Papers - FUNAHASHI Akira

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

Yamada T., Suetsugu Y., Deviatiiarov R., Gusev O., Cornette R., Nesmelov A., Hiroi N., Kikawada T., Funahashi A.

Scientific Reports (Scientific Reports)  8 ( 1 ) 17941 2018.12

Research paper (scientific journal), Joint Work, Accepted,  ISSN  2045-2322

　View Summary

© 2018, The Author(s). The larvae of the African midge, Polypedilum vanderplanki, can enter an ametabolic state called anhydrobiosis to overcome fatal desiccation stress. The Pv11 cell line, derived from P. vanderplanki embryo, shows desiccation tolerance when treated with trehalose before desiccation and resumes proliferation after rehydration. However, the molecular mechanisms of this desiccation tolerance remain unknown. Here, we performed high-throughput CAGE-seq of mRNA and a differentially expressed gene analysis in trehalose-treated, desiccated, and rehydrated Pv11 cells, followed by gene ontology analysis of the identified differentially expressed genes. We detected differentially expressed genes after trehalose treatment involved in various stress responses, detoxification of harmful chemicals, and regulation of oxidoreduction that were upregulated. In the desiccation phase, L-isoaspartyl methyltransferase and heat shock proteins were upregulated and ribosomal proteins were downregulated. Analysis of differentially expressed genes during rehydration supported the notion that homologous recombination, nucleotide excision repair, and non-homologous recombination were involv

• Access to Document (DOI)

Convolutional neural network-based instance segmentation algorithm to acquire quantitative criteria of early mouse development

Y Tokuoka, TG Yamada, N Hiroi, TJ Kobayashi, K Yamagata, ...

BioRxiv, 324186  2018.06

Research paper (scientific journal), Joint Work, Accepted

• Access to Document (DOI)

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

T Hiraiwa, Y Nakai, TG Yamada, R Tanimoto, H Kimura, Y Matsumoto, ...

FEBS open bio 8 (12), 1920-1935  2018

Research paper (scientific journal), Joint Work, Accepted

Requirement of spatiotemporal resolution for imaging intracellular temperature distribution

N Hiroi, R Tanimoto, K Ii, M Ozeki, K Mashimo, A Funahashi

Biomedical Imaging and Sensing Conference 10251, 102510Q 10251 2017.04

Research paper (scientific journal), Joint Work, Accepted,  ISSN  978-1-5106-1004-0

• Access to Document (DOI)

Editorial: Quantitative Biology: Dynamics of Living Systems

Hiroi, Noriko, Draviam, Viji M., Funahashi, Akira

FRONTIERS IN PHYSIOLOGY 7   196 2016.06

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1664-042X

• Access to Document (DOI)

Simulation technology and its application in Systems Biology.

FUNAHASHI Akira, HIROI Noriko

Folia pharmacologica Japonica (The Japanese Pharmacological Society)  147 ( 2 ) 101 - 106 2016.02

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0015-5691

　View Summary

生命現象の理解には個別のコンポーネントについての理解に加え，それらの統合されたふるまいを知る必要がある．このような様々な分子のダイナミクスの背景にあるメカニズムを理解する上で強力なツールとなるのが数理モデルである．システムバイオロジーでは，数理モデルを用いて生命現象を司るメカニズムを理解する手法を頻用する．歴史的には解析的に解くことが可能なモデルが用いられたが，コンピュータの発達により，常微分方程式モデル，偏微分方程式モデル，確率モデル，これらのハイブリッドモデルなど多岐に渡る形式で記述されたモデルを数値計算によって解くようになった．こうした背景から，作成したモデルの正しい挙動を数値的に得るための，正確な数値計算技術が不可欠の要素となっている．本稿では，各モデル化手法の特徴を概説した後，システムバイオロジー研究において広く利用されている代表的なアプリケーション（シミュレータ）について，ソフトウェアの全体像から実装されているアルゴリズムまで，原典を挙げて解説する．数値計算手法の実装内容を正確に知ることは，ユーザにとってはモデルが備えるべき内容を理解し，結果を正しく解釈するために有用となる．また開発者にとっては，不必要な重複を避け，新しいブレークスルーを実現するための技術が何であるか，自らの創造性の発端を得るためにより重要な知識となるだろう．

• Access to Document (DOI)

Reconstitution of Developmental Dynamics of Mammalian Embryogenesis from 3D Confocal Microscope Images

KOBAYASHI Tetsuya, OZEKI Mitsunori, YAMAGATA Kazuo, Funahashi Akira

IEICE technical report. (The Institute of Electronics, Information and Communication Engineers)  114 ( 482 ) 1 - 6 2015.03

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0913-5685

　View Summary

Reconstruction of developmental dynamics of mammalian preimplantation embryos from bioimaging data by using image analysis is now becoming an important challenge in the fields of basic science and assisted reproductive technology. In this work, we firstly review the recent progress on the image analysis techniques to reconstruct cell lineage from bioimaging data, and then introduce our recent result on the tracking of developmental dynamics of mammalian embryo by using integer programing.

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

Tamura, Naoka, Simon, Judith E., Nayak, Arnab, Shenoy, Rajesh, Hiroi, Noriko, Boilot, Viviane, Funahashi, Akira, Draviam, Viji M.

