News

• Yusuke Hiki Takahiro Yamada Akira Funahashi
• 13 Feb 2024
• Paper

A paper entitled: "Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches" is published in Frontiers in Immunology.

• Shohei Tada Yoshitaka Yamazaki
• 8 Feb 2024
• Paper

Our paper entitled: "Switching from weak to strong cortical attachment of microtubules accounts for the transition from nuclear centration to spindle elongation in metazoans." by Shohei Tada, Yoshitaka Yamazaki et al. is published in Heliyon.

• Akira Funahashi
• 1 Nov 2023
• Grant, CREST

The research project on Innovative Measurement and Analysis, in which we are participating as co-researchers, has been accepted by the funding program JST CREST.

• Yuki Tsukada
• 1 Nov 2023
• Grant, CREST

The research project on Cell Control, in which we are participating as co-researchers, has been accepted by the funding program JST CREST.

• Yuki Tsukada
• 01 Nov 2023
• Invited Talk

Yuki Tsukada was invited to deliver talk at the Neural Coding and Combinatorics, ICERM workshop. His talk title was "Decoding a compact neural circuit of Caenorhabditis elegans".

• Taichi Kanazawa
• 11 Oct 2023
• Selected Talk

Taichi Kanazawa was selected to deliver talk at 22nd International Conference on Systems Biology. His talk title was "Design and implementation of four-dimensional bright-field microscopy image segmentation algorithm of mouse embryos".

• Takashi Morikura
• 11 Oct 2023
• Selected Talk

Takashi Morikura was selected to deliver talk at 22nd International Conference on Systems Biology. His talk title was "Automatic quantitative evaluation for the performance of in vitro testis tissues using anomaly detection-based ensemble model with error-correcting output codes".

• Yusuke Hiki
• 11 Oct 2023
• Selected Talk

Yusuke Hiki was selected to deliver talk at 22nd International Conference on Systems Biology. His talk title was "Inference of gene regulatory network overcoming low performance for real world data".

• Takahiro Yamada Akira Funahashi
• 11 Aug 2023
• Paper

A paper entitled: "Titanium Culture Vessel Presenting Temperature Gradation for the Thermotolerance Estimation of Cells" is published in Cyborg and Bionic Systems.

• Ryo Joel Nakatani
• 12 May 2023
• Paper

A commentary on the paper published in Scientific Reports by Ryo Joel Nakatani, Masahiro Itabashi, et al. was posted on PodScholars.

• Akira Funahashi
• 10 Mar 2023
• Paper

A paper entitled: "SBML level 3 package: spatial processes, version 1, release 1" is published in Journal of Integrative Bioinformatics.

• Akira Funahashi
• 25 Feb 2023
• Invited Talk

Akira Funahashi was invited to deliver talk at the Measurement Informatics Seminars(情報計測オンラインセミナーシリーズ). His talk title was "深層学習による定量的な体外受精胚評価手法の開発 (in Japanese)".

• Risa Okubo Takahiro Yamada
• 15 Dec 2022
• Selected Talk

Risa Okubo was selected to deliver talk at 10th Annual workshop on Quantitative Biology Japan (定量生物学の会 第10回年会). Her talk title was "転写因子-DNA 相互作用を考慮した
深層学習による遺伝子制御ネットワーク推定アルゴリズムの構築(in Japanese)".

• Yuta Tokuoka
• 18 Nov 2022
• News

Our research result on "An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos." was featured in Nikkan Kogyo Shimbun website. "近畿大など、AIで出生につながる良好な受精卵評価 分類精度83.87％ (in Japanese)".

• Yuta Tokuoka
• 2 Nov 2022
• Paper

Our paper entitled: "An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos." by Yuta Tokuoka et al. is published in Artificial Intelligence in Medicine.

• Ryo Joel Nakatani Masahiro Itabashi
• 26 Oct 2022
• Paper

Our paper entitled: "Intercellular interaction mechanisms promote diversity in intracellular ATP concentration in Escherichia coli populations." by Ryo Joel Nakatani, Masahiro Itabashi et al. is published in Scientific Reports.

