Identifying Key Regulatory Genes in Drug Resistance Acquisition: Modeling Pseudotime Trajectories of Breast Cancer Single-Cell Transcriptome

Keita Iida, Mariko Okada

Cancers　Vol. 16　No. 10　p. 1884-1884　2024/05/15　Research paper (scientific journal)

ErbB2/HER2 governs CDK4 inhibitor sensitivity and timing and irreversibility of G1/S transition by altering c-Myc and cyclin D function

Ayaka Nagasato Ichikawa, Ken Murakami, Kazuhiro Aoki, Mariko Okada

bioRxiv　2024/05/14　Research paper (scientific journal)

Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging

Masatoshi Haga, Keita Iida, Mariko Okada

iScience　Vol. 27　No. 5　p. 109708-109708　2024/05　Research paper (scientific journal)

Extending BioMASS to construct mathematical models from external knowledge

Kiwamu Arakane, Hiroaki Imoto, Fabian Ormersbach, Mariko Okada

Bioinformatics Advances　Vol. 4　2024/04/04　Research paper (scientific journal)

Clonal Origin and Lineage Ambiguity in Mixed Neuroendocrine Carcinoma of the Uterine Cervix.

Masamune Masuda, Keita Iida, Sadahiro Iwabuchi, Mie Tanaka, Satoshi Kubota, Hiroyuki Uematsu, Kunishige Onuma, Yoji Kukita, Kikuya Kato, Shoji Kamiura, Aya Nakajima, Roberto Coppo, Mizuki Kanda, Kiyoshi Yoshino, Yutaka Ueda, Eiichi Morii, Tadashi Kimura, Jumpei Kondo, Mariko Okada-Hatakeyama, Shinichi Hashimoto, Masahiro Inoue

The American journal of pathology　2023/12/14　Research paper (scientific journal)

Inference of Genetic Networks from Steady-State and Pseudo Time-Series of Single-Cell Gene Expression Data using Modified Random Forests

Shuhei Kimura, Hirotaka Kitajima, Masato Tokuhisa, Mariko Okada

2023 IEEE Symposium Series on Computational Intelligence (SSCI)　Vol. 45　p. 1579-1586　2023/12/05　Research paper (international conference proceedings)

Omics-Based Mathematical Modeling Unveils Pathogenesis of Periodontitis in an Experimental Murine Model

C. Fujihara, K. Murakami, Shigeyuki Magi, D. Motooka, T. Nantakeeratipat, A. Canela, Reiko Tanaka, M. Okada, S. Murakami

Journal of Dental Research　2023/12　Research paper (scientific journal)

A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression

Hiroaki Imoto, Nora Rauch, Ashish J. Neve, Fahimeh Khorsand, Martina Kreileder, Leonidas G. Alexopoulos, Jens Rauch, Mariko Okada, Boris N. Kholodenko, Oleksii S. Rukhlenko

Biomolecules　Vol. 13　No. 8　p. 1212-1212　2023/08/02　Research paper (scientific journal)

LncRNA ZNNT1 induces p53 degradation by interfering with the interaction between p53 and the SART3-USP15 complex

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

PNAS Nexus　2023/07/04　Research paper (scientific journal)

Quantitative Imaging Analysis of NF-κB for Mathematical Modeling Applications

Wibisana, Johannes Nicolaus, Inaba, Takehiko, Sako, Yasushi, Okada, Mariko

Methods in molecular biology (Clifton, N.J.)　p. 253-266　2023/04/20　Research paper (scientific journal)

NFκB nuclear dynamics orchestrate inflammatory aging

Sho Tabata, Keita Matsuda, Kenshiro Nagai, Yoshihiro Izumi, Masatomo Takahashi, Yasutaka Motomura, Ayaka Ichikawa Nagasato, Shuichi Shimma, Kazuyo Moro, Takeshi Bamba, Mariko Okada

bioRxiv　2023/04/18

Type 2 helper T cells convert into Interleukin-13-expressing follicular helper T cells after antigen repriming

Yasuyo HARADA, Takanori SASAKI, Johannes Nicolaus WIBISANA, Mariko OKADA-HATAKEYAMA, Chaohong LIU, Hideki UENO, Peter D. BURROWS, Masato KUBO

Translational and Regulatory Sciences　Vol. 早期公開中　2023/02　Research paper (scientific journal)

Distinct but interchangeable subpopulations of colorectal cancer cells with different growth fates and drug sensitivity

Roberto Coppo, Jumpei Kondo, Keita Iida, Mariko Okada, Kunishige Onuma, Yoshihisa Tanaka, Mayumi Kamada, Masayuki Ohue, Kenji Kawada, Kazutaka Obama, Masahiro Inoue

iScience　Vol. 26　No. 2　p. 105962-105962　2023/02　Research paper (scientific journal)

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

Hiroaki IMOTO, Mariko OKADA

Seibutsu Butsuri　Vol. 63　No. 6　p. 320-324　2023/01　Research paper (scientific journal)

Inference of Genetic Networks using Random Forests: Performance Improvement using a New Variable Importance Measure

S.Kimura, Y.Takeda, M.Tokuhisa, M.Okada

Chem-Bio Informatics Journal, Vol.22　Vol. 88　No. 109　2022/12/29　Research paper (scientific journal)

Systems biology of protein network

Mariko Okada

Biophysical Reviews　Vol. 14　No. 6　p. 1231-1232　2022/12/13　Research paper (scientific journal)

TGF-β generates a population of cancer cells residing in G1 phase with high motility and metastatic potential via KRTAP2-3

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

Cell Reports　Vol. 40　No. 13　2022/09/27　Research paper (scientific journal)

Protocol for stratification of triple-negative breast cancer patients using in silico signaling dynamics

Hiroaki Imoto, Sawa Yamashiro, Ken Murakami, Mariko Okada

STAR Protocols　Vol. 3　No. 3　p. 101619-101619　2022/09/16　Research paper (scientific journal)

ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes

Keita Iida, Jumpei Kondo, Johannes Nicolaus Wibisana, Masahiro Inoue, Mariko Okada

Bioinformatics　Vol. 38　No. 18　p. 4330-4336　2022/09/15　Research paper (scientific journal)