BIOLOGY OPEN 4 ( 2 ) 155 - 169 2015.02

Research paper (scientific journal), Joint Work, Accepted,  ISSN  2046-6390

• Access to Document (DOI)

Bioimage Analysis for Quantitative Biology and Its Application to Mammalian Embryogenesis

KOBAYASHI Tetsuya J., BASHAR Md. Khayrul, FUNAHASHI Akira, FUJIMORI Toshihiko, YAMAGATA Kazuo

Medical Imaging Technology (The Japanese Society of Medical Imaging Technology)  33 ( 3 ) 84 - 89 2015

Joint Work, Accepted,  ISSN  0288450X

　View Summary

Driven by the rapid development of bioimaging, image analysis is now attracting much attention as the technology to extract quantitative information from bioimaging data. In this article, we briefly review recent applications of image analysis to bioimaging data, and introduce our ongoing research on the reconstruction of developmental dynamics of mammalian preimplantation embryos from bioimaging data.

• Access to Document (DOI)
• CiNii Research

増大特集 生命動態システム科学 Ⅰ.定量生物学 1.分子・細胞の計測 1)基本技術 (2)生命現象のシステムレベルでの理解に向けた基盤技術開発

舟橋 啓

生体の科学 (株式会社医学書院)  65 ( 5 ) 388 - 389 2014.10

Joint Work, Accepted,  ISSN  03709531

• Access to Document (DOI)
• CiNii Research

Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system

Takumi Hiraiwa, Tadamasa Kimura, Yuma Takenaka, Ryo Tanamoto, Hiroki Ota, Hiroshi Kimura, Yoshihiro Taguchi, Norihisa Miki, Yoshinori Matsumoto, Kotaro Oka, Akira Funahashi, Noriko Hiroi

IEEE 27th International Conference on Micro Electro Mechanical Systems (MEMS)    264 - 267 2014.01

Research paper (international conference proceedings), Joint Work, Accepted

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

Noriko Hiroi, Maciej Swat, Akira Funahashi

Frontiers in physiology (Frontiers Media SA)  5   128 2014

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1664-042X

• Access to Document (DOI)

Modeling and simulation using CellDesigner

Matsuoka Yukiko, Funahashi Akira, Ghosh Samik, Kitano Hiroaki

Methods in molecular biology (Clifton, N.J.) 1164   121 - 145 2014

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1064-3745

　View Summary

<p>In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN. </p>

• Access to Document (DOI)

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

Corrigan, Adam M., Shrestha, Roshan L., Zulkipli, Ihsan, Hiroi, Noriko, Liu, Yingjun, Tamura, Naoka, Yang, Bing, Patel, Jessica, Funahashi, Akira, Donald, Athene, Draviam, Viji M.

CELL CYCLE 12 ( 16 ) 2643 - 2655 2013.08

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1538-4101

• Access to Document (DOI)

in vivo oriented modeling with consideration of intracellular crowding

N Hiroi, K Iba, A Tabira, T Okuhara, T Kubojima, T Hiraiwa, T J Kobayashi, K Oka, A Funahashi

35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) 2013   2716 - 2719 2013.07

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  1557-170X

• Access to Document (DOI)

The systems biology simulation core algorithm

Keller, Roland, Doerr, Alexander, Tabira, Akito, Funahashi, Akira, Ziller, Michael J., Adams, Richard, Rodriguez, Nicolas, Le Novere, Nicolas, Hiroi, Noriko, Planatscher, Hannes, Zell, Andreas, Draeger, Andreas

BMC SYSTEMS BIOLOGY 7   2643 - 2655 2013.07

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1752-0509

• Access to Document (DOI)

LibSBMLSim: a reference implementation of fully functional SBML simulator

TAKIZAWA Hiromu, NAKAMURA Kazushige, TABIRA Akito, CHIKAHARA Yoichi, MATSUI Tatsuhiro, HIROI Noriko, FUNAHASHI Akira

BIOINFORMATICS 29 ( 11 ) 1474 - 1476 2013.06

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1367-4803

• Access to Document (DOI)

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

Viji M Draviam, Akira Funahashi, Noriko Hiroi, Akatsuki Kimura, Tetsuya J Kobayashi

Frontiers in physiology (Frontiers Media SA)  3   479 2013.01

Research paper (scientific journal), Joint Work, Accepted

• Access to Document (DOI)

Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms In Vivo

TAKIZAWA Hiromu, HIROI Noriko, FUNAHASHI Akira

PLOS ONE 7 ( 12 ) e51000 2012.12

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1932-6203

• Access to Document (DOI)

Software support for SBGN maps: SBGN-ML and LibSBGN

van Iersel, Martijn P., Villeger, Alice C., Czauderna, Tobias, Boyd, Sarah E., Bergmann, Frank T., Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I., Mi, Huaiyu, Moodie, Stuart L., Kitano, Hiroaki, Le Novere, Nicolas, Schreiber, Falk

BIOINFORMATICS 28 ( 15 ) 2016 - 2021 2012.08

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1367-4803

• Access to Document (DOI)