• Yuta Tokuoka
• 11 Sep 2022
• Invited Talk

Yuta Tokuoka was invited to deliver talk at the 8th Annual Meeting of The Society of Reproductive Biology for Young Scientists (第8回 生殖若手の会). His talk title was "深層学習が捉えた胚の動的形態変化を利用したマウス胚出生予測 (in Japanese)".

• Akira Funahashi
• 8 Sep 2022
• Invited Talk

Akira Funahashi was invited to deliver talk at the 165th Annual Meeting of The Japanese Society of Veterinary Science (第165回日本獣医学会学術集会). His talk title was "生物学者が機械学習を導入するための基礎知識 (in Japanese)".

• Hazumi Kubota
• 29 Jun 2022
• News

Our research result on "Symbolic Integration by Integrating Learning Models With Different Strengths and Weaknesses" was featured in The Penmark website.

• Mamoru Tomiyama
• 16 June 2022
• Poster Presentation

Mamoru Tomiyama made a poster presentation at the 36th Annual Conference of the Japanese Society for Artificial Intelligence. His talk title was "Neural Architecture Searchの探索空間削減を目指した深層学習モデルの部分構造解析 (in Japanese)".

• Takayuki Nakamura
• 18 May 2022
• News

Our research result on "Temperature elevation detection in migrating cells" was featured in Nikkei Newspaper website. "神奈川工科大・慶大・東大・自然科学研究機構、傷を治しに向かう細胞は向かわない細胞より温度が高いことの確認に成功 (in Japanese)".

• Yuta Tokuoka
• 13 May 2022
• Invited Talk

Yuta Tokuoka was invited to deliver talk at the 78th Annual Meeting of The Japanese Society of Microscopy (日本顕微鏡学会 第78回学術講演会). His talk title was "深層学習が捉えた胚の動的形態変化を利用したマウス胚出生予測 (in Japanese)".

• Akira Funahashi
• 7 May 2022
• Paper

A paper entitled: "BioSimulators: a central registry of simulation engines and services for recommending specific tools" is published in Nucleic Acids Research.

• Takayuki Nakamura
• 3 May 2022
• Paper

Our paper entitled: "Temperature elevation detection in migrating cells" by Takayuki Nakamura et al. is published in Optics Continuum.

• Hazumi Kubota
• 29 Apr 2022
• Paper

Our paper entitled: "Symbolic Integration by Integrating Learning Models with Different Strengths and Weaknesses" by Hazumi Kubota et al. is published in IEEE Access.

• Akira Funahashi
• 13 Apr 2022
• Grant, ABiS

The second phase of ABiS(Advanced Bioimaging Support) is about to begin!

• Akira Funahashi
• 6 Apr 2022
• Paper

A paper entitled: "High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance" is published in NAR Genomics and Bioinformatics.

• Yusuke Hiki
• 8 Mar 2022
• CREST, Award

Yusuke Hiki received the Laboratory Director's Award in the AIP Challenge Program (CREST). His talk title was "遺伝子制御の時間的変化を考慮した深層学習による遺伝子制御ネットワーク推定手法の提案(in Japanese)".

• Akira Funahashi
• 15 Dec 2021
• Invited Talk

Akira Funahashi was invited to deliver talk at the JBRAIC (日本乳腺人工知能研究会). His talk title was "深層学習と医学研究(in Japanese)".

• Akira Funahashi
• 19 Oct 2021
• Paper

A paper entitled: "COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms" is published in Molecular Systems Biology.

• Takahiro G. Yamada
• 15 Oct 2021
• Paper

Our paper entitled: "SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models" by Takahiro G. Yamada et al. is published in MDPI Processes.

• Akira Funahashi
• 5 Oct 2021
• Paper

A paper entitled: "Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells" is published in Scientific Reports.

• Akira Funahashi
• 21 Sep 2021
• Grant, CREST

The research project on BioDX, in which we are participating as co-researchers, has been accepted by the funding program JST CREST.

• Akira Funahashi
• 7 Aug 2021
• Invited Talk

Akira Funahashi was invited to deliver talk at the Japanese Society for Quantitative Biology Summer 2021. His talk title was "機械学習と定量生物学(in Japanese)".