Encoding and decoding NF-κB nuclear dynamics

Wibisana, Johannes Nicolaus, Okada, Mariko

Current opinion in cell biology　Vol. 77　p. 102103-102103　2022/08/01　Research paper (scientific journal)

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

Johannes N. Wibisana, Takehiko Inaba, Hisaaki Shinohara, Noriko Yumoto, Tetsutaro Hayashi, Mana Umeda, Masashi Ebisawa, Itoshi Nikaido, Yasushi Sako, Mariko Okada

PLoS Genetics　Vol. 18　No. 6　p. e1010235-e1010235　2022/06/01　Research paper (scientific journal)

A text-based computational framework for patient -specific modeling for classification of cancers

Imoto, Hiroaki, Yamashiro, Sawa, Okada, Mariko

iScience　p. 103944-103944　2022/03/10　Research paper (scientific journal)

Systems approaches to investigate the role of NF-κB signaling in aging

Haga, Masatoshi, Okada, Mariko

The Biochemical journal　Vol. 479　No. 2　p. 161-183　2022/01/28　Research paper (scientific journal)

IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells

Minami Ando, Shigeyuki Magi, Masahide Seki, Yutaka Suzuki, Takeya Kasukawa, Diane Lefaudeux, Alexander Hoffmann, Mariko Okada

npj Syst Biol Appl　Vol. 7　No. 42　p. 1-15　2021/12/01　Research paper (scientific journal)

Distinct and interchangeable growing patterns in colorectal cancer stem-like cells are regulated by Musashi-1

Roberto Coppo, Jumpei Kondo, Keita Iida, Mariko Okada, Kunishige Onuma, Yoshihisa Tanaka, Mayumi Kamada, Masayuki Ohue, Kenji Kawada, Kazutaka Obama, Masahiro Inoue

bioRxiv　2021/11/26

Essential Role of STAT3 Signaling in Hair Follicle Homeostasis

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

Frontiers in Immunology　Vol. 12　p. 663177-663177　2021/11/11　Research paper (scientific journal)

A combination approach of pseudotime analysis and mathematical modeling for understanding drug-resistant mechanisms

Shigeyuki Magi, Sewon Ki, Masao Ukai, Elisa Domínguez-Hüttinger, Atsuhiko T Naito, Yutaka Suzuki, Mariko Okada

Scientific Reports　Vol. 11　No. 1　p. 18511-18511　2021/09/16　Research paper (scientific journal)

p52Shc regulates the sustainability of ERK activation in a RAF-independent manner

Ryo Yoshizawa, Nobuhisa Umeki, Akihiro Yamamoto, Mariko Okada, Masayuki Murata, Yasushi Sako

Molecular Biology of the Cell　p. mbc.E21-01　2021/07/14　Research paper (scientific journal)

Reengineering protein-phosphorylation switches

Kholodenko, Boris N, Okada, Mariko

Science (New York, N.Y.)　Vol. 373　No. 6550　p. 25-26　2021/07/02　Research paper (scientific journal)

Building patient‐specific models for receptor tyrosine kinase signaling networks

Kyoichi Ebata, Sawa Yamashiro, Keita Iida, Mariko Okada

The FEBS Journal　2021/05/14　Research paper (scientific journal)

Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions

Tomomi Kanazawa, Hiroki Michida, Yuki Uchino, Akari Ishihara, Suxiang Zhang, Sho Tabata, Yutaka Suzuki, Akira Imamoto, Mariko Okada

The FEBS Journal　2021/04/22　Research paper (scientific journal)

Mathematical Modeling and Transcriptome Profiling of Breast Cancer Cells During Tamoxifen Treatment Reveal Multiple Trajectories for Resistant Subtypes

Shigeyuki Magi, Sewon Ki, Masao Ukai, Atsuhiko Naito, Yutaka Suzuki, Mariko Okada

2021/01/13

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A, Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C, FANTOM consortium, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel J L, Wasserman, Wyeth W, Bréhélin, Laurent, Lecellier, Charles-Henri

Nature communications　2021　Research paper (scientific journal)

Inference of Genetic Networks From Time-Series and Static Gene Expression Data: Combining a Random-Forest-Based Inference Method With Feature Selection Methods

Shuhei Kimura, Ryo Fukutomi, Masato Tokuhisa, Mariko Okada

Frontiers in Genetics　Vol. 11　No. 595912　2020/12　Research paper (scientific journal)

A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway

Hiroaki Imoto, Suxiang Zhang, Mariko Okada

Cancers　Vol. 12　No. 10　p. 2878-2878　2020/10/07　Research paper (scientific journal)

The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression.

Hiroki Michida, Hiroaki Imoto, Hisaaki Shinohara, Noriko Yumoto, Masahide Seki, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Takeya Kasukawa, Yutaka Suzuki, Mariko Okada-Hatakeyama

Cell Reports　Vol. 31　No. 9　2020/06/02　Research paper (scientific journal)

Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach

Chiang, Sufeng, Shinohara, Hisaaki, Huang, Jia-Hsin, Tsai, Huai-Kuang, Okada, Mariko

FEBS letters　Vol. 594　No. 10　p. 1477-1496　2020/05　Research paper (scientific journal)

2SBP: overview of the trans-omics session-measure × analyze metabolic adaptation of biological systems-at the 2019 BSJ Meeting in Miyazaki

Okada, Mariko, Bamba, Takeshi

Biophysical reviews　2020/03　Research paper (scientific journal)

ATF7-Dependent Epigenetic Changes Are Required for the Intergenerational Effect of a Paternal Low-Protein Diet

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, Shunsuke Ishii

Molecular Cell　2020/03　Research paper (scientific journal)

Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis.

