Research summary


    How do cells choose and process the information they need from a pool of thousands of genes? How can it ensure the specificity of the reaction in a small inner cell environment that is filled with very similar substrates? To answer these questions, we focus on dynamics of molecules and genes in cells and analyze them by combining wet lab experiments and mathematical models. We would like to clarify the quantitative relationship between the dynamics of signal transduction networks, transcriptional and epigenetic regulation and cell fate.

News
　　　

February 4, 2025 Our paper on epigenetic deep learning modeling has been published in Genes to Cells. Link
October 11, 2024 Our paper on comprehensive analysis of cellular signaling dynamics has been published in Bioinformatics Advances. Link
July 16, 2024 Our paper on cellular senescence has been published in The FEBS Journal. Link
April 15, 2024 Our paper on cancer drug resistance has been published in Cancers. Link
April 9, 2024 Our paper on skin aging has been published in iScience. Link
Press release (Japanese)
April 4, 2024 Our paper on automatic mathematical modeling has been published in Bioinformatics Advances. Link
February 8, 2024 Our joint paper with RIKEN has been published in Computational Modeling of Signaling Networks (Springer US). Link
December 22, 2023 Ken Murakami won the MBSJ2023 Best Science Pitch Award at The 46th Annual Meeting of the Molecular Biology Society of Japan. Congratulations! Link
November 16, 2023 Kiwamu Arakane won the student award at The 61st Annual Meeting of the Biophysical Society of Japan. Congratulations! Link
October 6, 2023 Our joint paper with School & Graduate School of Dentistry Osaka University has been published in Journal of Dental Research. Link
August 22, 2023 Our review paper has been published in The Biophysical Society of Japan. Link
July 4, 2023 Our joint paper with The University of Tokyo has been published in PNAS Nexus. Link
April 3, 2023 Ken Murakami has been selected for a JSPS research fellowship (DC2). Congratulations!
March 17, 2023 Hiroaki Imoto won the excellent research award from the Graduate School of Biological science, Osaka University. Congratulations! Photo
February 28, 2023 Josephina Sampson (University of Leeds) stays our laboratory.
February 7, 2023 Kaho Itoh has been selected for the member of Murata Overseas Scholarship Foundation. Congratulations! Link
January 17, 2023 Our joint paper with Kyoto University has been published in iScience. Link
January 17, 2023 Mariko Okada's review paper was published in Biophysical Reviews. Link
January 4, 2023 Our joint paper with Tottori University has been published in Chem-Bio Informatics Journal. Link
December 9, 2022 Kaho Itoh (M2) won the first place for outstanding poster presentation at the 20th IPR Retreat 2022, Osaka University.
December 5, 2022 See our Japanese review article published in Jikken Igaku. Link
October 8, 2022 Masatoshi Haga and Mariko Okada gave talks in The 21st International Conference On Systems Biology (ICSB 2022) (Berlin, Germany). Link
September 28, 2022 Our joint paper with Tokyo Medical and Dental University has been published in Cell Reports. Link
August 12, 2022 Our new paper was published in STAR Protocols. Link
July 1, 2022 Shou Soeda has been appointed as specially appointed assistant professor.
June 13, 2022 Fabian Ormersbach (Universität Heidelberg) has joined in our laboratory as a research internship student.
June 8, 2022 Mariko Okada gave an invited talk in 1st International Symposium on Aihara Moonshot Project (Online). Link
June 3, 2022 Our new paper was published in PLOS Genetics. Link
May 27, 2022 Our NF-κB review paper was publishe in Current Opinion in Cell Biology. Link
May 17, 2022 Mariko Okada gave an invited talk in 8th Conference on Systems Biology of Mammalian Cells in Heidelberg, Germany. Link
March 10, 2022 Our new paper was published in iScience. Link
PR 1 (in Japanese), PR 2 (in Japanese)
February 5, 2022 Our review article on the role of NF-κB signaling in aging has been published in Biochemical Journal. Link
January 19, 2022 Zi Wang （M2 student) won the first place for outstanding presentation at the 2022 NTHU-OU Virtual Symposium on Biological and Medical Science. Link
