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

Yamada TG, Hiki Y, Hiroi NF, Shagimardanova E, Gusev O, Cornette R, Kikawada T, Funahashi A.

PLoS One. 2020 Mar 19;15(3):e0230218. doi: 10.1371/journal.pone.0230218. eCollection 2020.


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

Ii K, Mashimo K, Ozeki M, Yamada TG, Hiroi N, Funahashi A.

Front Genet. 2019 Oct 22;10:1027. doi: 10.3389/fgene.2019.01027. eCollection 2019.


Predicting the future direction of cell movement with convolutional neural networks.

Nishimoto S, Tokuoka Y, Yamada TG, Hiroi NF, Funahashi A.

PLoS One. 2019 Sep 4;14(9):e0221245. doi: 10.1371/journal.pone.0221245. eCollection 2019.


mRNA Therapy Improves Metabolic and Behavioral Abnormalities in a Murine Model of Citrin Deficiency.

Cao J, An D, Galduroz M, Zhuo J, Liang S, Eybye M, Frassetto A, Kuroda E, Funahashi A, Santana J, Mihai C, Benenato KE, Kumarasinghe ES, Sabnis S, Salerno T, Coughlan K, Miracco EJ, Levy B, Besin G, Schultz J, Lukacs C, Guey L, Finn P, Furukawa T, Giangrande PH, Saheki T, Martini PGV.

Mol Ther. 2019 Jul 3;27(7):1242-1251. doi: 10.1016/j.ymthe.2019.04.017. Epub 2019 Apr 23.


Spatiotemporal observations of light propagation in multiple polarization states.

Inoue T, Matsunaka A, Funahashi A, Okuda T, Nishio K, Awatsuji Y.

Opt Lett. 2019 Apr 15;44(8):2069-2072. doi: 10.1364/OL.44.002069.


Pivotal role of inter-organ aspartate metabolism for treatment of mitochondrial aspartate-glutamate carrier 2 (citrin) deficiency, based on the mouse model.

Saheki T, Moriyama M, Kuroda E, Funahashi A, Yasuda I, Setogawa Y, Gao Q, Ushikai M, Furuie S, Yamamura KI, Takano K, Nakamura Y, Eto K, Kadowaki T, Sinasac DS, Furukawa T, Horiuchi M, Tai YH.

Sci Rep. 2019 Mar 12;9(1):4179. doi: 10.1038/s41598-019-39627-y.


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

Hiraiwa T, Yamada TG, Miki N, Funahashi A, Hiroi N.

J R Soc Interface. 2019 Mar 29;16(152):20180934. doi: 10.1098/rsif.2018.0934.


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

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

Sci Rep. 2018 Dec 18;8(1):17941. doi: 10.1038/s41598-018-36124-6.


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

Hiraiwa T, Nakai Y, Yamada TG, Tanimoto R, Kimura H, Matsumoto Y, Miki N, Hiroi N, Funahashi A.

FEBS Open Bio. 2018 Nov 9;8(12):1920-1935. doi: 10.1002/2211-5463.12525. eCollection 2018 Dec.


Ubiquitous distribution of fluorescent protein in muscles of four species and two subspecies of eel (genus Anguilla).

Funahashi A, Itakura T, Hassanin Abeer AI, Komatsu M, Hayashi S, Kaminishi Y.

J Genet. 2017 Mar;96(1):127-133.


Editorial: Quantitative Biology: Dynamics of Living Systems.

Hiroi N, Draviam VM, Funahashi A.

Front Physiol. 2016 Jun 2;7:196. doi: 10.3389/fphys.2016.00196. eCollection 2016. No abstract available.


Detection of Temperature Difference in Neuronal Cells.

Tanimoto R, Hiraiwa T, Nakai Y, Shindo Y, Oka K, Hiroi N, Funahashi A.

Sci Rep. 2016 Mar 1;6:22071. doi: 10.1038/srep22071.


Simulation technology and its application in Systems Biology.

Funahashi A, Hiroi N.