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, Mariko Okada

Life Science Alliance　Vol. 3　No. 2　2020/02　Research paper (scientific journal)

Feature Selection based on Random Forests and its Application to a Modeling of Sewage Treatment Plant

Shuhei Kimura, Masato Tokuhisa, Akiyuki Uemura, Mariko Okada

2019 International Conference on Technologies and Applications of Artificial Intelligence (TAAI)　2019/11　Research paper (international conference proceedings)

Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs

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

Nucleic acids research　Vol. 47　No. 16　p. 8838-8859　2019/09/19　Research paper (scientific journal)

Inference of genetic networks using random forests: Assigning different weights for gene expression data

Shuhei Kimura, Masato Tokuhisa, Mariko Okada

Journal of Bioinformatics and Computational Biology　Vol. 17　No. 04　p. 1950015-1950015　2019/08　Research paper (scientific journal)

Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers

Liu, Rui, Wang, Jinzeng, Ukai, Masao, Sewon, Ki, Chen, Pei, Suzuki, Yutaka, Wang, Haiyun, Aihara, Kazuyuki, Okada-Hatakeyama, Mariko, Chen, Luonan

Journal of molecular cell biology　2019/08　Research paper (scientific journal)

Signal-dependent regulation of early-response genes and cell cycle: a quantitative view

Hiroaki Imoto, Mariko Okada

Current Opinion in Systems Biology　Vol. 15　p. 100-108　2019/06　Research paper (scientific journal)

A hepatic post-transcriptional network comprised of CCR4-NOT deadenylase and FGF21 maintains systemic metabolic homeostasis

Masahiro Morita, Nadeem Siddiqui, Sakie Katsumura, Christopher Rouya, Ola Larsson, Takeshi Nagashima, Bahareh Hekmatnejad, Akinori Takahashi, Hiroshi Kiyonari, Mengwei, Zang, Ren_ St-Arnaud, Vincent Gigu_re, Ivan Topisirovic, Mariko Okada-Hatakeyama, Tadashi Yamamoto, Nahum Sonenberg

PNAS　Vol. 116 (16)　No. 16　p. 7973-7981　2019/03　Research paper (scientific journal)

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes

Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada, Tadashi Yamamoto

Development　Vol. 146: dev168146　No. 4　2019/02　Research paper (scientific journal)

Pulmonary phagocyte-derived NPY controls the pathology of severe influenza virus infection

Seiki Fujiwara, Midori Hoshizaki, Yu Ichida, Dennis Lex, Etsushi Kuroda, Ken Ishii, Shigeyuki Magi, Mariko Okada, Hiroyuki Takao, Masahiro Gandou, Hirotaka Imai, Ryujiro Hara, Herbert Herzog, Akihiko Yoshimura, Hitoshi Okamura, Josef Penninger, Arthur Slutsky, Stefan Uhlig, Keiji Kuba, Yumiko Imai

Nature Microbiology　Vol. 4　No. 2　p. 258-268　2019/02　Research paper (scientific journal)

Tamoxifen mechanically reprograms the tumor microenvironment via HIF-1A and reduces cancer cell survival

Cortes, Ernesto, Lachowski, Dariusz, Robinson, Benjamin, Sarper, Muge, Teppo, Jaakko S, Thorpe, Stephen D, Lieberthal, Tyler J, Iwamoto, Kazunari, Lee, David A, Okada-Hatakeyama, Mariko, Varjosalo, Markku T, Del Río Hernández, Armando E

EMBO reports　Vol. 20　No. 1　2019/01　Research paper (scientific journal)

Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-series and Static Gene Expression Data

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama

Proc. of the 18th IEEE International Conference on Bioinformatics and Bioengineering　p. 98-103　2018　Research paper (international conference proceedings)

High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA.

Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei

Methods in Molecular Biology　Vol. 1823　p. 167-183　2018　Research paper (scientific journal)

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.

Soh Ishiguro, Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei

RNA biology　Vol. 15　No. 7　p. 976-989　2018　Research paper (scientific journal)

Transcriptionally inducible pleckstrin homology-like domain, family a, member 1, attenuates ERBB receptor activity by inhibiting receptor oligomerization

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, Mariko Okada-Hatakeyama

Journal of Biological Chemistry　Vol. 293　No. 6　p. 2206-2218　2018　Research paper (scientific journal)

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment

Trisevgeni Rapakoulia, Xin Gao, Yi Huang, Michiel de Hoon, Mariko Okada-Hatakeyama, Harukazu Suzuki, Erik Arner

Bioinformatics　Vol. 33　No. 23　p. 3696-3700　2017/12　Research paper (scientific journal)

Inference of genetic networks from time-series of gene expression levels using random forests

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama

2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2017　2017/10/04　Research paper (international conference proceedings)

An integrated expression atlas of miRNAs and their promoters in human and mouse

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, Pal Saetrom, 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, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Michiel J. L. de Hoon

Nature Biotechnology　Vol. 35　No. 9　p. 872-+　2017/09　Research paper (scientific journal)

FANTOM5 CAGE profiles of human and mouse samples.

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, Yoshihide Hayashizaki

Scientific data　Vol. 4　p. 170112-170112　2017/08/29　Research paper (scientific journal)

Mathematical modeling of atopic dermatitis reveals "double-switch" mechanisms underlying 4 common disease phenotypes

Elisa Dominguez-Huttinger, Panayiotis Christodoulides, Kosuke Miyauchi, Alan D. Irvine, Mariko Okada-Hatakeyama, Masato Kubo, Reiko J. Tanaka

Journal of Allergy and Clinical Immunology　Vol. 139　No. 6　p. 1861-1872. e7　2017/06　Research paper (scientific journal)

Robustness analysis of the detailed kinetic model of an ErbB signaling network by using dynamic sensitivity

Hiroyuki Masunaga, Yurie Sugimoto, Shigeyuki Magi, Ryunosuke Itasaki, Mariko Okada-Hatakeyama, Hiroyuki Kurata

PLoS One　Vol. 12　No. 5　2017/05　Research paper (scientific journal)

Current status of mathematical modeling of cancer - from the viewpoint of cancer hallmarks

Shigeyuki Magi, Kazunari Iwamoto, Mariko Okada-Hatakeyama

Current Opinion in Systems Biology　Vol. 2　p. 39-48　2017/04/01

Positive Quadratic System Modeling Based on Singular Perturbation

OKAMOTO Yuji, IMURA Jun-ichi, OKADA-HATAKEYAMA Mariko

Transactions of the Society of Instrument and Control Engineers　Vol. 53　No. 3　p. 251-259　2017

Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge

Shuhei Kimura, Koji Kitazawa, Masato Tokuhisa, Mariko Okada-Hatakeyama

Chem-Bio Informatics Journal　Vol. 17　p. 53-71　2017　Research paper (scientific journal)

Protective neutralizing influenza antibody response in the absence of T follicular helper cells

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, Masato Kubo

Nature Immunology　Vol. 17　No. 12　p. 1447-1458　2016/12　Research paper (scientific journal)

ASBEL-TCF3 complex is required for the tumorigenicity of colorectal cancer cells

Kenzui Taniue, Akiko Kurimoto, Yasuko Takeda, Takeshi Nagashima, Mariko Okada-Hatakeyama, Yuki Katou, Katsuhiko Shirahige, Tetsu Akiyama

PNAS　Vol. 113　No. 45　p. 12739-12744　2016/11　Research paper (scientific journal)

Oscillation dynamics underlie functional switching of NF-κB for B-cell activation

Kentaro Inoue, Hisaaki Shinohara, Marcelo Behar, Noriko Yumoto, Gouhei Tanaka, Alexander Hoffmann, Kazuyuki Aihara, Mariko Okada-Hatakeyama

npj Systems Biology and Applications　Vol. 2　No. 16024　2016/10　Research paper (scientific journal)

MYU, a Target lncRNA for Wnt/c-Myc Signaling, Mediates Induction of CDK6 to Promote Cell Cycle Progression

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, Tetsu Akiyama

Cell Reports　Vol. 16　No. 10　p. 2554-2564　2016/09　Research paper (scientific journal)

A pre-metazoan origin of the CRK gene family and co-opted signaling network

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, Akira Imamoto

Scientific Reports　Vol. 6　No. 34349　2016/09　Research paper (scientific journal)

CD4 memory T cells develop and acquire functional competence by sequential cognate interactions and stepwise gene regulation

Tomohiro Kaji, Atsushi Hijikata, Akiko Ishige, Toshimori Kitami, Takashi Watanabe, Osamu Ohara, Noriyuki Yanaka, Mariko Okada, Michiko Shimoda, Masaru Taniguchi, Toshitada Takemori

International Immunology　Vol. 28　No. 6　p. 267-282　2016/06　Research paper (scientific journal)

Stimulus-Dependent Inhibitor of Apoptosis Protein Expression Prolongs the Duration of B Cell Signalling

Hisaaki Shinohara, Kentaro Inoue, Noriko Yumoto, Takeshi Nagashima, Mariko Okada-Hatakeyama

Scientific Reports　Vol. 6　No. 27706　2016/06　Research paper (scientific journal)

Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages

Keisuke Yoshida, Claire Renard-Guillet, Kentaro Inoue, Katsuhiko Shirahige, Mariko Okada-Hatakeyama, Shunsuke Ishii

Genomics Data　Vol. 7　p. 90-91　2016/03/01　Research paper (scientific journal)

Genetic network inference using hierarchical structure

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama

Frontiers in Physiology　Vol. 7　No. 57　2016/02/23　Research paper (scientific journal)

Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1

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, Tetsu Akiyama

PNAS　Vol. 113　No. 5　p. 1273-1278　2016/02　Research paper (scientific journal)

Observer Design of Positive Quadratic Systems

Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama

Proceedings of the 2016 European Control Conference (ECC’16)　p. 843-848　2016　Research paper (international conference proceedings)

Simultaneous Execution Method of Gene Clustering and Network Inference

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama

2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)　p. 1-7　2016　Research paper (international conference proceedings)

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R. R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, Mariko Okada-Hatakeyama, Jessica C. Mar

PLOS One　Vol. 10　No. 12　2015/12　Research paper (scientific journal)

Positive quadratic system approximate representation of nonlinear systems

Yuji Okamoto, Jun-Ichi Imura, Mariko Okada-Hatakeyama

IFAC-PapersOnLine　Vol. 28　No. 18　p. 65-70　2015/11/01　Research paper (international conference proceedings)

The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory

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, Shunsuke Ishii

Nature Immunology　Vol. 16　No. 10　p. 1034-+　2015/10　Research paper (scientific journal)

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

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, Mariko Okada-Hatakeyama, Cesare Furlanello

Scientific Reports　Vol. 5　No. 11999　2015/07　Research paper (scientific journal)

Signalling mechanisms regulating phenotypic changes in breast cancer cells

Natalia Volinsky, Cormac J. McCarthy, Alex von Kriegsheim, Nina Saban, Mariko Okada-Hatakeyama, Walter Kolch, Boris N. Kholodenko

Bioscience Report　Vol. 35　No. e0017　2015/04　Research paper (scientific journal)

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

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, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple

PLOS Computational Biology　Vol. 11　No. 4　2015/04　Research paper (scientific journal)

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Erik Arner, Carsten O. Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drablos, Andreas Lennartsson, Michelle Roennerblad, 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, David A. Hume, Alistair R. R. Forrest, Albin Sandelin, Piero Carninci, Yoshihide Hayashizaki

Science　Vol. 347　No. 6225　p. 1010-1014　2015/02　Research paper (scientific journal)

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity

Takeshi Nagashima, Norihiko Inoue, Noriko Yumoto, Yuko Saeki, Shigeyuki Magi, Natalia Volinsky, Alexander Sorkin, Boris N. Kholodenko, Mariko Okada-Hatakeyama

FEBS JOURNAL　Vol. 282　No. 4　p. 613-629　2015/02

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, Cong, FANTOM Consortium, Forrest, Alistair R R, Wagner, Günter P

Nature communications　2015　Research paper (scientific journal)

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Hurst, Laurence D, Ghanbarian, Avazeh T, Forrest, Alistair R R, FANTOM consortium, Huminiecki, Lukasz

PLoS biology　2015　Research paper (scientific journal)

Positive Quadratic System Representation of Molecular Interaction in a Cell

Yuji Okamoto, Jun-ichi Imura, Mariko Okada-Hatakeyama

2015 EUROPEAN CONTROL CONFERENCE (ECC)　p. 1554-1559　2015　Research paper (international conference proceedings)

Improvement of Reliabilities of Regulations using a Hierarchical Structure in a Genetic Network

