Yumoto, Yoshiyuki Sakaki, Mariko Hatakeyama. Phosphoproteome and transcriptome analyses of ErbB ligand-stimulated MCF-7 cells. Cancer Genomics and Proteomics. 5(3-4), 161-168. 2008. link [PubMed]

  • Takeshi Nagashima, Takahiro Suzuki, Shinji Kondo, Yoko Kuroki, Kaoru Takahashi, Kaori Ide, Aki Hasegawa, Tetsuro Toyoda, Toshio Kojima, Akihiko Konagaya, Harukazu Suzuki,Yoshihide Hayashizaki,Yoshiyuki Sakaki & Mariko Hatakeyama. Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 breast cancer cells. PLoS One. 3(3), e1803. doi: 10.1371/journal.pone.0001803, 2008. link [PubMed]

  • Takashi Nakakuki, Noriko Yumoto, Takashi Naka, Mikako Shirouzu, Shigeyuki Yokoyama and Mariko Hatakeyama. Topological analysis of MAPK cascade for kinetic ErbB signaling. PLoS One. 3(3), e1782. org/10.1371/journal.pone.0001782, 2008. link [PubMed]

  • Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura and Mariko Hatakeyama. Function approximation approach to the inference of reduced NGnet models of genetic networks. BMC Bioinformatics. 9, 23. doi: 10.1186/1471-2105-9-23, 2008. link [PubMed]

  • Marc R Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A Ogunnaike, Jan B. Hoek, Boris N Kholodenko. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analysis.  Mol. Syst. Biol. 3:144, 2007. link [PubMed]

  • Noriko Yumoto, Xiaomei Yu, and Mariko Hatakeyama. Expression of the ErbB4 receptor causes reversal regulation of PP2A in the Shc signal transduction pathway in human cancer cells. Molecular and Cellular Biochemistry. 285, 165–171. doi: 10.1007/s11010-005-9075-5, February, 2006. link [PubMed]

  • Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Okada. Function Approximation Approach to the Inference of Normalized Gaussian Network Models of Genetic Networks. Proceedings of the 2006 International Joint Conference on Neural Networks (IJCNN2006). 4525-4532. doi: 10.1109/IJCNN.2006.247017, 2006. link

  • Mariko Hatakeyama. System properties of ErbB receptor signaling for the understanding of cancer progression. Molecular BioSystems. 3(2), 111-116, doi: 10.1039/b612800a, 2007 link [PubMed]

  • Takeshi Nagashima, Hidetoshi Shimodaira, Kaori Ide, Takashi Nakakuki, Yukitaka Tani, Kaoru Takahashi, Noriko Yumoto and Mariko Hatakeyama. Quantitative Transcriptional Control of ErbB Receptor Signaling Undergoes Graded to Biphasic Response for Cell Differentiation. Journal of Biological Chemistry. 282(6):4045-4056, doi: 10.1074/jbc.A114.608653, 2007. link [PubMed]

  • Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, and Mariko Okada-Hatakeyama. Function approximation approach to the inference of neural network models of genetic networks. IPSJ Transactions on Bioinformatics. 48, 9-19, 2007. 

  • Takashi Naka, Mariko Okada-Hatakeyama, Naoto Sakamoto, Akihiko Konagaya. Compensation effect of the MAPK cascade on formation of phospho-protein gradients. Biosystems. 83, 167-177. doi: 10.1016/j.biosystems.2005.06.015, February, 2006. link [PubMed]

  • Atsushi Suenaga, Naoki Takada, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Kentaro Tomii, Noriaki Okimoto, Noriyuki Futatsugi, Tetsu Narumi, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya and Makoto Taiji. Novel mechanism of interaction of p85 subunit of PI3K and ErbB3 receptor-derived phosphotyrosyl peptides. Journal of Biological Chemistry. 280(2), 1321-1326. 2005. link [PubMed]

  • Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya. Genome-wide functional annotation environment for Thermus thermophilus in OBlGrid. Lecture Notes in Computer Science book series. 3370, 82-91. doi: 10.1007/978-3-540-32251-1_8, 2004. link

  • Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics. 21(7), 1154-1163. doi: 10.1093/bioinformatics/bti071, 2005. link [PubMed]

  • Yoshiyuki Sakaki, Boris N. Kholodenko, Hiroaki Kitano, Walter Kolch, Pierre De Meyts, Yosef Yarden, Hans V. Westerhoff, Steven Wiley, Mariko Hatakeyama. White Paper: The International Receptor Tyrosine Kinase Networks Consortium. Scientist . 19, 8-9, 2005. link

