Satya Arjunan: Difference between revisions
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==Background== | ==Background== | ||
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 | 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. | ||
At present, I am a Research Scientist at the RIKEN Quantitative Biology Center in Osaka, Japan. | |||
==Journal Publications== | ==Journal Publications== | ||
My Google Scholar | My Google Scholar page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here]. | ||
*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 Takahashi, K. [http://dx.doi.org/10.1101/079293 Multi-algorithm particle simulations with Spatiocyte]. Methods in Molecular Biology. In press. | ||
*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] | *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. | ||
*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] | * 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. | ||
*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] | * 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. (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] | |||
*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== | ||
*Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. (2010). [http://books.google.com/books?id=zCqHswQYAfgC&lpg=PT6&pg=PT363#v=onepage&q=&f=false In silico models for metabolic 'systems' engineering]. In: The Metabolic Pathway Engineering Handbook: Tools and Applications, Smolke, C. D., Palsson, B. and Lee, S. Y. (editors). CRC Press (Boca Raton, FL). [http://openwetware.org/images/b/b4/2010.selvarajoo.chapter.crc.press.pdf pdf] | *Selvarajoo, K., '''Arjunan, S. N. V.''' and Tomita, M. (2010). [http://books.google.com/books?id=zCqHswQYAfgC&lpg=PT6&pg=PT363#v=onepage&q=&f=false In silico models for metabolic 'systems' engineering]. In: The Metabolic Pathway Engineering Handbook: Tools and Applications, Smolke, C. D., Palsson, B. and Lee, S. Y. (editors). CRC Press (Boca Raton, FL). [http://openwetware.org/images/b/b4/2010.selvarajoo.chapter.crc.press.pdf pdf] | ||
*Arjunan, S. N. V. ( | *'''Arjunan, S. N. V.''' (2013). [http://www.ncbi.nlm.nih.gov/books/NBK84261/ A guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System]. In: E-Cell System: Basic Concepts and Applications, Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). Landes Bioscience and Springer Science+Business Media. [http://openwetware.org/images/0/05/2012.arjunan.chapter.landes.bioscience.pdf pdf] | ||
*Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). [http://www.landesbioscience.com/books/iu/id/953/?nocache=2071954650 E-Cell System: Basic Concepts and Applications]. Landes Bioscience and Springer Science+Business Media. | *'''Arjunan, S. N. V.''', Dhar, P. K. and Tomita, M. (editors). (2013). [http://www.landesbioscience.com/books/iu/id/953/?nocache=2071954650 E-Cell System: Basic Concepts and Applications]. Landes Bioscience and Springer Science+Business Media. | ||
==Contact== | ==Contact== | ||
Revision as of 18:29, 5 October 2016
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.
- Arjunan, S. N. V. and Takahashi, K. Multi-algorithm particle simulations with Spatiocyte. Methods in Molecular Biology. In press.
- Watabe, M., Arjunan, S. N. V., Fukushima, S., Iwamoto, K., Kozuka, J., Matsuoka, S., Shindo, Y., Ueda, M. and Takahashi, K. (2015). A Computational Framework for Bioimaging Simulation. PLoS ONE 10(7): e0130089.
- Shimo, H., Arjunan, S. N. V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., Tomita M. and Takahashi, K. (2015). Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS Computational Biology 2015, 11:e1004210.
- 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 8(3): e56310.
- Arjunan, S. N. V. and Tomita, M. (2010). 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 pdf.
- Arjunan, S. N. V. and Tomita, M. (2009). 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. pdf
- Yeo, Z. X., Wong, S. T., Arjunan, S. N. V., Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions. PLoS ONE 2(8): e776. pdf
- Takahashi, K., Arjunan, S. N. V. and Tomita, M. (2005). Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico. FEBS Letters 579(8): 1783-1788. pdf,
Books and Book Chapters
- Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. (2010). In silico models for metabolic 'systems' engineering. In: The Metabolic Pathway Engineering Handbook: Tools and Applications, Smolke, C. D., Palsson, B. and Lee, S. Y. (editors). CRC Press (Boca Raton, FL). pdf
- Arjunan, S. N. V. (2013). A guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System. In: E-Cell System: Basic Concepts and Applications, Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). Landes Bioscience and Springer Science+Business Media. pdf
- Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). (2013). E-Cell System: Basic Concepts and Applications. Landes Bioscience and Springer Science+Business Media.
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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