Kiwamu Arakane, Hiroaki Imoto, Fabian Ormersbach, Mariko Okada.
Extending BioMASS to construct mathematical models from external knowledge.
Bioinformatics Advances, 2024.
DOI: 10.1093/bioadv/vbae042.
Link
2023
Johannes Nicolaus Wibisana, Takehiko Inaba, Yasushi Sako, Mariko Okada.
Quantitative Imaging Analysis of NF-κB for Mathematical Modeling Applications.
Computational Modeling of Signaling Networks (Springer US), 2023.
DOI: 10.1007/978-1-0716-3008-2_11.
Link
Kenzui Taniue, Takeaki Oda, Tomoatsu Hayashi, Yuki Kamoshida, Yasuko Takeda, Anzu Sugawara, Yuki Shimoura, Lumi Negishi, Takeshi Nagashima, Mariko Okada-Hatakeyama, Yoshifumi Kawamura, Naoki Goshima, Nobuyoshi Akimitsu, Tetsu Akiyama.
LncRNA ZNNT1 induces p53 degradation by interfering with the interaction between p53 and the SART3-USP15 complex.
PNAS Nexus, 2023.
DOI: 10.1093/pnasnexus/pgad220.
Link
Chiharu Fujihara, Ken Murakami, Shigeyuki Magi, Daisuke Motooka, Teerachate Nantakeeratipat, Andres Canela, Reiko J Tanaka, Mariko Okada.
Omics-Based Mathematical Modeling Unveils Pathogenesis of Periodontitis in an Experimental Murine Model.
Journal of Dental Research, 2023.
DOI: 10.1177/002203452311965.
Link
Hiroaki Imoto, Nora Rauch, Ashish J. Neve,Fahimeh Khorsand, Martina Kreileder, Leonidas G. Alexopoulos, Jens Rauch, Mariko Okada, Boris N. Kholodenko, Oleksii S. Rukhlenko.
A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression.
Biomolecules, 2023.
DOI: 10.3390/biom13081212.
Link
Masatoshi Haga, Keita Iida, Mariko Okada.
Positive and negative feedback regulation of the TGF-β1-SMAD4 axis explains two equilibrium states in human skin aging.
bioRxiv, 2023.
DOI: 10.1101/2023.07.18.546970.
Link
Kenzui Taniue, Takeaki Oda, Tomoatsu Hayashi, Yuki Kamoshida, Yasuko Takeda, Anzu Sugawara, Yuki Shimoura, Lumi Negishi, Takeshi Nagashima, Mariko Okada-Hatakeyama, Yoshifumi Kawamura, Naoki Goshima, Nobuyoshi Akimitsu, Tetsu Akiyama.
LncRNA ZNNT1 induces p53 degradation by interfering with the interaction between p53 and the SART3-USP15 complex.
PNAS Nexus, 2023.
DOI: https://doi.org/10.1093/pnasnexus/pgad220.
Link
Roberto Coppo, Jumpei Kondo, Keita Iida, Mariko Okada, Kunishige Onuma, Yoshihisa Tanaka, Mayumi Kamada, Masayuki Ohue, Kenji Kawada, Kazutaka Obama, Masahiro Inoue.
Distinct but interchangeable subpopulations of colorectal cancer cells with different growth fates and drug sensitivity.
iScience, 2023.
DOI: https://doi.org/10.1016/j.isci.2023.105962.
Link
Reviews
井元 宏明, 岡田 眞里子.
生化学反応過程を記述した文章による実行可能な数理モデルの生成と患者固有モデリングへの応用.
生物物理, 日本生物物理学会, pp. 320-324, 2023年8月22日.
Link
飯田 渓太, 粕川 雄也.
リファレンスゲノムにマッピングする方法① 〜HISAT2 + StringTie.
実験医学別冊: 改訂版RNA-Seqデータ解析 WETラボのための超鉄板レシピ（坊農 秀雅／編）, 羊土社, pp. 53-65, 2023年9月28日.
Link
2022
Shuhei Kimura, Yahiro Takeda, Masato Tokuhisa, Mariko Okada.
Inference of genetic networks using random forests: Performance improvement using a new variable importance measure.
