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 Senior Scientific Software Engineer at the Victor Chang Cardiac Research Institute in Sydney and a Visiting Scientist at the RIKEN Center for Biosystems Dynamics Research in Osaka. | |||
==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]. | ||
* 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 | *Watabe, M., Yoshimura, H., '''Arjunan, S. N. V.''', Kaizu, K. & Takahashi, K. (2020). [https://doi.org/10.1103/PhysRevE.102.032413 Signaling activations through G-protein-coupled-receptor aggregations]. Physical Review E 102: 032413 | ||
*'''Arjunan, S. N. V.''' and Tomita, M. (2010). [ | *'''Arjunan, S. N. V.''', Miyauchi, A., Iwamoto, K. & Takahashi, K. (2020). [https://doi.org/10.1186/s12859-019-3338-8 pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems]. BMC Bioinformatics 21, 33. | ||
*Watabe, M., '''Arjunan, S. N. V.''', Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). [https://doi.org/10.1103/PhysRevE.100.062407 Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization]. Physical Review E 100, 062407 | |||
*Watabe, M., '''Arjunan, S. N. V.''', Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). [https://doi.org/10.1103/PhysRevE.100.010402 Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements]. Physical Review E 100, 010402(R) | |||
*Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and '''Arjunan, S. N. V.''' (2019). [https://doi.org/10.1103/PhysRevE.99.042411 Surface reaction-diffusion kinetics on lattice at the microscopic scale]. Physical Review E 99, 042411 | |||
*Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and '''Arjunan, S. N. V.''' (2018). [https://doi.org/10.1103/PhysRevE.98.032418 Reaction-diffusion kinetics on lattice at the microscopic scale]. Physical Review E 98: 032418. | |||
*'''Arjunan, S. N. V.''' and Takahashi, K. (2017) [https://doi.org/10.1007/978-1-4939-7015-5_16 Multi-algorithm particle simulations with Spatiocyte]. Methods in Molecular Biology, 1611: 219-236. | |||
*Watabe, M., '''Arjunan, S. N. V.''', Fukushima, S., Iwamoto, K., Kozuka, J., Matsuoka, S., Shindo, Y., Ueda, M. and Takahashi, K. (2015). [https://doi.org/10.1371/journal.pone.0130089 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). [https://doi.org/10.1371/journal.pcbi.1004210 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). [https://doi.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). [https://doi.org/10.1007/s11693-009-9047-2 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). [ | *Yeo, Z. X., Wong, S. T., '''Arjunan, S. N. V.''', Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). [https://doi.org/10.1371/journal.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). [ | *Takahashi, K., '''Arjunan, S. N. V.''' and Tomita, M. (2005). [https://doi.org/10.1016/j.febslet.2005.01.072 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). [ | *'''Arjunan, S. N. V.''', Dhar, P. K. and Tomita, M. (editors). (2013). [https://link.springer.com/book/10.1007%2F978-1-4614-6157-9 E-Cell System: Basic Concepts and Applications]. Landes Bioscience and Springer Science+Business Media. | ||
==Contact== | ==Contact== | ||
Satya Nanda Vel Arjunan <br> | Satya Nanda Vel Arjunan <br> | ||
satya.arjunan@[].com [gmail] <br> | satya.arjunan@[].com [gmail] <br> | ||
<font size=1> | <font size=1> |
Latest revision as of 14:39, 13 February 2024
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 Senior Scientific Software Engineer at the Victor Chang Cardiac Research Institute in Sydney and a Visiting Scientist at the RIKEN Center for Biosystems Dynamics Research in Osaka.
Journal Publications
My Google Scholar page can be found here.
- Watabe, M., Yoshimura, H., Arjunan, S. N. V., Kaizu, K. & Takahashi, K. (2020). Signaling activations through G-protein-coupled-receptor aggregations. Physical Review E 102: 032413
- Arjunan, S. N. V., Miyauchi, A., Iwamoto, K. & Takahashi, K. (2020). pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems. BMC Bioinformatics 21, 33.
- Watabe, M., Arjunan, S. N. V., Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization. Physical Review E 100, 062407
- Watabe, M., Arjunan, S. N. V., Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements. Physical Review E 100, 010402(R)
- Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and Arjunan, S. N. V. (2019). Surface reaction-diffusion kinetics on lattice at the microscopic scale. Physical Review E 99, 042411
- Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and Arjunan, S. N. V. (2018). Reaction-diffusion kinetics on lattice at the microscopic scale. Physical Review E 98: 032418.
- Arjunan, S. N. V. and Takahashi, K. (2017) Multi-algorithm particle simulations with Spatiocyte. Methods in Molecular Biology, 1611: 219-236.
- 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]
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