• Akira Funahashi
• 28 May 2021
• Paper

A paper entitled: "Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11" is published in International Journal of Molecular Sciences.

• Akira Funahashi
• 23 Mar 2021
• Invited Talk

Akira Funahashi was invited to deliver talk at the Data Driven Biology Workshop. His talk title was "深層学習が駆動する定量生物学の新展開(in Japanese)".

• Takahiro G. Yamada
• 26 Mar 2021
• Award

Takahiro G. Yamada received the Fujiwara Award for his outstanding achievement in research on systems biology. The title of his doctoral dissertation was "Gene regulatory network inference of desiccation tolerance system in Pv11 cells.".

• Takahiro Yamada
• 11 Feb 2021
• Invited Talk

Takahiro Yamada was invited to deliver talk at the 40th Scienc-ome. His talk title was "限界を超えた能力を生命に付与したい ー設計図志向な生物学を目指してー (in Japanese)".

• Yuta Tokuoka
• 27 Jan 2021
• News

Our research on QCANet has been featured in SigOpt's blog.

• Akira Funahashi
• 14 Dec 2020
• Book

The book on Machine Learning and Life Sciences "機械学習を生命科学に使う！" was published.

• Yuta Tokuoka
• 6 Nov 2020
• News

Our research results on QCANet were published in Asahi Newspaper. "AI analysis may lead to improved chance of success of IVF pregnancy : The Asahi Shimbun".

• Yuta Tokuoka
• 20 Oct 2020
• Paper

Our paper entitled: "3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis" by Yuta Tokuoka et al. is published in npj Systems Biology and Applications.

• Akira Funahashi
• 19 Oct 2020
• Grant, CREST

The research project on Mathematical Information Platform, in which we are participating as co-researchers, has been accepted by the funding program JST CREST.

• Akira Funahashi
• 10 Oct 2020
• Award

Yuta Tokuoka was awarded the Best Poster Award at the Society of Reproductive Biology for Young Scientists(第7回 生殖若手の会).

• Akira Funahashi
• 5 Oct 2020
• Invited Talk

Akira Funahashi was invited to deliver keynote speech at the "Computational Modeling in Biology" Network (COMBINE) 2020. His talk title was "CellDesigner: A modeling tool for biochemical networks".

• Ryo Nakatani
• 22 Sep 2020
• Invited Talk

Ryo Nakatani was invited to deliver talk at 2020 Japanese Society for Mathematical Biology annual meeting (JSMB 2020, 2020年度 日本数理生物学会年会). His talk title was "一細胞系譜解析による低グルコース培養下大腸菌集団のATP濃度多様性の解明 (in Japanese)".

• Chikahiro Imashiro, Yuta Tokuoka
• 15 Sep 2020
• Paper

Our paper entitled: "Direct cell counting using macro-scale smartphone images of cell aggregates" by Chikahiro Imashiro, Yuta Tokuoka et al. is published in IEEE Access.

• Akira Funahashi
• 9 Sep 2020
• Invited Talk

Akira Funahashi was invited to deliver talk at The 81st Japan Society of Applied Physics Autumun Meeting 2020(第81回 応用物理学会 秋季学術講演会). His talk title was "ライブセルイメージングと深層学習を用いた胚発生過程定量システムの構築 (in Japanese)".

• Akira Funahashi
• 26 Aug 2020
• Paper

A paper entitled: "SBML Level 3: an extensible format for the exchange and reuse of biological models" is published in Molecular Systems Biology.

• Akira Funahashi
• 5 May 2020
• Paper

A paper entitled: "COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms" is published in Scientific Data.

• Takahiro Yamada
• 19 Mar 2020
• Paper

Our paper entitled: "Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11" by Takahiro Yamada et al. is published in PLOS ONE.

• Akira Funahashi
• 13 Mar 2020
• Book

The book (Cell Biology by the Numbers) we translated was published (数でとらえる細胞生物学).

• Tsuyoshi Iwasaki
• 3 Feb 2020
• Paper

Our paper entitled: "Neural Differentiation Dynamics Controlled by Multiple Feedback Loops in a Comprehensive Molecular Interaction Network" by Tsuyoshi Iwasaki et al. is published in MDPI Processes.