Chem-Bio Informatics Journal, 2022.
DOI: https://doi.org/10.1273/cbij.22.88.
Link
Kazuki Takahashi, Katarzyna A. Podyma-Inoue, Maki Saito, Shintaro Sakakitani, Akinari Sugauchi, Keita Iida, Sadahiro Iwabuchi, Daizo Koinuma, Kyoko Kurioka, Toru Konishi, Susumu Tanaka, Atsushi Kaida, Masahiko Miura, Shinichi Hashimoto, Mariko Okada, Toshihiro Uchihashi, Kohei Miyazono, Tetsuro Watabe.
TGF-β generates a population of cancer cells residing in G1 phase with high motility and metastatic potential via KRTAP2-3.
Cell Reports, 2022.
DOI: https://doi.org/10.1016/j.celrep.2022.111411.
Link
Hiroaki Imoto, Sawa Yamashiro, Ken Murakami, Mariko Okada.
Protocol for stratification of triple-negative breast cancer patients using in silico signaling dynamics.
STAR Protocols, 2022.
DOI: 10.1016/j.xpro.2022.101619.
Link
Keita Iida, Jumpei Kondo, Johannes N. Wibisana, Masahiro Inoue, Mariko Okada.
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes.
Bioinformatics, 2022.
DOI: 10.1093/bioinformatics/btac541.
Link
Keita.
ASURAT: Functional annotation-driven unsupervised clustering for single-cell data.
Bioconductor, 2022.
DOI: https://doi.org/10.18129/B9.bioc.ASURAT.
Link
Johannes N. Wibisana, Takehiko Inaba, Hisaaki Shinohara, Noriko Yumoto, Tetsutaro Hayashi, Mana Umeda, Masashi Ebisawa, Itoshi Nikaido, Yasushi Sako, Mariko Okada.
Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers.
PLOS Genetics, 2022.
DOI: https://doi.org/10.1371/journal.pgen.1010235.
Link
Hiroaki Imoto, Sawa Yamashiro, Mariko Okada.
A text-based computational framework for patient-specific modeling for classification of cancers.
iScience, 2022.
DOI: https://doi.org/10.1016/j.isci.2022.103944.
Link
Reviews
Mariko Okada.
Systems biology of protein network.
Biophysical Reviews, 2022.
DOI: https://doi.org/10.1007/s12551-022-01023-8.
Link
飯田 渓太, 岡田 眞里子.
空間トランスクリプトームと1細胞トランスクリプトームの統合解析.
実験医学別冊: 空間オミクス解析スタートアップ実践ガイド（鈴木 穣／編）, 羊土社, pp. 175-182, 2022年12月5日.
Link
Johannes Nicolaus Wibisana, Mariko Okada.
Encoding and decoding NF-κB nuclear dynamics.
Current Opinion in Cell Biology, 2022.
DOI: https://doi.org/10.1016/j.ceb.2022.102103.
Link
Masatoshi Haga, Mariko Okada.
Systems approaches to investigate the role of NF-κB signaling in aging.
Biochemical Journal, 2022.
DOI: https://doi.org/10.1042/BCJ20210547.
Link
2021
Minami Ando, Shigeyuki Magi, Masahide Seki, Yutaka Suzuki, Takeya Kasukawa, Diane Lefaudeux, Alexander Hoffmann, Mariko Okada.
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.
npj systems biology and applications, 2021.
DOI: https://doi.org/10.1038/s41540-021-00204-7.