  • Yoshiyuki Sakaki, Boris N. Kholodenko, Mariko Okada-Hatakeyama, Hiroaki Kitano, Walter Kolch, Pierre De Meyts, Yosef Yarden, Hans V. Westerhoff, Steven Wiley. International consortium on systems biology of receptor tyrosine kinase regulatory networks. IEE proceedings-Systems Biology. 152(2), 53-60. doi: 10.1049/ip-syb:20059002, 2005. link [PubMed]

  • Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama. Inference of genetic networks using neural network models. 2005 IEEE Congress on Evolutionary Computation Proceedings Vol. 2. 1738-1745. doi: 10.1109/CEC.2005.1554898, 2005 link

  • Aki Hasegawa, Kazumi Matsumura, Yu Gyoubai, Mariko Hatakeyama, Akihiko Konagaya. Software-aided mass spectrometry analysis for identification of protein-protein interaction in signal transduction pathways. Proceedings of the International Workshop on Biomedical Data Engineering (BMDE2005). 44-51. doi: 10.1109/ICDE.2005.286, 2005. link

  • Yoshiyuki Sakaki, Boris N. Kholodenko, Mariko Okada-Hatakeyama, Hiroaki Kitano, Walter Kolch, Pierre De Meyts, Yosef Yarden, Hans V. Westerhoff, Steven Wiley. The RTK consortium white paper. The-Scientist, 19, 8-9. 2005.

  • Shuhei Kimura, Mariko Hatakeyama and Akihiko Konagaya. Inference of S-system models of genetic networks from noisy time-series data. Chem-Bio Informatics Journal. 4, 1-14. 2004. link

  • Mariko Hatakeyama, Noriko Yumoto, Xiaomei Yu, Mikako Shirouzu, Shigeyuki Yokoyama & Akihiko Konagaya. Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase. Oncogene. 23, 5023-5031, 2004. link

  • Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi & Akihiko Konagaya. OBIYagns: A grid-based biochemical simulator with parameter estimator. Bioinformatics. 20(10):1646-1648, 2004. link [PubMed]

  • Atsushi Suenaga, Anatoly B. Kiyatkin, Mariko Hatakeyama, Noriyuki Futatsugi, Noriaki Okimoto, Yoshinori Hirano, Tetsu Narumi, Atsushi Kawai, Ryutaro Susukita, Takahiro Koishi, Hideaki Furusawa, Kenji Yasuoka, Naoki Takada, Yousuke Ohno, Makoto Taiji, Toshikazu Ebisuzaki, Jan B. Hoek, Akihiko Konagaya & Boris N. Kholodenko. Tyr317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations. The Journal of Biological Chemistry. 279(6): 4657-4662, 2004. link [PubMed]

  • Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama and Kenji Satou. The superstructure towards Open Bioinformatics Grid. New Generation Computing, Computing Paradigms and Computational Intelligence. 22, 167-176. 2004.

  • Shuhei Kimura, Mariko Hatakeyama, Takuji Kawasaki, Takashi Naka, Akihiko Konagaya. Parameter estimation for the simulation of biochemical pathways. Proceedings of 15th IASTED International Conference on Modelling and Simulation. 266-271, 2004. link

  • Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya. Inference of S-system models for genetic networks by using a genetic local search. Proceedings of 2003 Congress on Evolutionary Computation. 631-638. 2003. link

  • Atsushi SuenagaMio IchikawaMariko HatakeyamaXiaomei YuNoriyuki FutatsugiTetsu NarumiKazuhiko FukuiTakaho TeradaMakoto TaijiMikako ShirouzuShigeyuki Yokoyama and Akihiko Konagaya. Molecular Dynamics, Free Energy, and SPR Analyses of the Interactions Between the SH2 Domain of Grb2 and ErbB Phosphotyrosyl Peptides. Biochemistry (U.S). 42(18), 5195-5200. org/10.1021/bi034113h, 2003. link [PubMed]

  • Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Noriko Yumoto, Mio Ichikawa, Jae-Hoon Kim, Kazuki Saito, Mihoro Saeki, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya. A computational model on the modulation of MAPK and Akt pathways in heregulin induced ErbB signaling.  Biochemical Journal. 373(Pt2), 451-463, doi:10.1042/BJ20021824, 2003. link [PubMed]


  • Japanese Review


  • 篠原久明, 井上健太郎, 岡田眞里子. B細胞の免疫応答を制御するシグナル活性の閾値決定機構. 感染 炎症 免疫. 45(1), 78-81. 2015.

  • 篠原久明・井上健太郎・岡田眞里子. B細胞受容体シグナル伝達系における正のフィードバック制御によるNF-κBの活性化のスイッチ様の応答. ライフサイエンス 新着論文レビュー. doi: 10.7875/first.author.2014.082 link

  • 岡田眞里子. ゲノムから見た乳がんのシグナル伝達とシステム生物学. 実験医学増刊 ゲノム医学・生命科学研究 総集編. 31(15), 118 – 125. 2013年9月.