Shuhei Kimura, Mariko Okada-Hatakeyama

2015 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)　p. pp. 485-491　2015　Research paper (international conference proceedings)

Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus

Naoki Iwanaga, Kaori Ide, Takeshi Nagashima, Takeo Tomita, Yoshihiro Agari, Akeo Shinkai, Seiki Kuramitsu, Mariko Okada-Hatakeyama, Tomohisa Kuzuyama, Makoto Nishiyama

Extremophiles　Vol. 18　No. 6　p. 995-1008　2014/11　Research paper (scientific journal)

A Fast Parameter Estimation Method for Inferring Reduced S-system Models of Genetic Networks

Shuhei Kimura, Munehiro Furuta, Masanao Sato, Mariko Okada-Hatakeyama

Proceedings of 2014 International Conference on Information Systems and Computing Technology　p. 45-50　2014/10

Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-kappa B activation

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

Science　Vol. 344　No. 6185　p. 760-764　2014/05　Research paper (scientific journal)

Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells

Hiroko Yukinaga, Clara Shionyu, Eishu Hirata, Kumiko Ui-Tei, Takeshi Nagashima, Shinji Kondo, Mariko Okada-Hatakeyama, Honda Naoki, Michiyuki Matsuda

Journal of Cell Science　Vol. 127　No. 8　p. 1805-1815　2014/04　Research paper (scientific journal)

A promoter-level mammalian expression atlas.

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 Furino, 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, Furni 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, Shohei Noma, Tadasuke Noazaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohimiya, 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, 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, Takaai 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 Toyodo, Tetsuro Toyoda, Elvind Valen, Marc van de Wetering, Linda M van den Berg, Roberto Verado, 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, Yoshihide Hayashizaki

Nature　Vol. 507　No. 7493　p. 462-470　2014/03/27　Research paper (scientific journal)

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Morikawa, Hiromasa, Ohkura, Naganari, Vandenbon, Alexis, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R R, Standley, Daron M, Date, Hiroshi, Sakaguchi, Shimon, FANTOM Consortium

Proceedings of the National Academy of Sciences of the United States of America　2014　Research paper (scientific journal)

An effective method for the inference of reduced S-system models of Genetic Networks

Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

IPSJ Transactions on Bioinformatics　Vol. 7　p. 30-38　2014　Research paper (scientific journal)

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

Tomohiro Kaji, Koji Furukawa, Akiko Ishige, Itsumi Toyokura, Masaki Nomura, Mariko Okada, Yoshimasa Takahashi, Michiko Shimoda, Toshitada Takemori

International Immunology　Vol. 25　No. 12　p. 683-695　2013/12　Research paper (scientific journal)

Inference of Vohradsky's Models of Genetic Networks by Solving Two-Dimensional Function Optimization Problems

Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

PLOS One　Vol. 8　No. 12　2013/12　Research paper (scientific journal)

Capturing drug responses by quantitative promoter activity profiling

Kazuhiro Kajiyama, Mariko Okada-Hatakeyama, Yoshihide Hayashizaki, Hideya Kawaji, Hirokazu Suzuki

CPT: Pharmacometrics & Systems Pharmacology　Vol. 2(9)　No. e77　2013/09　Research paper (scientific journal)

Statistical significance of combinatorial regulations

Aika Terada, Mariko Okada-Hatakeyama, Koji Tsuda, Jun Sese

PNAS　Vol. 110　No. 32　p. 12996-13001　2013/08　Research paper (scientific journal)

Functional analysis of a novel long ncRNA involved in the tumorigenicity of colorectal cancer

Taniue Kenzui, Akiko Kurimoto, Hironobu Sugimasa, Emiko Nasu, Takeshi Nagashima, Mariko Okada-Hatakeyama, Tetsu Akiyama

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC　Vol. Article_in_Cancer Research Vol. 73 (8 Supplement)　p. 1831-1831　2013/04

Individual hematopoietic stem cells in human bone marrow of patients with aplastic anemia or myelodysplastic syndrome stably give rise to limited cell lineages

Takamasa Katagiri, Hiroshi Kawamoto, Takashi Nakakuki, Ken Ishiyama, Mariko Okada-Hatakeyama, Shigeki Ohtake, Yu Seiki, Kohei Hosokawa, Shinji Nakao

Stem Cells　Vol. 31　No. 3　p. 536-546　2013/03　Research paper (scientific journal)

3P179 Dynamic Signal Response of Rigorous PI3K Heterodimer in Living Cells(12. Cell biology,Poster)

Pack Chan-Gi, Saeki Yuko, Okada Mariko, Sako Yasushi

Seibutsu Butsuri　Vol. 53　No. 1　2013

Methods for the Analysis of Intracellular Signal Transduction Systems

Takashi Nakakuki, Mariko Okada-Hatakeyama

Technological Advancements in Biomedicine for Healthcare Applications　Vol. 34　p. 347-353　2013

Computational design of small peptide inhibitors of Protein-Protein interactions in CRK-SH2 mediated intracellular signaling

Junya Yamagishi, Noriaki Okimoto, Takuma Kasai, Atsushi Suenaga, Mariko Okada, Akira Imamoto, Makoto Taiji

Models in Bioscience and Materials Research　p. 155-166　2013/01

Development of an efficient parameter estimation method for the inference of Vohradský's neural network models of genetic networks

Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

Proceedings of the International Joint Conference on Neural Networks　p. 2676-2681　2013　Research paper (international conference proceedings)

Phase responses of oscillating components in a signaling pathway

Masaki Nomura, Mariko Okada-Hatakeyama

Frontiers in Physiology　Vol. 4　No. 68　2013　Research paper (scientific journal)

Distinct cellular pathways select germline-encoded and somatically mutated antibodies into immunological memory

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

The Journal of Experimental Medicine　Vol. 209　No. 11　p. 2079-2097　2012/10　Research paper (scientific journal)

Dynamically varying interactions between heregulin and ErbB proteins detected by single-molecule analysis in living cells

Michio Hiroshima, Yuko Saeki, Mariko Okada-Hatakeyama, Yasushi Sako

PNAS　Vol. 109　No. 35　p. 13984-13989　2012/08

Catching transcriptional regulation by thermostatistical modeling

Till D. Frank, Alex Cheong, Mariko Okada-Hatakeyama, Boris N. Kholodenko

Physical Biology　Vol. 9　No. 4　p. 1-11　2012/08　Research paper (scientific journal)