Link
Kosuke Miyauchi, Sewon Ki, Masao Ukai, Yoshie Suzuki, Kentaro Inoue, Wataru Suda, Takeshi Matsui, Yoshihiro Ito, Kenya Honda, Haruhiko Koseki, Osamu Ohara, Reiko J. Tanaka, Mariko Okada-Hatakeyama, Masato Kubo. Essential Role of STAT3 Signaling in Hair Follicle Homeostasis. Frontiers in immunology, 2021. Link
Ryo Yoshizawa, Nobuhisa Umeki, Akihiro Yamamoto, Mariko Okada, Masayuki Murata, Yasushi Sako. p52Shc regulates the sustainability of ERK activation in a RAF-independent manner. Mol Biol Cell, 2021. Link
Boris N. Kholodenko, Mariko Okada. Reengineering protein-phosphorylation switches. Science, 2021. Link
Tomomi Kanazawa, Hiroki Michida, Yuki Uchino, Akari Ishihara, Suxiang Zhang, Sho Tabata, Yutaka Suzuki, Akira Imamoto, Mariko Okada. Cell Shape‐Based Chemical Screening Reveals an Epigenetic Network Mediated by Focal Adhesions. FEBS Journal, 2021. Link
Shigeyuki Magi, Sewon Ki, Masao Ukai, Atsuhiko Naito, Yutaka Suzuki, Mariko Okada. Mathematical Modeling and Transcriptome Profiling of Breast Cancer Cells During Tamoxifen Treatment Reveal Multiple Trajectories for Resistant Subtypes. Scientific Reports, 2021. Link
Reviews
Kyoichi Ebata, Sawa Yamashiro, Keita Iida, Mariko Okada. Building patient-specific models for receptor tyrosine kinase signaling networks. FEBS Journal, 2021. Link
Johannes Nicolaus Wibisana, 飯田 渓太, 岡田 眞里子.
免疫系の１細胞解析による転写制御機構の予測.
医学のあゆみ 1細胞解析・技術と応用（企画 菅野 純夫）Vol. 276, No. 10, pp. 983-988, March 6, 2021.
Link
2020
Hiroaki Imoto, Suxiang Zhang, Mariko Okada. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers. 12(10), 2878, 2020. Link
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 Rep. 31, 9, 107724, 2020. Link
Sufeng Chiang, Jia-Hsin Huang, Huai-Kuang Tsai and Mariko Okada. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. 594(10): 1477-1496. doi: 10.1002/1873-3468.13757, 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]
Shuhei Kimura, Ryo Fukutomi, Masato Tokuhisa, Mariko Okada. Inference of genetic networks from time-series and static gene expression data: combining a random-forest-based inference method with feature selection methods. Frontiers in Genetics. doi: 10.3389/fgene.2020.595912, 11: 595912, 2020. Link
Hideki Tokunaga, Keita Iida, Atsushi Hozawa, Soichi Ogishima, Yoh Watanabe, Shogo Shigeta, Muneaki Shimada, Yumi Yamaguchi-Kabata, Shu Tadaka, Fumiki Katsuoka, Shin Ito, Kazuki Kumada, Yohei Hamanaka, Nobuo Fuse, Kengo Kinoshita, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda. Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2). PLoS One. doi: 10.1371/journal.pone.0236907, January, 2021. Link
Article
岡田眞里子. キャリアデザイン談話室（1）キャリアの決め時と決め方. 生物物理. 60(5), 303-304. 2020. Link
Review
岡田眞里子、井元宏明. 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. 京都大学数理解析研究所 講究録「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-」. No.2166, 7-11, 2020 Link
Book Chapter
Johannes Nicolaus Wibisana, Takehiko Inaba, Yasushi Sako, Mariko Okada. Quantitative imaging analysis of NF-κB for mathematical modelling applications. Computational Modeling of Signaling Networks (Edited by Lan Nguyen). Methods in Molecular Biology, Springer Nature. 2020, in press.
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. Proc. Natl. Acad. Sci. USA. 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 Intl. Conf. on Technologies and Applications of Artificial Intelligence (TAAI 2019). doi: 10.1109/TAAI48200.2019.8959859, January, 2020. Link
Up to 2018
Rui Liu, Jinzeng Wang, Masao Ukai, Ki Sewon, Pei Chen, Yutaka Suzuki, Haiyun Wang, Kazuyuki Aihara, Mariko Okada-Hatakeyama*, Luonan Chen* *co-corresponding authors. Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. J. Mol. Cell. Biol. 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 Intl. Conf. on Bioinformatics and Bioengineering (BIBE). 98-103. doi: 10.1109/BIBE.2018.00026, December, 2018. link[PubMed]
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 J. 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 Conf. 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
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]
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 Rep. 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. Proc. Natl. Acad. Sci. USA. 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 physiol. 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. Proc. Natl. Acad. Sci. USA. 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 Rep. 6: 34349. doi: 10.1038/srep34349, PMID: 27686861, September, 2016. Link[PubMed]
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 Comp. Biol. 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. Proc. of the 2015 Intl. Joint Conf. 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 Rep. 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. Intl. 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. J. 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. Proc. Natl. Acad. Sci. USA. 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 Rep. 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. Proc. of 2014 Intl. Conf. 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 J. 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 Rep. 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 in Physiol. 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. Proc: 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. Proc. of the 2013 Intl. Joint Conf. on Neural Networks. 2676-2681, August, 2013.
Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda, and Jun Sese. Statistical significance of combinatorial regulations. Proc. Natl. Acad. Sci. USA. 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. Intl. 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 Biol. 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. J. Exp. Med. 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 Intl. Joint Conf. 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. Proc. Natl. Acad. Sci. USA. 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. EMBO J. 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]
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. J. Biol. Chem. 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. Proc. 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. Intl. Conf. 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. Proc. of the IJCNN (the Intl. Joint Conf. 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. Proc. of the IJCNN (the Intl. Joint Conf. 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. J. Bioinformatics and Computational Biology. 8(4), 661-677. doi: 10.1142/S0219720010004859, 2010. Link
Takashi Nakakuki, Marc R Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A Ogunnaike, Mariko Okada-Hatakeyama*, Boris N Kholodenko* *co-corresponding authors. 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 J. 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 J. 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]
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 #co-first authors. 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. Proc. of the 2006 Intl. Joint Conf. 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. J. Biol. Chem. 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. J. Biol. Chem. 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. The 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. Proc. of the Intl. 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
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. J. Biol. Chem. 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. Proc. of 15th IASTED Intl. Conf. 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. Proc. of 2003 Congress on Evolutionary Computation. 631-638. 2003. Link
Atsushi Suenaga, Mio Ichikawa, Mariko Hatakeyama, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi, Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu, Shigeyuki 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 J. 373(Pt2), 451-463, doi:10.1042/BJ20021824, 2003. Link[PubMed]
Mariko Okada.
Modelling Cell Signaling using LLM and AI.
The 6th ExCELLS Symposium.
January 22, 2024, National Institutes of Natural Science, Okazaki Conference Center, Aichi. Invited Talk.
2023
International Conference Presentation
Oral presentation
Masatoshi Haga, Mariko Okada.
Data-driven mathematical modeling of human skin aging.
NET SKIN MODELS, European Network for Skin Engineering and Modeling.
September 14, 2023, Online. Invited talk.
Mariko Okada.
A Computational Platform for Patient-specific Modeling.
OKO International Symposium 2023, Mathematical Biology from genes to cells to humans.
August 28, 2023, Shiran Kaikan, Kyoto. Invited talk.
Mariko Okada.
Encoding and decoding of NF-kB nuclear dynamics and cell fate regulation.
Uehara International Symposium 2023 Big Data-Driven Approaches with AI in Life.
June 5, 2023, Tokyo International Forum, Tokyo. Invited talk.
Mariko Okada.
Encoding and decoding of NFBk transcriptional regulation.
CSTI 2023 Cell Signalling and its Therapeutic Implications Cape Shanck.
May 17, 2023, Victoria, Australia. Invited talk. Link
Ayaka Ichikawa.
Regulatory mechanism of G1/S cell cycle transition via ErbB signaling network.
Japan-Korea Bilateral Symposium between IPR and SNU on Structure and Folding of Disease Related Proteins.
January 13, 2023, Seoul National University, Korea.
Poster presentation
Ken Murakami, Mariko Okada.
Detection of enhancer activity at the single-cell level by deep learning method.
14th International Workshop on Advanced Genomics.
October 4-6, 2023, Hitotsubashi Koudou, Tokyo.
Keita Matsuda, Sho Tabata, Mariko Okada.
Data-driven functional analysis of NFκB-dependent gene regulation in inflammatory aging.
OKO International Symposium 2023, Mathematical Biology from genes to cells to humans.
August 28, 2023, Shiran Kaikan, Kyoto.