  • 岡田眞里子. がんシグナル伝達ネットワークの多階層制御. 実験医学. 31(18). 2013年11月.

  • 岡田眞里子. シグナル伝達系における制御の規則性と細胞応答の予測. ライフサイエンス 領域融合レビュー, 3, e001. doi: 10.7875/leading.author.3.e001, January 6, 2014. link

  • 畠山眞里子、中茎隆、仲隆. RTKシグナル伝達系のシステムバイオロジー -数理解析の基礎と創薬への応用. 実験医学. 24(16), 2530-2535,2006年10月.

  • 篠原久明, 井上健太郎, 岡田眞里子. B細胞受容体シグナル伝達系の正のフィードバック制御によるNF-κBのスイッチ様応答. ライフサイエンス新着論文レビュー. link

  • 岡田眞里子. がん細胞情報伝達のダイナミクスとシステムバイオロジー. 応用数理. 22 (3). 2012.

  • 岡田眞里子. 遺伝子ネットワークのスイッチが細胞運命を決定する. 実験医学増刊. 29 (12), 127-132. 2011.

  • 畠山眞里子. シグナル伝達系のシステムバイオロジー ~細胞制御の理論と予測~月刊バイオインダストリー. 25(12), 20-25. 2008.

  • 中茎隆、仲隆、畠山眞里子. 数理モデルを用いた細胞内シグナル伝達系の解析 ~ポストゲノム時代におけるシステムバイオロジー研究の最前線. 計測と制御. 47(2), 132-138. 2008.

  • 畠山眞里子. 癌細胞を用いたシグナル伝達研究における多数リン酸化蛋白解析. 分子消化器病. 4, 233-238. 2007.

  • 畠山眞里子. 生命の謎に“システム解析”で迫る -生物現象を定式化してデザインする研究. 化学. 62, 52-56. 2007.

  • 畠山眞里子. 細胞制御理解に向けたRTKシグナル伝達系の統合システム解析. 実験医学. 25 (11), 1649-1655. 2007.


2020


    International Conference Presentation


    Oral presentation
  • Mariko Okada, Reclassification of cancer subtypes based on the dynamic behaviors. The 1st International Symposium on Human InformatiX, February 27-28, 2020. ATR, Kyoto. Invited talk

  • Johannes Nicolaus Wibisana. NF-κB mediated transcriptional regulation in B cell. Japan-Korea Bilateral Symposium between IPR and SNU on Advanced Analysis of Protein Function and Structure, January 31, 2020, College of Pharmacy, Seoul National University

  • Mariko Okada. Reclassification of cancer subtypes based on the dynamic behaviors. The 1st International Symposium on Human InformatiX, February 27, 2020, Advanced Telecommunications Research Institute International, Kyoto

  • Poster presentation
  • Hiroki Michida, Hiroaki Imoto, Takeya Kasukawa, Mariko Okada. The number of transcription factor molecules loading at an enhancer determines gene expression quantity. The 1st International Symposium on Human InformatiX, February 27, 2020, Advanced Telecommunications Research Institute International, Kyoto

  • Domestic Conference Presentation


    Oral presentation
  • 井元宏明. 生物学研究を加速する細胞モデリング基盤の紹介. 第16回 生物数学の理論とその応用 ~生命現象の定量的理解に向けて~, January 27-31, 2020, 京都大学 数理解析研究所420号室

  • 岡田 眞里子. 細胞制御メカニズム理解のための数理モデル構築とツール開発. 第16回 生物数学の理論とその応用 ~生命現象の定量的理解に向けて~, January 27-31, 2020, 京都大学 数理解析研究所420号室

2019


    International Conference Presentation


    Oral presentation
  • Mariko Okada. Quantitative analysis of immune response using Omics and imaging. 1st International Symposium on Inflammation Cellular Society, November 26-27, 2019, The University of Tokyo. Invited talk

  • Mariko Okada. Cooperative mechanism in epigenetic network controls gene expression quantity. Bioinformatics Seminar, Academia Sinica, Nov 20, 2019, Taiwan. Invited talk

  • Mariko Okada. Analyze immune response using Omics and imaging. ICSB 2019@OIST Trans-Omics workshop –The 3rd International Symposium for Trans-Omics– October 31, 2019, Okinawa

  • Mariko Okada. Quantitative analysis of biological networks using mathematical models. The 9th International Congress on Industrial and Applied Mathematics (ICIAM 2019) The CJK-SIAMs joint mini-symposium on Mathematical Biology - July15-19, 2019, Valencia, Spain

  • Mariko Okada. Quantitative analysis of transcription using Omics and imaging. Trans-Omics workshop –The 3rd International Symposium for Trans-Omics–, International Conference of Systems Biology, October 31, 2019, OIST, Okinawa

  • Hiroaki Imoto, Kyouichi Ebata, Su xiang Zhang, Shigeyuki Magi, Mariko Okada. Model-based identification of ErbB network principles among cell types. International Conference of Systems Biology, November 1-5, 2019, OIST, Japan

  • Poster presentation
  • Keita Iida, Takeya Kasukawa, Mariko Okada. Bioinformatic processing of single-cell RNA-seq data for genome-wide parameter estimation upon eukaryotic gene expressions. International Conference of Systems Biology, November 1-5, 2019, OIST, Japan

  • Kyoichi Ebata, Sawa Yamashiro, Hiroaki Imoto, Oleksii Rukhlenko, Boris Kholodenko, Mariko Okada. A Multi-layer Analysis of Signal-dependent Cell Cycle Progression. International Conference of Systems Biology, November 1-5, 2019, OIST, Japan

  • Hiroki Michida, Minami Ando, Shigeyuki Magi, Mariko Okada. A NF-κB - p38 MAPK crosstalk shapes oscillatory gene expression. International Conference of Systems Biology, November 1-5, 2019, OIST, Japan

  • Johannes Nicolaus Wibisana, Takehiko Inaba, Yasushi Sako, Mariko Okada. Multi-dimensional analysis of NF-κB nuclear dynamics. International Conference of Systems Biology, November 1-5, 2019, OIST, Japan


  • Domestic Conference Presentation


    Oral presentation
  • 岡田眞里子. 創薬を加速する細胞モデリング基盤の構築. JST未来社会創造事業 キックオフ会議, 2019年12月10日, 東京市ヶ谷

  • Mariko Okada. Model-based understanding of cell proliferation. The 42nd Annual Meeting of the Molecular Biology Society of Japan, December 3-6, 2019, 福岡

  • Mariko Okada. Analyze Omics data using kinetic model. The 57th Annual Meeting of the Biophysical Society of Japan. MeasurexAnalyze Metabolic Adaptation of Biological Systems, Sept 26, 2019 宮崎

  • 岡田眞里子. 炎症疾患の代謝アダプテーション. 第3回代謝オミクス領域会議, 2019年7月3日, 福岡

  • Quantitative evaluation of kinase activities and transcriptional regulation using mathematical model. 数理モデルを用いたキナーゼと転写の定量的評価. 第92回日本薬理学会年会, 2019年3月14日, 大阪

  • 岡田 眞里子. Quantitative evaluation of kinase activities and transcriptional regulation using mathematical model. The 92nd Annual Meeting of the Japanese Pharmacological Society, March 14-16, 2019 Osaka (invited talk)

  • Minami Ando. Biological significance of the oscillatory dynamics of NF-kB for target gene expression. Japan-Korea Symposium on Multi-Scale Structural Life Science and the Advanced Technologies, March 15, 2019, Osaka University (oral presentation)

  • Hiroaki Imoto. ErbBシグナル伝達経路と細胞周期の統合数理モデルを用いた細胞応答の予測. RIKEN Symposium “Behavior and Logic of Cellular Systems XI,” March 28-29, 2019, Saitama (oral presentation)

  • Hiroki Michida. NF-kB - p38 MAPK クロストークによる遺伝子発現動態制御の解明. RIKEN Symposium “Behavior and Logic of Cellular Systems XI,” March 28-29, 2019, Saitama (oral presentation)

  • 間木重行. 時系列・一細胞解析から見える抗がん剤耐性獲得過程, 大阪大学蛋白質研究所セミナー「がん研究の新機軸」, July 4-5, 2019, 大阪大学微生物研究所 谷口記念講堂

  • 飯田 渓太. 1細胞レベルの確率遺伝子発現モデリング、解析、パラメータ推定. 社会創造数学セミナーシリーズ(第100回HMMCセミナー), July 11, 2019, 北海道大学

  • 飯田 渓太. 一般化超幾何関数を用いた遺伝子発現モデルの解表示とその応用可能性について. 第64回京都大学応用数学セミナー, October 23, 2019, 京都大学

  • 金沢 朋美. Elucidating mechanisms of cell morphology regulation by Crk gene family. 第18回IPRリトリート, November 21-22, 2019, 大阪大学銀杏会館

  • Johannes Nicolaus Wibisana. Multi-dimensional analysis of NF-κB nuclear dynamics. 第18回IPRリトリート, November 21-22, 2019, 大阪大学銀杏会館

  • 飯田渓太. Probabilistic model of eukaryotic gene expressions. 2019年度応用数学合同研究集会, December 12-14, 2019, 龍谷大学瀬田キャンパス

  • Poster presentation
  • Minami Ando. Biological significance of the oscillatory dynamics of NF-kB for target gene expression. BDR Symposium 2019, March 25-27, 2019, Kobe (poster presentation)