• Maya Ooka
• 14 Dec 2019
• Paper

Our paper entitled: "Deep Learning for Non-Invasive Determination of the Differentiation Status of Human Neuronal Cells by Using Phase-Contrast Photomicrographs" by Maya Ooka et al. is published in MDPI Applied Sciences.

• Akira Funahashi
• 7 Nov 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at 群馬大学総合外科学講座 Translational Researchセミナー. His talk title was "人工知能と医学研究(in Japanese)".

• Ryo Nakatani
• 7 Nov 2019
• Selected Talk

Ryo Nakatani was selected to deliver talk at Quantitative Biology Japan Caravan 2019(定量生物学の会 北海道キャラバン 2019). His talk title was "一細胞系譜による低グルコース培養下大腸菌集団のATP濃度多様性生成機構の解明(in Japanese)".

• Kaito Ii
• 22 Oct 2019
• Paper

Our paper entitled: "XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images" by Kaito Ii et al. is published in Frontiers in Genetics.

• Akira Funahashi
• 18 Oct 2019
• Review

Our review article entitled: "Development of 3D imaging system with an electrically tunable lens (in Japanese)" by Akira Funahashi et al. is published in Experimental Medicine (実験医学).

• Akira Funahashi
• 5 Sep 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at 群馬大学数理データ科学教育研究センター主催第1回レギュラトリーサイエンスセミナー. His talk title was "腫瘍内不均一性を考慮した予後の予測に向けた深層学習ベースの組織画像解析(in Japanese)".

• Shori Nishimoto
• 5 Sep 2019
• Paper

Our paper entitled: "Predicting the future direction of cell movement with convolutional neural networks" by Shori Nishimoto et al. is published in PLOS ONE.

• Akira Funahashi
• 29 Aug 2019
• Invited Talk

Yuta Tokuoka and Akira Funahashi were invited to deliver talk at Grant-in-Aid for Scientific Research on Innovative Areas- Platforms for Advanced Technologies and Research Resources "Advanced Bioimaging Support(ABiS)" Training Course (新学術領域研究・学術研究支援基盤形成 「先端バイオイメージング支援プラットフォーム」AIによる生物画像解析トレーニングコース). Their talk title was "機械学習による画像分類(in Japanese)".

• Akira Funahashi
• 17 Jul 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at COMBINE 2019. His talk title was "CellDesigner: A modeling tool for biochemical networks".

• Akira Funahashi
• 1 Jul 2019
• Review

Our review article entitled: "Basis for diagnosis using image analysis and deep learning (in Japanese)" by Akira Funahashi et al. is published in Pathology and Clinical Medicine (病理と臨床).

• Akira Funahashi
• 28 May 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at AI Systems Medicine Research and Training Center, Yamaguchi University. His talk title was "畳み込みニューラルネットワークを用いた神経分化判別および特徴量解析(in Japanese)".

• Akira Funahashi
• 20 May 2019
• Software

CellDesigner version 4.4.2 released! CellDesigner is a modeling tool of biochemical networks.

• Akira Funahashi
• 20 May 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at Cardiovascular Meeting, Keio University School of Medicine. His talk title was "Deep Learning-based Quantitative Evaluation of Early Embryo in Fertility Treatments Perspective (in Japanese)".

• Shori Nishimoto
• 8 Mar 2019
• Invited Talk

Shori Nishimoto was invited to deliver talk at School of Veterinary Medicine and Science, University of Nottingham. His talk title was "Deep Learning Based Tissue Analysis for Predicting Cancer Outcomes Accounting for Intratumoral Heterogeneity".

• Akira Funahashi
• 8 Mar 2019
• Invited Talk

Akira Funahashi was invited to deliver talk at School of Veterinary Medicine and Science, University of Nottingham. His talk title was "Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development".

• Takumi Hiraiwa
• 6 Mar 2019
• Paper

Our paper entitled: "Activation of cell migration via morphological changes in focal adhesions depends on shear stress in MYCN-amplified neuroblastoma cells" by Takumi Hiraiwa et al. is published in Journal of the Royal Society Interface.