Keita Matsuda, Sho Tabata, Mariko Okada.
Data-driven functional analysis of NFκB-dependent gene regulation in inflammatory aging.
OKO International Symposium 2023, Mathematical Biology from genes to cells to humans.
August 28, 2023, Shiran Kaikan, Kyoto.
Kiwamu Arakane, Hiroaki Imoto, Mariko Okada.
Applying Text-Mined Knowledge from PubMed and PubMed Central to Signaling Pathways.
27th Annual International Conference on Research in Computational Molecular Biology.
April 18, 2023, Istanburl Mariott Sisli, Turkey.
Ken Murakami, Mariko Okada.
Detection of enhancer activity at the single-cell level by deep learning.
Keystone Symposia/Scientific Conference on Biomedical and Life Science Topics/Chromatin Architecture in Development and Human Health.
March 14, 2023, Fairmont Empress Victoria Conference Center, Canada.
Domestic Conference Presentation
Oral presentation
Mariko Okada.
数式フリーの数理モデリングによる細胞制御の解明 分子ネットワークの設計による生命現象の再構築と操作.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Kiwamu Arakane, Mariko Okada.
Extracting Intracellular Networks and Constructing Mathematical Models with Natural Language Processing.
The 61st Annual Meeting of the Biophysical Society of Japan.
November 16, 2023, Nagoya Congress Center, Aichi.
Keita Matsuda, Sho Tabata, Kazuyo Moro, Mariko Okada.
NFκB dynamics and gene regulation in inflammatory aging.
The 61st Annual Meeting of the Biophysical Society of Japan.
November 16, 2023, SNagoya Congress Center, Aichi.
Poster presentation
Shou Soeda, Keita Matsuda, Yoko Takada, Jun Adachi, Mariko Okada.
Mechanism of cell fate decision for inflammatory senescence induced by sustained activation of NF-κB.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Katsunari Saito, Ken Murakami, Kaho Itoh, Yutaka Suzuki, Yukiko Goda, Mariko Okada.
Multi-omics analysis of stimulus-response heterogeneity in hippocampal neural cells.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Kiwamu Arakane, Hiroaki Imoto, Mariko Okada.
自然言語処理による知識抽出とシグナル伝達系の数理モデルのデータ駆動的な構築.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Ken Murakami, Mariko Okada.
ディープラーニング手法を用いた一細胞レベルエンハンサー検出法の開発.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Ririn Rahmala Febri, Ayaka Ichikawa, Mariko Okada.
Understanding the ligand-specific of the HER2 signaling network in cell cycle G1/S transition.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Keita Matsuda, Sho Tabata, Kazuyo Moro, Mariko Okada.
NFκB dynamics and gene regulation in inflammatory aging.
The 46th Annual Meeting of the Molecular Biology Society of Japan.
December 6, 2023, Kobe Convention Center, Hyogo.
Katsunari Saito, Ken Murakami, Kaho Itoh, Yutaka Suzuki, Yukiko Goda, Mariko Okada.
Multi-omics analysis of stimulus-response heterogeneity in hippocampal neural cells.
The 61st Annual Meeting of the Biophysical Society of Japan.
November 16, 2023, Nagoya Congress Center, Aichi.
Keita Matsuda, Sho Tabata, Kazuyo Moro, Mariko Okada.
NFκB dynamics and gene regulation in inflammatory aging.
The 96th Annual Meeting of the Japanese Biochemical Society.
October 31-November 2, 2023, Fukuoka Convention Center, Fukuoka.
Ayaka Ichikawa, Ken Murakami, Kazuhiro Aoki, Mariko Okada.
Role of ErbB2 receptor expression on cell cycle progression and quiescence via Cyclin D1 and c-Myc.
The 96th Annual Meeting of the Japanese Biochemical Society.
October 31-November 2, 2023, Fukuoka Convention Center, Fukuoka.
Shou Soeda, Keita Matsuda, Yoko Takada, Jun Adachi, Mariko Okada.
Mechanism of cell fate decision for inflammatory senescence induced by sustained activation of NF-κB.
The 96th Annual Meeting of the Japanese Biochemical Society.
October 31-November 2, 2023, Fukuoka Convention Center, Fukuoka.
Ken Murakami, Mariko Okada.
ディープラーニング手法を用いた一細胞レベルエンハンサー検出法の開発.
The 82nd Annual Meeting of the Japanese Cancer Association.
September 22, 2023, Pacifico Yokohama, Kanagawa.
Katsunari Saitoh, Ken Murakami, Kaho Itoh, Yutaka Suzuki, Yukiko Goda, Mariko Okada.
Multi-omics analysis of stimulus-response heterogeneity in hippocampal neural cells.
Informatics in Biology, Medicine and Pharmacology 2023.
September 7, 2023, Kashiwanoha conference center, Chiba.
Keita Matsuda, Sho Tabata, Kazuyo Moro, Mariko Okada.
NFκB dynamics and gene regulation in inflammatory aging.
Informatics in Biology, Medicine and Pharmacology 2023.
September 7, 2023, Kashiwanoha conference center, Chiba.
Kiwamu Arakane, Hiroaki Imoto, Mariko Okada.
Applying natural language processing to extract intracellular networks for mathematical modeling.
OKO International Symposium 2023, Mathematical Biology from genes to cells to humans.
August 28, 2023, Shiran Kaikan, Kyoto.
荒金 究, 井元 宏明, 岡田 眞里子
テキストマイニングによる PubMed・PubMed Central からの遺伝子ネットワークの抽出.
AIロボット駆動科学シンポジウム2023.
July 6, 2023, 東京、国際フォーラム.
荒金 究, 井元 宏明, 岡田 眞里子
テキストマイニングによる PubMed・PubMed Central からの遺伝子ネットワークの抽出.
CREST「バイオDX」領域 第2回領域会議.
May 11, 2023, 理化学研究所 神戸キャンパス 融合連携イノベーション推進棟.
荒金 究, 井元 宏明, 岡田 眞里子
テキストマイニングによる PubMed・PubMed Central からの遺伝子ネットワークの抽出.
言語処理学会第29回年次大会(NLP2023).
March 15, 2023, 沖縄コンベンションセンター.
2022
International Conference Presentation
Oral presentation
Mariko Okada.
Gene expression heterogeneity arises from signaling networks.
The 21st International Conference On Systems Biology (ICSB 2022).
October 8, 2022, Berlin, Germany. Invited talk. Link
Masatoshi Haga, Tsuyoshi Ishii, Mariko Okada.
Data-driven mathematical modeling of human skin aging and its application for natural compound screening.
The 21st International Conference On Systems Biology (ICSB 2022).
October 8, 2022, Berlin, Germany. Link
Keita Iida.
Clustering single-cell and spatial transcriptomes through multifaceted biological aspects.
1st International Symposium on Aihara Moonshot Project.
June 8, 2022, Online.
Mariko Okada.
Non-genetic heterogeneity arising from biological networks.
1st International Symposium on Aihara Moonshot Project.
June 8, 2022, Online. Invited talk.
Mariko Okada.
Pasmopy - Patient-Specific Modeling in Python for Classification of Cancers.
8th Conference on Systems Biology of Mammalian Cells.
May 16, 2022, Heidelberg, Germany. Invited talk.
