Satya Arjunan

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==Background==
==Background==
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I completed my PhD in Systems Biology at the [http://www.iab.keio.ac.jp/ Institute for Advanced Biosciences], Keio University in 2009. My thesis can be found [http://openwetware.org/images/b/bc/2009.arjunan.keio.pdf here]. I developed a multicompartmental spatiotemporal stochastic simulation algorithm, called [http://spatiocyte.org Spatiocyte], with applications in bacterial division site placement control. I am also a member of the [http://www.e-cell.org/ E-Cell Project]. In the past, I have worked on protein secondary structure prediction and distributed parallel computing. I completed my MSc in Computer Science and BEng in Electronics Engineering at Universiti Teknologi Malaysia.
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I completed my PhD in Systems Biology at the [http://www.iab.keio.ac.jp/ Institute for Advanced Biosciences], Keio University in 2009. My thesis can be found [http://openwetware.org/images/b/bc/2009.arjunan.keio.pdf here]. I developed a stochastic particle simulation method, called [http://spatiocyte.org Spatiocyte], with applications in bacterial division site placement control. I am also a member of the [http://www.e-cell.org/ E-Cell Project]. In the past, I have worked on protein secondary structure prediction and distributed parallel computing. I completed my MSc in Computer Science and BEng in Electronics Engineering at Universiti Teknologi Malaysia.
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Currently I am a postdoc at the RIKEN Quantitative Biology Center in Osaka, Japan.
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At present, I am a Research Scientist at the RIKEN Quantitative Biology Center in Osaka, Japan.
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==Journal Publications==
==Journal Publications==
My Google Scholar page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here].
My Google Scholar page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here].
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* Abdullah, A., Deris, S., Anwar, S. and '''Arjunan, S. N. V.''' (2013). An evolutionary Firefly Algorithm for the estimation of nonlinear biological model parameters. PLoS ONE. (in press)
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*'''Arjunan, S. N. V.''' and Takahashi, K. [http://dx.doi.org/10.1101/079293 Multi-algorithm particle simulations with Spatiocyte]. Methods in Molecular Biology. In press.
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*Watabe, M., '''Arjunan, S. N. V.''', Fukushima, S., Iwamoto, K., Kozuka, J., Matsuoka, S., Shindo, Y., Ueda, M. and Takahashi, K. (2015). [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130089 A Computational Framework for Bioimaging Simulation]. PLoS ONE 10(7): e0130089.
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* Shimo, H., '''Arjunan, S. N. V.''', Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., Tomita M. and Takahashi, K. (2015). [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004210 Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes]. PLoS Computational Biology 2015, 11:e1004210.
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* Abdullah, A., Deris, S., Anwar, S. and '''Arjunan, S. N. V.''' (2013). [http://dx.plos.org/10.1371/journal.pone.0056310 An evolutionary Firefly Algorithm for the estimation of nonlinear biological model parameters]. PLoS ONE 8(3): e56310.
*'''Arjunan, S. N. V.''' and Tomita, M. (2010). [http://www.springerlink.com/content/438375471t332vx6 A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation]. Systems and Synthetic Biology 4(1): 35-53 [http://www.springerlink.com/content/438375471t332vx6/fulltext.pdf pdf].
*'''Arjunan, S. N. V.''' and Tomita, M. (2010). [http://www.springerlink.com/content/438375471t332vx6 A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation]. Systems and Synthetic Biology 4(1): 35-53 [http://www.springerlink.com/content/438375471t332vx6/fulltext.pdf pdf].
*'''Arjunan, S. N. V.''' and Tomita, M. (2009). [http://precedings.nature.com/documents/3526/version/1 Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System]. International Journal of Computer Science and Information Security. 3(1): 211–216. [http://precedings.nature.com/documents/3526/version/1/files/npre20093526-1.pdf pdf]
*'''Arjunan, S. N. V.''' and Tomita, M. (2009). [http://precedings.nature.com/documents/3526/version/1 Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System]. International Journal of Computer Science and Information Security. 3(1): 211–216. [http://precedings.nature.com/documents/3526/version/1/files/npre20093526-1.pdf pdf]
*Yeo, Z. X., Wong, S. T., '''Arjunan, S. N. V.''', Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000776 Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions]. PLoS ONE 2(8): e776. [http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=3EA7966B9EA32BC46DFCD562DE1DCDB0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0000776&representation=PDF pdf]
*Yeo, Z. X., Wong, S. T., '''Arjunan, S. N. V.''', Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000776 Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions]. PLoS ONE 2(8): e776. [http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=3EA7966B9EA32BC46DFCD562DE1DCDB0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0000776&representation=PDF pdf]
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*Takahashi, K., '''Arjunan, S. N. V.''' and Tomita, M. (2005). [http://www.sciencedirect.com/science/article/pii/S0014579305001857 Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico]. FEBS Letters 579(8): 1783-1788. [http://www.e-cell.org/ecell/papers/takahashi2005.pdf pdf]
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*Takahashi, K., '''Arjunan, S. N. V.''' and Tomita, M. (2005). [http://www.sciencedirect.com/science/article/pii/S0014579305001857 Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico]. FEBS Letters 579(8): 1783-1788. [http://www.e-cell.org/ecell/papers/takahashi2005.pdf pdf],
==Books and Book Chapters==
==Books and Book Chapters==

Current revision

Image:satya.arjunan.png


Contents

Background

I completed my PhD in Systems Biology at the Institute for Advanced Biosciences, Keio University in 2009. My thesis can be found here. I developed a stochastic particle simulation method, called Spatiocyte, with applications in bacterial division site placement control. I am also a member of the E-Cell Project. In the past, I have worked on protein secondary structure prediction and distributed parallel computing. I completed my MSc in Computer Science and BEng in Electronics Engineering at Universiti Teknologi Malaysia.

At present, I am a Research Scientist at the RIKEN Quantitative Biology Center in Osaka, Japan.

Journal Publications

My Google Scholar page can be found here.

Books and Book Chapters

Contact

Satya Nanda Vel Arjunan
satya.arjunan@[].com [gmail]
Laboratory for Biochemical Simulation
RIKEN Quantitative Biology Center
OLABB, Osaka University
6-2-3, Furuedai, Suita
Osaka 565-0874, JAPAN
Phone: +81-6-6155-0111
http://www.qbic.riken.jp/english/index.html

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