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

by Hiroaki Imoto, Suxiang Zhang, Mariko Okada
Published 2020-10-01

Inference of Vohradský's models of genetic networks by solving two-dimensional function optimization problems.

by Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama
Published 2013-01-01

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

by Shuhei Kimura, Ryo Fukutomi, Masato Tokuhisa, Mariko Okada
Published 2020-12-01

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

by Hiroyuki Masunaga, Yurie Sugimoto, Shigeyuki Magi, Ryunosuke Itasaki, Mariko Okada-Hatakeyama, Hiroyuki Kurata
Published 2017-01-01

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

by Keisuke Yoshida, Claire Renard-Guillet, Kentaro Inoue, Katsuhiko Shirahige, Mariko Okada-Hatakeyama, Shunsuke Ishii
Published 2016-03-01

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

by Shigeyuki Magi, Sewon Ki, Masao Ukai, Elisa Domínguez-Hüttinger, Atsuhiko T Naito, Yutaka Suzuki, Mariko Okada
Published 2021-09-01

HSF1 is required for induction of mitochondrial chaperones during the mitochondrial unfolded protein response

by Arpit Katiyar, Mitsuaki Fujimoto, Ke Tan, Ai Kurashima, Pratibha Srivastava, Mariko Okada, Ryosuke Takii, Akira Nakai
Published 2020-06-01

Signalling mechanisms regulating phenotypic changes in breast cancer cells

by Natalia Volinsky, Cormac J. McCarthy, Alex von Kriegsheim, Nina Saban, Mariko Okada‑Hatakeyama, Walter Kolch, Boris N. Kholodenko
Published 2015-03-01

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

by Hiroki Michida, Hiroaki Imoto, Hisaaki Shinohara, Noriko Yumoto, Masahide Seki, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Takeya Kasukawa, Yutaka Suzuki, Mariko Okada-Hatakeyama
Published 2020-06-01

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

by 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
Published 2016-09-01

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

by 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, Jessica C Mar
Published 2015-01-01

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

by 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, FANTOM Consortium, Levon M Khachigian, Mariko Okada-Hatakeyama, Colin A Semple
Published 2015-04-01