Nihon Yakurigaku Zasshi. 2016 Feb;147(2):101-6. doi: 10.1254/fpj.147.101. Review. Japanese. No abstract available.


Eel green fluorescent protein is associated with resistance to oxidative stress.

Funahashi A, Komatsu M, Furukawa T, Yoshizono Y, Yoshizono H, Orikawa Y, Takumi S, Shiozaki K, Hayashi S, Kaminishi Y, Itakura T.

Comp Biochem Physiol C Toxicol Pharmacol. 2016 Mar-Apr;181-182:35-9. doi: 10.1016/j.cbpc.2015.12.009. Epub 2015 Dec 30.


Lysosomal localization of Japanese medaka (Oryzias latipes) Neu1 sialidase and its highly conserved enzymatic profiles with human.

Ryuzono S, Takase R, Oishi K, Ikeda A, Chigwechokha PK, Funahashi A, Komatsu M, Miyagi T, Shiozaki K.

Gene. 2016 Jan 10;575(2 Pt 2):513-523. doi: 10.1016/j.gene.2015.09.028. Epub 2015 Oct 8.


The principles of whole-cell modeling.

Karr JR, Takahashi K, Funahashi A.

Curr Opin Microbiol. 2015 Oct;27:18-24. doi: 10.1016/j.mib.2015.06.004. Epub 2015 Jun 24. Review.


Acceleration of discrete stochastic biochemical simulation using GPGPU.

Sumiyoshi K, Hirata K, Hiroi N, Funahashi A.

Front Physiol. 2015 Feb 13;6:42. doi: 10.3389/fphys.2015.00042. eCollection 2015.


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

Nakai Y, Ozeki M, Hiraiwa T, Tanimoto R, Funahashi A, Hiroi N, Taniguchi A, Nonaka S, Boilot V, Shrestha R, Clark J, Tamura N, Draviam VM, Oku H.

Rev Sci Instrum. 2015 Jan;86(1):013707. doi: 10.1063/1.4905330.


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

Tamura N, Simon JE, Nayak A, Shenoy R, Hiroi N, Boilot V, Funahashi A, Draviam VM.

Biol Open. 2015 Jan 16;4(2):155-69. doi: 10.1242/bio.201410413.


Modeling and simulation using CellDesigner.

Matsuoka Y, Funahashi A, Ghosh S, Kitano H.

Methods Mol Biol. 2014;1164:121-45. doi: 10.1007/978-1-4939-0805-9_11.


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

Hiroi N, Swat M, Funahashi A.

Front Physiol. 2014 Apr 4;5:128. doi: 10.3389/fphys.2014.00128. eCollection 2014.


In vivo oriented modeling with consideration of intracellular crowding.

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

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2716-9. doi: 10.1109/EMBC.2013.6610101.


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

Corrigan AM, Shrestha RL, Zulkipli I, Hiroi N, Liu Y, Tamura N, Yang B, Patel J, Funahashi A, Donald A, Draviam VM.

Cell Cycle. 2013 Aug 15;12(16):2643-55. doi: 10.4161/cc.25671. Epub 2013 Jul 16.


Brief report: the smiles of a child with autism spectrum disorder during an animal-assisted activity may facilitate social positive behaviors--quantitative analysis with smile-detecting interface.

Funahashi A, Gruebler A, Aoki T, Kadone H, Suzuki K.

J Autism Dev Disord. 2014 Mar;44(3):685-93. doi: 10.1007/s10803-013-1898-4.


The systems biology simulation core algorithm.

Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A.

BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55.


LibSBMLSim: a reference implementation of fully functional SBML simulator.

Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157. Epub 2013 Apr 5.


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

Draviam VM, Funahashi A, Hiroi N, Kimura A, Kobayashi TJ.

Front Physiol. 2013 Jan 11;3:479. doi: 10.3389/fphys.2012.00479. eCollection 2012. No abstract available.


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

Takizawa H, Hiroi N, Funahashi A.