  • Hiroaki Imoto. ErbBシグナル伝達経路と細胞周期の統合数理モデルを用いた細胞応答の予測, RIKEN Symposium “Behavior and Logic of Cellular Systems XI,” March 28-29, 2019, Saitama (poster presentation)

  • Hiroki Michida. NF-kB - p38 MAPK クロストークによる遺伝子発現動態制御の解明, RIKEN Symposium “Behavior and Logic of Cellular Systems XI,” March 28-29, 2019, Saitama (poster presentation)

  • Hiraoki Imoto, Kyouichi Ebata,Shigeyuki Magi, Suxiang Zhang, Mariko Okada. A comprehensive model of heterogeneous cell cycle responses , 第57回日本生物物理学会年会, September 24-26, 2019, 宮崎シーガイアコンベンションセンター

  • Kyoichi Ebata, Hiroaki Imoto, Sawa Yamashiro, Mariko Okada. Quantitative Analysis of Signal-dependent Cell Cycle Regulation, 第57回日本生物物理学会年会, September 24-26, 2019, 宮崎シーガイアコンベンションセンター

  • Suxiang Zhang, Shigeyuki Magi, Mariko Okada. Crosstalk between estrogen receptor and ErbB signaling pathways in breast cancer cells. the 78th Annual Meeting of the Japanese Cancer Association, September 26-28, 2019,京都国際会館

  • 張 素香. The novel roles of Crk gene family in mouse development. 第18回IPRリトリート, November 21-22, 2019, 大阪大学銀杏会館

  • Suxiang Zhang, Sewon Ki, Sayaka Inoue, Akira Imamoto, Mariko Okada. Investigation of the function of CRK gene family in TGF-β signaling response, 第42回日本分子生物学会大会, December 3-6, 2019, 福岡国際会議場

  • Sawa Yamashiro, Hiroaki Imoto, Kyoichi Ebata, Keita Iida, Mariko Okada. Reclassification of signal-dependent breast cancer subtypes. 第42回日本分子生物学会大会, December 3-6, 2019, 福岡国際会議場

2018


    International Conference Presentation


  • Signal-dependent transcriptional regulation for cell fate control, Mariko Okada-Hatakeyama, 3rd Symposium on Complex Biodynamics & Networks, Singapore, December 10-12, 2018. (invited talk)

  • Time-series analysis on the process of acquiring resistance for estrogen receptor antagonist in breast cancer cells, Shigeyuki Magi, Sewon Ki, Masao Ukai, Yutaka Suzuki, Mariko Okada, 3rd Symposium on Complex Biodynamics & Networks, Matrix Building, Biopolis, Singapore, December 10-12, 2018. (oral presentation)

  • Biological significance of the oscillatory dynamics of NF-kB for target gene expression, Minami Ando, 3rd Symposium on Complex Biodynamics & Networks, Matrix Building, Biopolis, Singapore, December 10-12, 2018. (poster presentation)

  • Quantitative Transcription Control Mediated by Signaling Network, Mariko Okada-Hatakeyama, The 19th International Conference on Systems Biology (ICSB 2018), Lyon, France, October 28-November 1, 2018. (invited talk)

  • Quantitative analysis of transcriptional regulation, Mariko Okada-Hatakeyama, Seminar at Chinese Academy of Sciences, Shanghai, Chinese Academy of Sciences, Shanghai, October 17-19, 2018. (invited talk)

  • Biological significance of the oscillatory dynamics of NF-kB for target gene expression, Minami Ando, Shigeyuki Magi, Kazunari Iwamoto, Mariko Okada, The 91st Annual Meeting of the Japanese Biochemical Society, Kyoto, September 24-26, 2018. (poster presentation)

  • Data-driven modelling of cellular network, Mariko Okada-Hatakeyama, The 2018 International Conference on Computational Systems B Biology (ISB 2018), Guiyang, China, August 18-21, 2018. (invited talk)

  • Quantitative transcriptional control of NF-kB, Mariko Okada-Hatakeyama, Seminar at UCLA Biology Institute, Los Angeles, USA, July 17, 2018. (oral presentation)

  • Quantitative transcriptional control of NF-kB, Mariko Okada-Hatakeyama, ISMB 2018, Chicago, Chicago, USA, July 6-10, 2018. (oral presentation)

  • Modeling of signal-transcriptional network, Mariko Okada-Hatakeyama, 18th World Congress of Basic and Clinical Pharmacology (WCP2018 Kyoto), Kyoto, July 1-6, 2018. (invited talk)

  • Pulmonary phagocyte-derived NPY controls the pathology of severe influenza virus infection, Yumiko Imai, the 18th World Congress of Basic and Clinical Pharmacology (WCP2018), Kyoto, July 1-6, 2018. (oral presentation)