• Yuta Tokuoka
• 26 Feb 2019
• Invited Talk

Yuta Tokuoka was invited to deliver talk at Engineering Network Workshop - Fusion of tolerance function of life and engineering -. His talk title was "深層学習が駆動するPv11生存細胞スクリーニング(in Japanese)".

• Mikiko Motomuro
• 22 Feb 2019
• Selected Talk

Mikiko Motomuro was selected to deliver talk at The Seventh Annual Winter Q-bio meeting. Her talk title was "Mechanical Modeling of Cell Migration During the Early Embryogenesis of C. elegans to Reveal the Mechanism for Controlling Cell Arrangement".

• Takayuki Nakamura
• 21 Feb 2019
• Selected Talk

Takayuki Nakamura was selected to deliver talk at The Seventh Annual Winter Q-bio meeting. His talk title was "Analysis of Intracellular Temperature Effect on Wound Healing Process".

• Takahiro G Yamada
• 18 Dec 2018
• Paper

Our paper entitled: "Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery" by Takahiro G Yamada et al. is published in Scientific Reports.

• Akira Funahashi
• 14 Dec 2018
• Invited Talk

Akira Funahashi was invited to deliver talk at AI Systems Medicine Research and Training Center, Yamaguchi University. His talk title was "深層学習が明らかにする細胞顕微鏡画像解析の新展開(in Japanese)".

• Noriko Hiroi
• 21 Sep 2018
• Invited Talk

Noriko Hiroi was invited to deliver talk at Keio University International Symposium on Advanced Technologies for Mechano-biology and Regenerative Medicine. Her talk title was "Quantitative analysis of sensitivity to Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device".

• Takumi Hiraiwa
• 16 Sep 2018
• Paper

Our paper entitled: "Quantitative analysis of sensitivity to a Wnt3a gradient in determination of the pole‐to‐pole axis of mitotic cells by using a microfluidic device" by Takumi Hiraiwa et al. is published in FEBS Open Bio.

• Takahiro Yamada
• 14 Sep 2018
• Selected Talk

Takahiro Yamada was selected to deliver talk at SICE Annual Conference 2018 (SICE 2018). His talk title was "Mathematical Modeling Identifies the Conditions Required for RNA-Based Oscillator".

• Yoshitaka Yamazaki
• 13 Sep 2018
• Selected Talk , Award

Yoshitaka Yamazaki was selected to deliver talk at 2nd Keio Life Science Symposium. He also received a research encouragement award! His talk title was "In silico 及び in vivo 実験による有糸分裂期中心体位置制御機構の解明(in Japanese)".

• Takahiro G Yamada
• 6 Sep 2018
• Invited Talk

Takahiro G Yamada was invited to deliver talk at CELLab-SOCU Summer Symposium. His talk title was "カラカラに乾燥しても死なないネムリユスリカの神秘に転写制御ネットワークから迫る(in Japanese)".

• Akira Funahashi
• 27 Jul 2018
• Invited Talk

Akira Funahashi was invited to deliver talk at The 36th Annual Meeting of Japan Society of Fertilization and Implantation. His talk title was "ディープラーニングを用いたマウス発生過程における定量的指標の獲得(in Japanese)".

• Akira Funahashi
• 17 Jul 2018
• Invited Talk

Akira Funahashi was invited to deliver talk at 関西医科大学大学院. (in Japanese)

• Takahiro Yamada
• 23 May 2018
• Invited Talk

Takahiro Yamada was invited to deliver talk at Life of Genomes 2018. His talk title was "Inferring a Polypedilum vanderplanki transcriptional regulatory network for rehydration process from time-series RNA-seq data".

• Akira Funahashi
• 15 Mar 2018
• Invited Talk

Akira Funahashi was invited to deliver talk at 自然科学研究機構新分野創成センター合同シンポジウム 「分野横断・分野融合研究による生命創成を探究する新しい科学の創成」. His talk title was "深層学習が明らかにする細胞顕微鏡画像解析の新展開(in Japanese)".

• Akira Funahashi
• 1 Mar 2018
• Invited Talk

Akira Funahashi was invited to deliver talk at SYSBIO 2018 Advanced Lecture Course on Systems Biology. His talk title was "CellDesigner: A process diagram editor for gene-regulatory and biochemical networks".

• Akira Funahashi
• 5 Dec 2017
• Software

LibSBMLSim version 1.4.0 released! LibSBMLSim enables you to write your own SBML capable simulator with a few lines of code.

• Takahiro Yamada
• 28 Aug 2017
• Award

Takahiro Yamada received a poster prize in the 1st Keio Life Science Symposium. His poster title was "時系列RNA-seqデータに基づくネムリユスリカ乾燥耐性機構の転写制御ネットワークの同定(in Japanese)".

• Yuta Tokuoka
• 11 Aug 2017
• Selected Talk

Yuta Tokuoka was selected to deliver talk at 18th International Conference on Systems Biology (ICSB 2017). His talk title was "Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network".

• Noriko Hiroi
• 23 Jun 2017
• Invited Talk

Noriko Hiroi was invited to deliver talk at EMERGING RESEARCH CHALLENGES IN BIOLOGY. Her talk title was "Asymmetric division, cell migration, and differentiation control in microfluidic devices".

• Noriko Hiroi
• 20 Jun 2017
• Invited Talk

Noriko Hiroi was invited to deliver talk at EMN Europe Meeting on Quantum. Her talk title was "The foundation of Biothermology from the point of view of nano/microscale thermophysical properties of biopolymers".

• Noriko Hiroi
• 24 Apr 2017
• Invited Talk

Noriko Hiroi was invited to deliver talk at Biomedical Imaging and Sensing Conference. Her talk title was "Requirement of spatiotemporal resolution for imaging intracellular temperature distribution".

• Noriko Hiroi
• 14 Apr 2017
• Conference

We had "International Workshop on Quantitative Biology 2017" at Keio University.

• Yuta Tokuoka
• 8 Jan 2017
• Selected Talk

Yuta Tokuoka was selected to deliver talk at 8th Annual workshop on Quantitative Biology Japan (定量生物学の会 第8回年会). His talk title was "深層学習を用いた3次元蛍光顕微鏡画像セグメンテーションアルゴリズムの提案(in Japanese)".

• Matthew Higashionna
• 14 Dec 2016
• Invited Talk

Matthew Higashionna was invited to deliver talk at International Symposium on Micro-Nano Science and Technology 2016 (MNST 2016). His talk title will be "Quantification of the effect of shear stress on the differentiation of SH-SY5Y cells".

• Noriko Hiroi
• 27 May 2016
• Paper

Our editorial article entitled: "Quantitative Biology: Dynamics of living systems" by Noriko Hiroi et al. is published in Frontiers in Physiology (Systems Biology).

• Ryuichi Tanimoto
• 1 Mar 2016
• Paper

Our paper entitled: "Detection of Temperature Difference in Neuronal Cells" by Ryuichi Tanimoto et al. is published in Scientific Reports.

• Akira Funahashi
• 10 Feb 2016
• Review

Our review entitled: "Simulation technology and its application in Systems Biology (in Japanese)" by Akira Funahashi et al. is published in Folia Pharmacologica Japonica.

• Akira Funahashi
• 24 Jun 2015
• Review

A review entitled: "The principles of whole-cell modeling" by Jonathan R Karr et al. is published in Current Opinion in Microbiology.

• Akira Funahashi
• 26 May 2015
• Review

A review entitled: "Bioimage Analysis for Quantitative Biology and Its Application to Mammalian Embryogenesis (in Japanese)" by Tetsuya J Kobayashi et al. is published in Medical Imaging Technology.

• Kei Sumiyoshi
• 13 Feb 2015
• Paper

Our paper entitled: "Acceleration of discrete stochastic biochemical simulation using GPGPU" by Kei Sumiyoshi et al. is published in Frontiers in Physiology (Systems Biology).

• Yuichiro Nakai
• 21 Jan 2015
• Paper

Our paper entitled: "High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes" by Yuichiro Nakai et al. is published in Review of Scientific Instruments.