PLoS One. 2012;7(12):e51000. doi: 10.1371/journal.pone.0051000. Epub 2012 Dec 20.


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

Hiroi N, Okuhara T, Kubojima T, Iba K, Tabira A, Yamashita S, Okada Y, Kobayashi TJ, Funahashi A.

Front Physiol. 2012 Jul 23;3:293. doi: 10.3389/fphys.2012.00293. eCollection 2012.


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

Hiroi1 N, Klann M, Iba K, Heras Ciechomski Pd, Yamashita S, Tabira A, Okuhara T, Kubojima T, Okada Y, Oka K, Mange R, Unger M, Funahashi A, Koeppl H.

EURASIP J Bioinform Syst Biol. 2012 Jun 26;2012:7.


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

van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.

Bioinformatics. 2012 Aug 1;28(15):2016-21. Epub 2012 May 10.


[Relationship between performance rating and risk of low back pain in manufacturing line workers].

Higuchi Y, Funahashi A, Izumi H, Kumashinro M.

J UOEH. 2012 Mar 1;34(1):47-55. Japanese.


Cytochrome P450 1C1 complementary DNA cloning, sequence analysis and constitutive expression induced by benzo-a-pyrene in Nile tilapia (Oreochromis niloticus).

Hassanin AA, Kaminishi Y, Funahashi A, Itakura T.

Aquat Toxicol. 2012 Mar;109:17-24. doi: 10.1016/j.aquatox.2011.11.012. Epub 2011 Dec 1.


BioPAX support in CellDesigner.

Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD.

Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21.


Physiological environment induces quick response - slow exhaustion reactions.

Hiroi N, Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Oka K, Köhler G, Funahashi A.

Front Physiol. 2011 Sep 21;2:50. doi: 10.3389/fphys.2011.00050. eCollection 2011.


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

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.


The Systems Biology Graphical Notation.

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.

Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.


Limitations on work and attendance rates after employees with cancer returned to work at a single manufacturing company in Japan.

Ohguri T, Narai R, Funahashi A, Nishiura C, Yamashita T, Yarita K, Korogi Y.

J Occup Health. 2009;51(3):267-72. Epub 2009 Mar 19.


Psycho-educational Horseback Riding to Facilitate Communication Ability of Children with Pervasive Developmental Disorders.

Keino H, Funahashi A, Keino H, Miwa C, Hosokawa M, Hayashi Y, Kawakita K.

J Equine Sci. 2009;20(4):79-88. doi: 10.1294/jes.20.79. Epub 2010 Jan 19.


The effect of smoking prevalence at worksites on individual cessation behavior.

Nishiura C, Narai R, Ohguri T, Funahashi A, Yarita K, Hashimoto H.

J Occup Health. 2009;51(1):48-56. Epub 2008 Dec 5.


Integration of CellDesigner and SABIO-RK.

Funahashi A, Jouraku A, Matsuoka Y, Kitano H.

In Silico Biol. 2007;7(2 Suppl):S81-90.


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

Nordling TE, Hiroi N, Funahashi A, Kitano H.

Mol Biosyst. 2007 Aug;3(8):523-9. Epub 2007 Jun 27.


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

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.


A comprehensive pathway map of epidermal growth factor receptor signaling.

Oda K, Matsuoka Y, Funahashi A, Kitano H.

Mol Syst Biol. 2005;1:2005.0010. Epub 2005 May 25.


Using process diagrams for the graphical representation of biological networks.

Kitano H, Funahashi A, Matsuoka Y, Oda K.

Nat Biotechnol. 2005 Aug;23(8):961-6.


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

Funahashi A.

Tanpakushitsu Kakusan Koso. 2003 Jun;48(7):810-6. Review. Japanese. No abstract available.


[Comparison of the effects of accelerated heavy ions and X-rays on the development of rat brain].

Inouye M, Funahashi A, Nakamura E, Takahashi S, Kubota Y, Takagishi Y, Hayasaka S, Murata Y.

Biol Sci Space. 1998 Nov;12(3):188-9. Japanese. No abstract available.


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