  • Pulmonary phagocyte-derived NPY and Y1 receptor axis controls the pathology of severe influenza virus infection, Yumiko Imai, World Congress of Basic and Clinical Pharmacology, Kyoto, July 1-6, 2018. (oral presentation)

  • Dynamic changes in host nuclear system to influenza virus infection, Yumiko Imai, JMCB symposium, Shanghai, China, June 8-10, 2018. (oral presentation)

  • Integrative analysis to reveal transcriptional regulation of NF-kB, Mariko Okada-Hatakeyama, IMS-JSI International Symposium on Immunology 2018 "Checkpoint in medical science and its technology, Tokyo, June 7-8, 2018. (invited talk)

  • Host chromatin 4D response to influenza virus infection, Yumiko Imai, Chromatin OS International Meeting, Stockholm, Sweden, May 20, June 1, 2018. (oral presentation)

  • Understanding negative feedback mechanism of ErbB signaling using mathematical modeling of cell population dynamics, Shigeyuki Magi, International IPR Seminar on "Frontiers of Multiscale Structural Biology: Order-disorder transitions and dynamic membrane interactions", Osaka, May 9-10, 2018. (oral presentation)

  • Modeling and Omics analysis of NF-kB system, Mariko Okada-Hatakeyama, IPR Seminar "BioNetworks in Health and Diseases", Osaka, April 18-19, 2018. (oral presentation)


  • Domestic Conference Presentation


  • ErbBシグナル伝達経路と細胞周期の統合数理解析, Hiroaki Imoto, Kazunari Iwamoto, Mariko Okada, 理研シンポジウム「細胞システムの動態と論理X」, Saitama, April 12-14, 2018. (poster presentation)

  • 情報化学的アプローチによるNF-kBの転写発現制御機能の解明, Minami Ando, 理研シンポジウム「細胞システムの動態と論理X」, Saitama, April 12-13, 2018. (oral presentation)

  • 細胞接着を起点とした細胞代謝応答ネットワークの実験・情報学的解明, Mariko Okada-Hatakeyama, 長瀬科学技術振興財団平成29年度研究成果発表会, Osaka, April 26, 2018. (oral presentation)

  • 細胞ネットワークの数理モデリングと疾患研究への応用, Mariko Okada-Hatakeyama, 公開シンポジウム「医療情報分析の実際」, Osaka, May 28-June 1, 2018. (oral presentation)

  • 炎症疾患の代謝アダプテーション, Mariko Okada-Hatakeyama, 新学術研究「代謝オミクス」第2回 領域会議, Tokyo, June 11, 2018. (oral presentation)

  • 疾患システム科学の考え方とデータ解析への応用, Mariko Okada-Hataleyama, 第43回東北眼疾患病態研究会 , Tohoku University, Miyagi, July 23, 2018. (invited talk)

  • ウイルス感染に対する宿主エピゲノム応答, Yumio Imai, 未来医療教育研究機構セミナー, Chiba University, 医学部第2講義室, August 24, 2018. (invited talk)

  • がん細胞の遺伝子変異不均一性に関する数理モデル解析, Kazunari Iwamoto and Mariko Okada-Hatakeyama, 新学術領域研究「数理シグナル」第2回若手ワークショップ, Shiga, August 31-September 2, 2018. (oral presentation)

  • Biological significance of the oscillatory dynamics of NF-kB for target gene expression, Minami Ando, Shigeyuki Magi, Kazunari Iwamoto, Mariko Okada, The 56th Annual Meeting of the Biophysical Society of Japan, Okayama University, September 15-17, 2018. (oral presentation)

  • Model-based prediction of ErbB signaling activities on cell cycle entry, Hiroaki Imoto, Kazunari Iwamoto, Shigeyuki Magi, Suxiang Zhang, Mariko Okada-Hatakeyama, The 56th Annual Meeting of the Biophysical Society of Japan, Okayama University, September 15-17, 2018. (oral presentation)

  • Experimental Validation of a Mathematical Model of ErbB Receptor Signaling to Cell Cycle, Kyoichi Ebata, Hiroaki Imoto, Kazunari Iwamoto, Shigeyuki Magi, Suxiang Zhang, Mariko Okada-Hatakeyama, The 56th Annual Meeting of the Biophysical Society of Japan, Okayama University, September 15-17, 2018. (poster presentation)

  • Investigation of the crosstalk mechanism between two damped oscillators, NF-kB and p38 MAP kinase, Hiroki Michida, Minami Ando, Kazunari Iwamoto, Shigeyuki Magi, Mariko Okada-Hatakeyama, The 56th Annual Meeting of the Biophysical Society of Japan, Okayama University, September 15-17, 2018. (poster presentation)

  • Mechanisms of biphasic transcriptional responses in cell fate regulation, Mariko Okada-Hatakeyama, RIKEN Center for Sustainable Resource Science (CSRS) Seminar, Yokohama, September 21, 2018. (invited talk)

  • Understanding biological systems from multi-order kinetics, Mariko Okada-Hatakeyama, The 91st Annual Meeting of the Japanese Biochemical Society「多次元速度論からの生物の理解」, Kyoto, September 24-26, 2018. (oral presentation)

  • Biological significance of the oscillatory dynamics of NF-kB for target gene expression, Minami Ando, Shigeyuki Magi, Kazunari Iwamoto, Mariko Okada-Hatakeyama, The 91st Annual Meeting of the Japanese Biochemical Society, Kyoto, September 24-26, 2019. (oral presentation)

  • Predictions of cellular responses with a mathematical model integrating ErbB signaling and cell cycle, Hiroaki Imoto, Kazunari Iwamoto, Shigeyuki Magi, Suxiang Zhang, Mariko Okada-Hatakeyama, The 91st Annual Meeting of the Japanese Biochemical Society, Kyoto, September 24-26, 2019. (oral presentation)

  • Integrated analysis of Crk gene family controlling cell functions, Tomomi Kanazawa, Kazunari Iwamoto, Shigeyuki Magi, Suxiang Zhang, Akira Imamoto, Mariko Okada-Hatakeyama, The 91st Annual Meeting of the Japanese Biochemical Society, Kyoto, September 24-26, 2019. (poster presentation)

  • ウイルス感染に対する宿主核内システムの応答機構 , Yumiko Imai, 関西ライフサイエンス・リーディングサイエンティストセミナー, Grand Front Osaka, September 27, 2018. (oral presentation)

  • Time-series analysis on the process of acquiring tamoxifen resistance in breast cancer cells, Shigeyuki Magi, Yutaka Suzuki, Mariko Okada-Hatakeyama, The 77th Annual Meeting of the Japanese Cancer Association, Osaka, September 27-29, 2018. (oral presentation)

  • Heterogeneity of cellular responses in breast cancer cells, Zhang Suxiang, The 77th Annual Meeting of the Japanese Cancer Association, Osaka, September 27-29, 2018. (poster presentation)

  • 神経ペプチドによるインフルエンザ重症化の制御機構, Yumiko Imai, 心血管膜輸送研究会2018, Aichi, November 1-2, 2018. (oral presentation)

  • ウイルス感染に対する宿主核内システムの応答機構, Yumiko Imai, The 46th Annual Meeting of the Japanese Society of Clinical Immunology, Nagano, November 8-10, 2018. (oral presentation)

  • Dynamics and regulatory principles of biological networks, Mariko Okada-Hatakeyama, The 60th Anniversary of the Institute for Protein Research, Osaka, November 16, 2018. (oral presentation)

  • 細胞システム解析の考え方と基礎・応用, Mariko Okada-Hatakeyama, The 16th Symposium of Japan Consortium for Glycobiology and Glycotechnology, Tokyo, November 26-27, 2018. (invited talk)

  • 乳がんのタモキシフェン耐性獲得過程の時系列解析, Shigeyuki Magi, Sewon Ki, Masao Ukai, Yutaka Suzuki, Mariko Okada-Hatakeyama, The 41st Annual Meeting of the Molecular Biology Society of Japan, Yokohama, November 28-30, 2018. (poster presentation)

  • NF-kB - p38 MAPK crosstalk mechanism regulating gene expression dynamics, Hiroki Michida, Minami Ando, Shigeyuki Magi, Mariko Okada-Hatakeyama, The 41st Annual Meeting of the Molecular Biology Society of Japan, Yokohama, November 28-30, 2018. (poster presentation)

  • 貪食細胞由来の神経ペプチドによるインフルエンザ重症化機構, Yumiko Imai, The 28th Annual Meeting of Japanese Association of Cardiovascular Pharmacology, Tokyo, December 7, 2018. (oral presentation)

  • Biological significance of the oscillatory dynamics of NF-kB for target gene expression, Minami Ando, The 17th IPR Retreat, Osaka University, December 20-21, 2018. (poster presentation)

  • Model-based prediction of ErbB signaling activities on irreversible G1/S transition, Hiroaki Imoto, The 17th IPR Retreat, Osaka University, December 20-21, 2018. (oral presentation)

  • Quantitative Analysis of Signal-mediated Cell Cycle Regulation, Kyoichi Ebata, The 17th IPR Retreat, Osaka University, December 20-21, 2018. (poster presentation)

  • NF-kB - p38 MAPK crosstalk mechanism regulating gene expression dynamics, Hiroki Michida, Minami Ando, Shigeyuki Magi, Mariko Okada-Hatakeyama, The 17th IPR Retreat, Osaka University, December 20-21, 2018. (oral presentation)

2017


    International Conference Presentation


  • Systems biology of signaling network, Mariko Okada-Hatakeyama, Seminar at Centre for Molecular Medicine, JNU New Delhi, India (New Delhi), March 7, 2018. (oral presentation)

  • An input-output relationship of signaling-epigenetic regulation, Mariko Okada-Hatakeyama, Symposium on Chromosome Biology and Cell Signaling. Joint IPR Seminar by IISER TVM and Osaka Univ, India (Trivandrum), March 5, 2018. (oral presentation)

  • Formation of NF-kappa B super enhancer regulated by chromatin structural changes, Kazunari Iwamoto, Australian National University (ANU) & IPR 2nd Joint Symposium 2017 “PROTEIN STRUCTURE AND FUNCTION”, Osaka, December 3-5, 2017. (invited talk)

  • Trans-Omics analysis of NF-κB regulation, Mariko Okada-Hatakeyama, CREST & Scientific Research on Innovative Areas Symposium. “The 1st International Symposium for Trans-Omics”, Tokyo, December 21-22. (invited talk)

  • Mathematical modeling of cancer signaling network, Mariko Okada-Hatakeyama, The Third Trilateral Workshop for Frontier Protein Studies 2017, China (Shanghai), August 31-September 2, 2017. (invited talk)

  • Analysis of Omics data using kinetic model, Mariko Okada-Hatakeyama, Seminar at Dept. of Bioengineering, UK(London), May 18, 2017. (invited talk)


  • Domestic Conference Presentation


  • Classic yet unique dynamic properties of NF-κB gene regulation, Mariko Okada-Hatakeyama, OIST-JST Joint Seminar, Okinawa, November 28, 2017. (invited talk)

  • 細胞の形態と代謝ネットワーク, Mariko Okada-Hatakeyama, 11th Metabolome Symposium, Osaka, November 14, 2017. (invited talk)

  • システムバイオロジーとバイオデータベース, Mariko Okada-Hatakeyama, NBDC Workshop, Tokyo, November 13 ,2017. (invited talk)

  • 細胞形態と代謝を繋ぐシグナル軸の同定, Mariko Okada-Hatakeyama, Astellas Foundation for Research on Metabolic Disorders 平成29年度研究報告会, Tokyo, October 21, 2017. (invited talk)

  • NF-κB転写因子の動態と機能, Mariko Okada-Hatakeyama, Kyushu University MIB Seminar, Fukuoka, August 10, 2017. (invited talk)

  • シグナル伝達の数理モデル化と細胞変換, Mariko Okada-Hatakeyama, 新学術領域「数理シグナル」第1回若手ワークショップ, Shizuoka, August 7, 2017. (invited talk)

  • 「システムバイオロジーと創薬」, Mariko Okada-Hatakeyama, Biogrid Workshop2017, Osaka, May 27, 2017. (invited talk)

  • シグナル依存的なクロマチン構造変化によるスーパーエンハンサーの制御機構, Kazunari Iwamoto, 日本生物工学会バイオインフォマティクス相談部会 第一回講演会, Osaka, December 26, 2017. (oral presentation)

  • スーパーエンハンサーを介した転写因子NF-κBの遺伝子発現制御機構の解明, Kazunari Iwamoto, 第5回NGS現場の会, Miyagi, May 22-24, 2017. (oral presentation)

  • シグナルの定量解析と数理モデルによる分子制御機構の同定, Shigeyuki Magi, 第64回日本生化学会近畿支部例会, Osaka, May 27, 2017. (oral presentation)

  • 細胞モデリングとAI - オミクス研究から実用的システム生物学の構築へ, Mariko Okada-Hatakeyama, ConBio2017, Hyogo, December 7, 2017. (oral presentation)

  • A new integrated mathematical model of the ErbB signaling and transcriptional regulation reveals the key reactions to determine the ErbB responses, Hiroaki Imoto, The 55th Annual Meeting of the Biophysical Society of Japan, Kumamoto, September 19-21. (poster presentation)

  • A new integrated mathematical model of the ErbB signaling and transcriptional regulation reveals the key reactions to determine the ErbB responses, Hiroaki Imoto, IPR Retreat 2017, Osaka, December 12-13, 2017. (poster presentation)

  • 次世代シーケンシング法によるNF-kB標的遺伝子の転写制御機構の解明, Minami Ando, IPR Retreat 2017, Osaka, December 12-13, 2017. (oral presentation)

  • 乳がん細胞におけるタモキシフェン耐性獲得過程の時系列解析, Shigeyuki Magi, 第1回がんと代謝研究会・若手の会, Tokyo, January 16, 2018. (oral presentation)

  • 乳がんの内分泌療法抵抗性獲得過程の時系列解析, Shigeyuki Magi, The 90th Annual Meeting of the Japanese Biochemical Society, Kobe, December 6, 2017. (poster presentati on)