• Akira Funahashi
• 16 Jan 2015
• Paper

A paper entitled: "A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset" is published in Biology Open.

• Akira Funahashi
• 16 Jul 2014
• Book

A book chapter entitled: "Modeling and simulation using CellDesigner" is published in Methods in Molecular Biology.

• Noriko Hiroi
• 4 Apr 2014
• Paper

Our paper entitled: "Assessing uncertainty in model parameters based on sparse and noisy experimental data" by Noriko Hiroi et al. is published in Frontiers in Physiology (Systems Biology).

• Noriko Hiroi
• 25 Nov 2013
• Conference

We had "International Workshop on Quantitative Biology 2013" at Osaka University.

• Akira Funahashi
• 23 Aug 2013
• Paper

A paper entitled: "Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance" is published in Cell Cycle.

• Akira Funahashi
• 5 Jul 2013
• Paper

A paper entitled: "The systems biology simulation core algorithm" is published in BMC Systems Biology.

• Noriko Hiroi
• 4 Jul 2013
• Invited Talk

Noriko Hiroi was invited to deliver talk at The 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’13). Her talk title was "In Vivo Oriented Modeling with Consideration of Intracellular Crowding".

• Akira Funahashi
• 28 Jun 2013
• Invited Talk

Akira Funahashi was invited to deliver talk on CellDesigner at The 2nd HD Physiology International Symposium.

• Akira Funahashi
• 7 May 2013
• Invited Talk

Akira Funahashi and Noriko Hiroi were invited to organize a two days workshop on CellDesigner at Monash University, Australia.

• Hiromu Takizawa
• 5 Apr 2013
• Paper

Our paper entitled: "LibSBMLSim: a reference implementation of fully functional SBML simulator" by Hiromu Takizawa et al. is published in Bioinformatics.

• Akira Funahashi
• 28 Jan 2013
• Software

LibSBMLSim version 1.1.0 released! LibSBMLSim enables you to write your own SBML capable simulator with a few lines of code.

• Hiromu Takizawa
• 20 Dec 2012
• Paper

Our paper entitled: "Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms In Vivo" by Hiromu Takizawa et al. is published in PLoS ONE.

• Akira Funahashi
• 7 Dec 2012
• Paper

A General Commentary Article entitled: "Meeting Report of the International Workshop on Quantitative Biology 2012: Mesoscopic and microscopic worlds meet." by Viji M. Draviam et al. is published in Frontiers in Physiology (Systems Biology).

• Akira Funahashi
• 25 Nov 2012
• Conference

We had "5th Annual Meeting of The Japanese Society for Quantitative Biology (Q-BioJP)" at the University of Tokyo.

• Noriko Hiroi
• 22 Nov 2012
• Conference

We had "International Workshop on Quantitative Biology 2012" at the University of Tokyo.

• Noriko Hiroi
• 23 Jul 2012
• Paper

Our paper entitled: "Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments" by Noriko Hiroi et al. is published in Frontiers in Fractal Physiology.

• Noriko Hiroi
• 26 Jun 2012
• Paper

Our paper entitled: "From Microscopy Data to in silico Environments for in vivo Oriented Simulations" by Noriko Hiroi et al. is published in EURASIP Journal on Bioinformatics and Systems Biology.

• Akira Funahashi
• 10 May 2012
• Paper

A paper entitled: "Software support for SBGN maps: SBGN-ML and LibSBGN" by Martijn P. van Iersel et al. is published in Bioinformatics.

• Akira Funahashi
• 4 Apr 2012
• Software

LibSBMLSim version 1.0.0 released! LibSBMLSim enables you to write your own SBML capable simulator with a few lines of code.

• Akira Funahashi
• 21 Oct 2011
• Paper

A paper entitled: "BioPAX support in CellDesigner" by Huaiyu Mi et al. is published in Bioinformatics.

• Akira Funahashi
• 15 Sep 2011
• News

Our paper was featured on a Japanese news site.

• Noriko Hiroi
• 13 Mar 2011
• Paper

Our paper entitled: "Physiological environment induce quick response - slow exhaustion reactions" by Noriko Hiroi et al. is published in Frontiers in Physiology (Systems Biology).