An ErbB receptor-mediated AP-1 regulatory network is modulated by STAT3 and c-MYC during calcium-dependent keratinocyte differentiation

Yuko Saeki, Takeshi Nagashima, Shuhei Kimura, Mariko Okada-Hatakeyama

Experimental Dermatology　Vol. 21　No. 4　p. 293-298　2012/04　Research paper (scientific journal)

Inference of S-system models of genetic networks by solving one-dimensional function optimization problems

Shuhei Kimura, D. Araki, Koki Matsumura, Mariko Okada-Hatakeyama

Mathematical Biosciences　Vol. 235　No. 2　p. 161-170　2012/02　Research paper (scientific journal)

Inference of S-system Models of Genetic Networks by Solving Linear Programming Problems and Sets of Linear Algebraic Equations

Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama

2012 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)　p. 1-8　2012　Research paper (international conference proceedings)

Obesity resistance and increased hepatic expression of catabolism-related mRNAs in Cnot3(-/+) mice

Masahiro Morita, Yuichi Oike, Takeshi Nagashima, Tsuyoshi Kadomatsu, Mitsuhisa Tabata, Toru Suzuki, Takahisa Nakamura, Nobuaki Yoshida, Mariko Okada, Tadashi Yamamoto

The EMBO Journal　Vol. 30　No. 22　p. 4678-4691　2011/11　Research paper (scientific journal)

A rank-based statistical test for measuring synergistic effects between two gene sets

Yuichi Shiraishi, Mariko Okada-Hatakeyama, Satoru Miyano

Bioinformatics　Vol. 27　No. 17　p. 2399-2405　2011/09　Research paper (scientific journal)

Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity

Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai, Mariko Okada-Hatakeyama

BMC Systems Biology　Vol. 5　No. 29　p. 1-14　2011/02　Research paper (scientific journal)

3L1534 ErbB signaling-Quantification of protein diffusion and interaction networks in MCF7 cells using FCS and FCCS(Cell biology 5,The 49th Annual Meeting of the Biophysical Society of Japan)

Pack Chan-Gi, Saeki Yuko, Hiroshima Michio, Okada Mariko, Sako Yasushi

Seibutsu Butsuri　Vol. 51　2011

AGLSDC: a Genetic Local Search Suitable for Parallel Computation

S.Kimura, T.Nakakuki, S.Kirita, M.Okada

SICE Journal of Control, Measurement, and System Integration　Vol. 4　No. 2　p. 105-113　2011　Research paper (scientific journal)

Efficient parameter estimation for the inference of s-system models of genetic networks: Proposition of further problem decomposition and alternate function optimization

Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama

Chem-Bio Informatics Journal　Vol. 11　No. 1　p. 24-40　2011　Research paper (scientific journal)

Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway

Saswati Dana, Takashi Nakakuki, Mariko Hatakeyama, Shuhei Kimura, Soumyendu Raha

Computer Methods and Programs in Biomedicine　Vol. 101　No. 1　p. 1-22　2011/01　Research paper (scientific journal)

Integrated Quantitative Analysis of the Phosphoproteome and Transcriptome in Tamoxifen-resistant Breast Cancer

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

The Journal of Biological Chemistry　Vol. 286　No. 1　p. 818-829　2011/01　Research paper (scientific journal)

Particle simulation of epidermal growth factor receptor in prostate cancer cells

Ryusuke Kenmochi, Tatsunori Hanai, Takashi Nakakuki, Mariko Okada, Chiharu Ishii

IFAC Proceedings Volumes (IFAC-PapersOnline)　Vol. 18　No. 1　p. 9633-9637　2011　Research paper (international conference proceedings)

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics

Takashi Nakakuki, Marc R. Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A. Ogunnaike, Mariko Okada-Hatakeyama, Boris N. Kholodenko

Cell　Vol. 141　No. 5　p. 884-896　2010/05　Research paper (scientific journal)

Inferring cluster-based networks from differently stimulated multiple time-course gene expression data

Yuichi Shiraishi, Shuhei Kimura, Mariko Okada

Bioinformatics　Vol. 26　No. 8　p. 1073-1081　2010/04　Research paper (scientific journal)

Bootstrap Analysis of Genetic Networks inferred by the Method Using LPMs

Shuhei Kimura, Koki Matsumura, Mariko Okada-Hatakeyama

Proceedings of the 2010 International Conference on Computational Science and its Applications　p. 296-299　2010/03

Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations.

Shuhei Kimura, Yuichi Shiraishi, Mariko Okada

J. Bioinform. Comput. Biol.　Vol. 8　No. 4　p. 661-677　2010　Research paper (scientific journal)

Effective Parameter Estimation for S-system Models using LPMs and Evolutionary Algorithms

Shuhei Kimura, Yusuke Amano, Koki Matsumura, Mariko Okada-Hatakeyama

2010 IEEE Congress on Evolutionary Computation (CEC)　p. 2034-2041　2010　Research paper (international conference proceedings)

Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells

Yuko Saeki, Takaho Endo, Kaori Ide, Takeshi Nagashima, Noriko Yumoto, Tetsuro Toyoda, Harukazu Suzuki, Yoshihide Hayashizaki, Yoshiyuki Sakaki, Mariko Okada-Hatakeyama

BMC Genomics　Vol. 10　2009/11　Research paper (scientific journal)

Mutation of epidermal growth factor receptor is associated with MIG6 expression

Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Atsushi Suenaga, Kaori Ide, Noriko Yumoto, Yoshimi Naruo, Kaoru Takahashi, Yuko Saeki, Makoto Taiji, Hiroshi Tanaka, Shih-Feng Tsai, Mariko Hatakeyama

FEBS Journal　Vol. 276　No. 18　p. 5239-5251　2009/09　Research paper (scientific journal)

Structural and Functional Basis of a Role for CRKL in a Fibroblast Growth Factor 8-Induced Feed-Forward Loop

Ji-Heui Seo, Atsushi Suenaga, Mariko Hatakeyama, Makoto Taiji, Akira Imamoto

Molecular and Cellular Biology　Vol. 29　No. 11　p. 3076-3087　2009/06　Research paper (scientific journal)

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

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, 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

Nature Genetics　Vol. 41　No. 5　p. 553-62　2009/05　Research paper (scientific journal)

Genetic network inference as a series of discrimination tasks

Shuhei Kimura, Satoshi Nakayama, Mariko Hatakeyama

Bioinformatics　Vol. 25　No. 7　p. 918-925　2009/04　Research paper (scientific journal)

Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor

Atsushi Suenaga, Mariko Hatakeyama, Anatoly B. Kiyatkin, Ravi Radhakrishnan, Makoto Taiji, Boris N. Kholodenko

Biophysical Journal　Vol. 96　No. 6　p. 2278-2288　2009/03　Research paper (scientific journal)

Inference of Genetic Networks using Linear Programming Machines: Application of A Priori Knowledge

S. Kimura, Y. Shiraishi, M. Hatakeyama

IJCNN: 2009 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS, VOLS 1- 6　p. 694-+　2009　Research paper (international conference proceedings)

Topological Analysis of MAPK Cascade for Kinetic ErbB Signaling

Takashi Nakakuki, Noriko Yumoto, Takashi Naka, Mikako Shirouzu, Shigeyuki Yokoyama, Mariko Hatakeyama

PLOS One　Vol. 3　No. 3　2008/03　Research paper (scientific journal)

Integrative Genome-Wide Expression Analysis Bears Evidence of Estrogen Receptor-Independent Transcription in Heregulin-Stimulated MCF-7 Cells

Takeshi Nagashima, Takahiro Suzuki, Shinji Kondo, Yoko Kuroki, Kaoru Takahashi, Kaori Ide, Noriko Yumoto, Aki Hasegawa, Tetsuro Toyoda, Toshio Kojima, Akihiko Konagaya, Harukazu Suzuki, Yoshihide Hayashizaki, Yoshiyuki Sakaki, Mariko Hatakeyama

PLOS One　Vol. 3　No. 3　2008/03　Research paper (scientific journal)

1S2-3 Pursuit of Quantitative to Qualitative Changes in Cellular Reaction Network by Experimental and Mathematical Approaches(1S2 New perspectives in Biophysics from Computational and Experimental Methods,The 46th Annual Meeting of the Biophysical Society of Japan)

Hatakeyama Mariko

Seibutsu Butsuri　Vol. 48　2008

Function approximation approach to the inference of reduced NGnet models of genetic networks

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama

BMC Bioinformatics　Vol. 9　No. 23　2008/01　Research paper (scientific journal)

Phosphoproteome and transcriptome analyses of ErbB ligand-stimulated MCF-7 cells

Takeshi Nagashima, Masaaki Oyama, Hiroko Kozuka-Hata, Noriko Yumoto, Yoshiyuki Sakaki, Mariko Hatakeyama

Cancer Genomics and Proteomics　Vol. 5　No. 3-4　p. 161-168　2008　Research paper (scientific journal)

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses

Marc R. Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A. Ogunnaike, Jan B. Hoek, Boris N. Kholodenko

Molecular Systems Biology　Vol. 3　No. 144　2007/11　Research paper (scientific journal)

Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation

Takeshi Nagashima, Hidetoshi Shimodaira, Kaori Ide, Takashi Nakakuki, Yukitaka Tani, Kaoru Takahashi, Noriko Yumoto, Mariko Hatakeyama

Journal of Biological Chemistry　Vol. 282　No. 6　p. 4045-4056　2007/02　Research paper (scientific journal)

System properties of ErbB receptor signaling for the understanding of cancer progression

Mariko Hatakeyama

Molecular Biosystems　Vol. 3　No. 2　p. 111-116　2007/02　Research paper (scientific journal)

In silico simulation of epidermal growth factor signaling in prostate cancer cells

Takashi Nakakuki, Kaori Ide, Noriko Yumoto, Takeshi Nagashima, Mariko Hatakeyama

GENSIPS'07 - 5th IEEE International Workshop on Genomic Signal Processing and Statistics　2007　Research paper (international conference proceedings)

Function Approximation Approach to the Inference of Neural Network Models of Genetic Networks

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama

IPSJ Transactions on Bioinformatics　Vol. 48　p. 9-19　2007

Inference of genetic networks using a reduced NGnet model

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Kotaro Yoshida, Koki Matsumura, Mariko Hatakeyama

2007 IEEE INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS, VOLS 1-6　p. 932-+　2007　Research paper (international conference proceedings)

Expression of the ErbB4 receptor causes reversal regulation of PP2A in the Shc signal transduction pathway in human cancer cells

Noriko Yumoto, Xiaomei Yu, Mariko Hatakeyama

Molecular and Cellular Biochemistry　Vol. 285　No. 1-2　p. 165-171　2006/04　Research paper (scientific journal)

Compensation effect of the MAPK cascade on formation of phospho-protein gradients

Takashi Naka, Mariko Hatakeyama, Naoto Sakamoto, Akihiko Konagaya

Biosystems　Vol. 83　No. 2-3　p. 167-177　2006/02　Research paper (scientific journal)

Modeling the ErbB signaling network in MCF-7 breast cancer cells and analysis of ligand-dependent responses

Marc R. Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Jan B. Hoek, Boris N. Kholodenko, Babatunde A. Ogunnaike

AIChE Annual Meeting, Conference Proceedings　2006　Research paper (international conference proceedings)

Function approximation approach to the inference of normalized Gaussian network models of genetic networks

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama

IEEE International Conference on Neural Networks - Conference Proceedings　p. 2218-2225　2006　Research paper (international conference proceedings)

Function approximation approach Gaussian network models to the inference of normalized of genetic networks

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama

2006 IEEE INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORK PROCEEDINGS, VOLS 1-10　p. 2218-+　2006　Research paper (international conference proceedings)

The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks

Sakaki, Yoshiyuki, Kholodenko, Boris N, Hatakeyama, Mariko, Kitano, Hiroaki, Kolch, Walter, De Meyts, Pierre, Yarden, Yosef, Westerhoff, Hans V, Wiley, H Steven

