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List of works by Akira Funahashi

3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis

scientific article published on 20 October 2020

A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset.

scientific article published on 16 January 2015

Acceleration of discrete stochastic biochemical simulation using GPGPU.

scientific article

Activation of cell migration via morphological changes in focal adhesions depends on shear stress in MYCN-amplified neuroblastoma cells

scientific article published on 01 March 2019

Assessing uncertainty in model parameters based on sparse and noisy experimental data

scientific article

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance

scientific article

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA

scientific article published on 01 January 2006

Deduction of intracellular sub-systems from a topological description of the network.

scientific article published on 27 June 2007

Detection of Temperature Difference in Neuronal Cells.

scientific article published on March 2016

Development of non-bias phenotypic drug screening for cardiomyocyte hypertrophy by image segmentation using deep learning

scientific article published in 2022

Editorial: Quantitative Biology: Dynamics of Living Systems

scientific article

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

scientific article

From microscopy data to in silico environments for in vivo-oriented simulations.

scientific article

High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance

scientific article published on 05 April 2022

High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes.

scientific article published on January 2015

Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11

scientific article published on 19 March 2020

In vivo oriented modeling with consideration of intracellular crowding.

scientific article

Integration of CellDesigner and SABIO-RK.

scientific article

LibSBMLSim: a reference implementation of fully functional SBML simulator ⬇️

scientific article published on April 5, 2013

Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo

scientific article

Meeting report of the International Workshop on Quantitative Biology 2012: mesoscopic and microscopic worlds meet ⬇️

scientific article published on January 11, 2013

Modeling and simulation using CellDesigner

scientific article published on 01 January 2014

Physiological Intracellular Crowdedness is Defined by the Perimeter-to-Area Ratio of Sub-Cellular Compartments

scientific article

Physiological environment induces quick response - slow exhaustion reactions.

scientific article published on 21 September 2011

Predicting the future direction of cell movement with convolutional neural networks

scientific article published on 04 September 2019

Quantitative analysis of sensitivity to a Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device

scientific article published on 09 November 2018

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SBML Models and MathSBML

Simulation technology and its application in Systems Biology.

scientific article published on January 2016

Software support for SBGN maps: SBGN-ML and LibSBGN.

scientific article

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

scientific article (publication date: 21 August 2010)

The principles of whole-cell modeling

scientific article published on 23 June 2015

The systems biology simulation core algorithm

scientific article

Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery

scientific article published in Scientific Reports

Using process diagrams for the graphical representation of biological networks

scientific article published on 01 August 2005

XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

scientific article published on 22 October 2019

[The ERATO Systems Biology Workbench and Systems Biology Markup Language: an integrated environment and standardization for systems biology]

scientific article published on 01 June 2003

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