Mariko Okada. A computational platform for mathematical modeling of cancer networks. The international Chemical Congress of Pacific Basin Societies 2021, December 21, 2021, Online conference
Poster presentation
Kaho Itoh, Hiroki Michida, Mariko Okada. Multi-omics analysis of immediate early genes regulation in neuron. The 44th Annual Meeting of the Japan Neuroscience Society, The 1st CJK International Meeting, September 28-31, 2021, Kobe Convention Center, Hyogo
永井 賢史郎, 井元 宏明, Ulrike Muenzner, Johannes Nicolaus Wibisana, 岡田 眞里子. Elucidation of the mechanism of COVID-19 severity with mathematical modeling. The 44th Annual Meeting of the Molecular Biology Society of Japan, December 1-3, 2021, PACIFICO Yokohama, Kanagawa
王 梓, 岡田 眞里子. A Dynamic Molecular Regulatory Network to Determine Hippocampal Cell Fate during Embrogenesis. The 44th Annual Meeting of the Molecular Biology Society of Japan, December 1-3, 2021, PACIFICO Yokohama, Kanagawa
伊藤 夏穂, 岡田 眞里子. Multi-omics analysis of immediate early genes regulation in neuron. 44th Annual Meeting of the Molecular Biology Society of Japan, December 1-3, 2021, PACIFICO Yokohama, Kanagawa
伊藤 夏穂, 岡田 眞里子. Quantitative analysis of immediate early genes regulation in neuron. The 59th Annual Meeting of the BSJ, November 25-27, 2021, Online conference
王 梓, 岡田 眞里子. A Dynamic Molecular Regulatory Network to Determine Hippocampal Cell Fate during Embrogenesis. The 59th Annual Meeting of the BSJ, November 25-27, 2021, Online conference
王 梓, 岡田 眞里子. A Dynamic Molecular Regulatory Network to Determine Hippocampal Cell Fate during Embrogenesis. IIBMP2021「2021年日本バイオインフォマティクス学会年会 ・第10回生命医薬情報学連合大会」, September 27-29, 2021, Online conference
山城 紗和, 井元 宏明, 岡田 眞里子. Classification of TNBC using a patient-specific ErbB network model. The 80th Annual Meeting of Japanese Cancer Association, September 30-October 2, 2021, PACIFICO Yokohama, Kanagawa
2020
International Conference Presentation
Oral presentation
Mariko Okada, Prediction and validation of NF-kB mediated gene expression mechanisms in B cells using bulk and single cell sequencing data. 8th Annual Meeting of the International Cytokine & Interferon Society, November 1-4, 2020. Invited talk
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
Ulrike Muenzner. Identifying Long Attractors in Boolean Networks Using A Priori Information. EURAXESS Japan meeting - "Publish and Prosper": European Research "Day & Night", January 7-9, 2020, Online conference
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
Hiroaki Imoto. Model-based prediction of ErbB signaling dynamics solely from the information about gene expression levels, The 58th Annual Meeting of the Biophysical Society of Japan, September 16-18, 2020, Online conference
Johannes Nicolaus Wibisana. NF-κB mediated transcriptional regulation in B cell, The 58th Annual Meeting of the Biophysical Society of Japan, September 16-18, 2020, Online conference
Masahiro Inoue, Mariko Okada-Hatakeyama, Shinichi Hashimoto, Tadashi Kimura, Jumpei Kondo. Lineage plasticity in a mixed tumor of neuroendocrine carcinoma/adenocarcinoma of the uterine cervix, The 79th Annual Meeting of the Japanese Cancer Assciation, October 1-3, 2020
Yu Chen, Sadahiro Iwabuchi, Tohru Kiyono, Shigeyuki Magi, Yasuhito Arai, Akihiko Yokoyama, Mariko Okada, Shinichi Hashimoto, Kentaro Semba, Rieko Ohki. Akt dysregulation by loss of PHLDA3 is an important
determinant of pancreatic neuroendocrine tumor progression, The 79th Annual Meeting of the Japanese Cancer Assciation, October 1-3, 2020
Hiroki Michida, Hiroaki Imoto, Takeya Kasukawa, Mariko Okada. Quantitative analysis of epigenetic regulation by NF-κB transcription factor, The 43rd Annual Meeting of the Molecular Biology Society of Japan, December 2-4, 2020
Teerachate Nantakeeratipat, Chiharu Fujihara, Johannes Nicolous Wibisana, Hiroaki Imoto, Keita Iida, Mariko Okada, Shinya Murakami. Building a mathematical model of periodontal disease, The 43rd Annual Meeting of the Molecular Biology Society of Japan, December 2-4, 2020
Masatoshi Haga, Tsuyoshi Ishii, Mariko Okada. Mathematical modeling of human skin aging based on time-course omics data, The 43rd Annual Meeting of the Molecular Biology Society of Japan, December 2-4, 2020
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
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
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)
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)
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)
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)
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)
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)
Copyright 2020 Laboratory for Cell Systems, Institute for Protein Research, Osaka University
All rights reserved. No reproduction or republication without written permission.