Systems biology　Vol. 2　No. 2　p. 53-60　2005/06　Research paper (scientific journal)

White paper: The International Receptor Tyrosine Kinase Networks Consortium

Y Sakaki, H Kitano, W Kolch, P De Meyts, Y Yarden, HV Westerhoff, HS Wiley, M Hatakeyama, J Schlessinger

The Scientist　Vol. 19　No. 8　p. 8-9　2005/04

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm

Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya

Bioinformatics　Vol. 21　No. 7　p. 1154-1163　2005/04　Research paper (scientific journal)

Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides

A Suenaga, N Takada, M Hatakeyama, M Ichikawa, XM Yu, K Tomii, N Okimoto, N Futatsugi, T Narumi, M Shirouzu, S Yokoyama, A Konagaya, M Taiji

Journal of Biological Chemistry　Vol. 280　No. 2　p. 1321-1326　2005/01　Research paper (scientific journal)

Software-aided mass spectrometry analysis for identification of protein-protein interaction in signal transduction pathways

Aki Hasegawa, Kazumi Kuriyama-Matsumura, Yu Xiaomei, Mariko Hatakeyama, Akihiko Konagaya

Proceedings - International Workshop on Biomedical Data Engineering, BMDE2005　Vol. 2005　2005　Research paper (international conference proceedings)

Inference of genetic networks using neural network models

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama

Proceedings of the 2005 IEEE Congress on Evolutionary Computation　Vol. 2　p. 1738-1745　2005　Research paper (international conference proceedings)

Genome-wide functional annotation environment for Thermus thermophilus in OBIGrid

Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya

GRID COMPUTING IN LIFE SCIENCE　Vol. 3370　p. 82-91　2005　Research paper (scientific journal)

OBIYagns: a grid-based biochemical simulator with a parameter estimator

Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya

Bioinformatics　Vol. 20　No. 10　p. 1646-1648　2004/07　Research paper (scientific journal)

Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase

Mariko Hatakeyama, Noriko Yumoto, Xiaomei Yu, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya

Oncogene　Vol. 23　No. 29　p. 5023-5031　2004/06　Research paper (scientific journal)

Tyr-317 phosphorylation increases shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations

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

Journal of Biological Chemistry　Vol. 279　No. 6　p. 4657-4662　2004/02　Research paper (scientific journal)

Clustering method for the Inference of S-system models of Genetic Networks

Kimura Shuhei, Hatakeyama Mariko, Matsumura Koki

Proceedings of the Annual Conference of Biomedical Fuzzy Systems Association　Vol. 17　p. 15-18　2004

Parameter estimation for the simulation of biochemical pathways

Shuhei Kimura, Mariko Okada-Hatakeyama, Takuji Kawasaki, Takashi Naka, Akihiko Konagaya

Proceedings of the Fifteenth IASTED International Conference on Modelling and Simulation　p. 266-271　2004　Research paper (international conference proceedings)

The superstructure toward open bioinformatics grid

Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou

New Generation Computing　Vol. 22　No. 2　p. 167-176　2004　Research paper (scientific journal)

Inference of S-system models of genetic networks from noisy time-series data

Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya

Chem-Bio Informatics Journal　Vol. 4　No. 1　p. 1-14　2004　Research paper (scientific journal)

OBIYagns: A Biochemical Simulator in Grid Environment

Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya

Genome Informatics 14 (Proceedings of GIW2003 -The 14th International Conference on Genome Informatics)　Vol. 14　p. 621-622　2003/12　Research paper (international conference proceedings)

A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling

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

Biochemical Journal　Vol. 373　p. 451-463　2003/07　Research paper (scientific journal)

Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of grb2 and ErbB phosphotyrosyl peptides

Atsushi Suenaga, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi, Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya

Biochemistry　Vol. 42　No. 18　p. 5195-5200　2003/05　Research paper (scientific journal)

Inference of S-system models of genetic networks using a genetic local search

S Kimura, M Hatakeyama, A Konagaya

Vol. 1-4　p. 631-638　2003　Research paper (international conference proceedings)

A Mathematical Modeling of Signal Transduction Cascade on Raf-Akt Cross-Talk

Mariko Hatakeyama, Shuhei Kimura, Noriko Yumoto, Mio Ichikawa, Takuji Kawasaki, Takashi Naka, Akihiko Konagaya

Genome Informatics 13 (Proceedings of GIW2002 -The 13th International Conference on Genome Informatics)　Vol. 13　p. 359-360　2002/12　Research paper (international conference proceedings)

Development of Biochemical System Simulator with Parameter Estimator

Takuji Kawasaki, Shuhei Kimura, Mariko Hatakeyama, Takashi Naka, Akihiko Konagaya

Genome Informatics 13 (Proceedings of GIW2002 -The 13th International Conference on Genome Informatics)　Vol. 13　p. 463-464　2002/12　Research paper (international conference proceedings)

Foci formation of MCF7 cells as an in vitro screening method for estrogenic chemicals

Enmin Zou, Mariko Hatakeyama, Fumio Matsumura

Environmental Toxicology and Pharmacology　Vol. 11　No. 2　p. 71-77　2002/03

Estrogenic action of β-HCH through activation of c-Neu in MCF-7 breast carcinoma cells

Mariko Hatakeyama, Daniel M. Tessier, Debra Y. Dunlap, Enmin Zou, Fumio Matsumura

Environmental Toxicology and Pharmacology　Vol. 11　No. 1　p. 27-38　2002/01

Comparison of the characteristic of estrogenic action patterns of beta-HCH and heregulin beta 1 in MCF-7 human breast cancer cells

Mariko Hatakeyama, Enmin Zou, Fumio Matsumura

Journal of Biochemical and Molecular Toxicology　Vol. 16　No. 5　p. 209-219　2002　Research paper (scientific journal)

Correlation between the activation of Neu tyrosine kinase and promotion of foci formation induced by selected organochlorine compounds in the MCF-7 model system

Mariko Hatakeyama, Fumio Matsumura

Journal of Biochemical and Molecular Toxicology　Vol. 13　No. 6　p. 296-302　1999　Research paper (scientific journal)