November 30, 2021 A joint seminar with the International Symposium on Evolutionary Genomics and Bioinformatics 2022 will be held at Taiwan, March 12 2022. Seminars
November 29, 2021 Kaho Itoh won the student award at the annual meeting of the 59th Biophysical Society of Japan. Congraturation! Link
November 22, 2021 Our new paper on patient-specific modeling has been published in SSRN.
November 11, 2021 Our joint paper with RIKEN has been published in Frontiers in Immunology.
September 29, 2021 Zi Wang won the excellent poster award at IIBMP2021.
July 14, 2021 See our new paper published in Mol Biol Cell.
July 13, 2021 See our new paper released on bioRxiv .
July 2, 2021 Perspective article on Science.
June 11, 2021 See our new paper released on bioRxiv.
April 9, 2021 See our new paper published in FEBS Journal.
April 9, 2021 See our new paper published in Research Square.
March 18, 2021 Zi Wang has been selected for the Rotary Yoneyama Memorial Foundation scholarship. Congratulations!
March 9, 2021 See our new paper published in FEBS Journal.
March 9, 2021 See our Japanese review article published in Igaku no ayumi.
December 2, 2020 Masatoshi Haga, Hiroki Michida, and Keng Teerachate Nantakeeratipat gave poster presentations in The 43rd Annual Meeting of the Molecular Biology Society of Japan. (December 2-4th, 2020).
December 23, 2020 See our new paper published in Frontiers in Genetics.
November 20, 2020 Hiroaki Imoto gave a poster presentation in EMBL conference - From Functional Genomics to Systems Biology (November 16-19th, 2020)
November 5, 2020 IPR seminar “オミクス解析における実験と数理の協働” is going to be held on January 15th, 2021 via Zoom and hosted by Keita Iida and Ayaka Ichikawa.
October 12, 2020 The Japanese review by Okada & Imoto has been released at the Kokyuroku of the Research Institute for Mathematical Sciences, Kyoto University.
October 7, 2020 The paper by Imoto et al. has been published in Cancers.
Press Release
Osaka UniversityJST
October 1, 2020 An Japanese essay on career for young researchers by Okada has been released in Seibutsu Butsuri Journal.
September 18, 2020 Johannes Nicolaus Wibisana won the student presentation award at the annual meeting of the Biophysical Society of Japan.
June 23, 2020 Series of lectures by Prof. Boris Kholodenko will be held online on July. more info
June 2, 2020 Hiroki Michida's paper has been published in Cell Reports.
Osaka University Press Release
May 1, 2020 Specially appointed associate professor Tabata has joined in our laboratory.
April 10, 2020 Specially appointed assistant professor Ulrike Muenzner has joined in our laboratory.
March 26, 2020 Keita Iida has been selected for The 2019 MSJ Prize for Exellent Applied Mathematicians. Congratulations!
February 26, 2020 Nico has been selected for the Honjo International Scholarship Foundation scholarship. Congratulations!
February 26, 2020 Hiroaki Imoto has been selected for a JSPS research fellowship (DC1). Congratulations!
January 20, 2020 Sufeng Chiang's paper was accepted for publication in FEBS letters. This is a significant achievement of the joint research with National Taiwan University.
January 16, 2020 The paper from the results of joint research with the University of Chicago was accepted by Life Science Alliance.
The Nihon Keizai Shimbun（online edition）Press Release
November 20, 2019 Sufeng Chiang, who stayed at our laboratory, successfully obtained a doctorate from National Taiwan University.
November 5, 2019 Nico, Kyoichi Ebata, Hiroki Michida, Hiroaki Imoto, and Keita Iida participated in ICSB 2019 @ OIST.
October 1, 2019 Ayaka Ichikawa has been appointed as researcher.
September 26, 2019 Hiroaki Imoto won the student presentation award at the annual meeting of the Biophysical Society of Japan.
September 13, 2019 We are hiring students → Recruitment
April 11, 2019 Hiroaki Imoto's paper was accepted for publication in Current Opinion in Systems Biology.
April 1, 2019 Keita Iida has been appointed as assistant professor.
March 11, 2019 Update (Website)
December 3, 2018 Update (Photos)
September 19, 2018 Update (Photos)
March 27, 2018 Mariko Okada has achieved an award of The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology.