Orhan Karsligil: Difference between revisions
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[[Image:orhan.jpg|frame|Dr. Orhan Karsligil [mailto://orhan@karsligil.com Orhan's email]]] | [[Image:orhan.jpg|frame|Dr. Orhan Karsligil [mailto://orhan@karsligil.com Orhan's email]]] | ||
== | ==About Me== | ||
I am a research scholar working in [http://openwetware.org/wiki/Stephanopoulos_Lab Prof. Gregory Stephanopoulos' lab]. I am mostly interested in complex networks and pattern discovery. You can read more on my background and previous research at my online [http://karsligil.homeip.net:8000/~okarsligil/wordpress/about-me/ resume] | I am a research scholar working in [http://openwetware.org/wiki/Stephanopoulos_Lab Prof. Gregory Stephanopoulos' lab]. I am mostly interested in complex networks and pattern discovery. You can read more on my background and previous research at my online [http://karsligil.homeip.net:8000/~okarsligil/wordpress/about-me/ resume] | ||
For now you can visit my blog at: [http://www.karsligil.com Orhan's Blog] for more information. I will update this site with my current research and research resources. | For now you can visit my blog at: [http://www.karsligil.com Orhan's Blog] for more information. I will update this site with my current research and research resources. | ||
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==My Simple Blog== | |||
11/03/06 | |||
*Done a presentation on Elementary Flux Modes | |||
*Starting on the code for Unsupervised Multiresolution Smoother (UMS) | |||
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__HIDER__<br> | |||
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Old days will go here | |||
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==My Research Ideas== | ==My Research Ideas== | ||
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##Motifs with gaps | ##Motifs with gaps | ||
##Motif search covering reversed sequences | ##Motif search covering reversed sequences | ||
##Multiresolution Motif Search Algorithms | |||
#3D structure and motifs | #3D structure and motifs | ||
##Not shape but proximity motifs | ##Not shape but proximity motifs | ||
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##Motif searches</td> | ##Motif searches</td> | ||
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==My Publications and Presentations== | ==My Publications and Presentations== | ||
===Current Work=== | ===Current Work=== | ||
Group Presentation, Literature Review on "Multidimensional Signatures in Antimicrobial Peptides". You can get the pdf for the presentation [http://okarsligil.googlepages.com/LR02162006.pdf from here]. | * Group Presentation, Literature Review on "Multidimensional Signatures in Antimicrobial Peptides". You can get the pdf for the presentation [http://okarsligil.googlepages.com/LR02162006.pdf from here]. | ||
* Review of Elementary Mode Analysis. A short summary. You can get the pdf for the summary from [http://www.openwetware.org/images/2/28/Elementary_Mode_Analysis.pdf here] | |||
** More detailed information for the presentation [[http://www.openwetware.org/wiki/Orhan_Karsligil:ElementaryModes]] | |||
* Multiscale Data Smoothing Algorithm (Draft). A multiscale thresholding strategy followed with an optimization step to minimize jumps in the data. You can find the description of the algorithm in the following [http://www.openwetware.org/images/2/2e/Multiscale_Data_Smoothing.pdf PDF presentation] | |||
===Process Design and Control Days=== | ===Process Design and Control Days=== | ||
Thesis under Prof. George Stephanopoulos on [https://dspace.mit.edu/bitstream/1721.1/16749/1/47663206.pdf “Multiscale Modeling, Identification, and Model Predictive Control of Processing Systems.”] (May 2000) | * Thesis under Prof. George Stephanopoulos on [https://dspace.mit.edu/bitstream/1721.1/16749/1/47663206.pdf “Multiscale Modeling, Identification, and Model Predictive Control of Processing Systems.”] (May 2000) | ||
“Multi-Scale Modeling, Estimation and Control of Processing Systems”, George Stephanopoulos, Matthew Dyer, and Orhan Karsligil, Computers and Chemical Engineering, 21, p. S797-S803 (1997) | * “Multi-Scale Modeling, Estimation and Control of Processing Systems”, George Stephanopoulos, Matthew Dyer, and Orhan Karsligil, Computers and Chemical Engineering, 21, p. S797-S803 (1997) | ||
“Multi-Scale Considerations in Linear and Nonlinear Estimation and Control”, George Stephanopoulos, Orhan Karsligil and Matthew Dyer, in Nonlinear Model-Based Control, R. Berber and C. Kravaris (editors), Kluwer (1998) | * “Multi-Scale Considerations in Linear and Nonlinear Estimation and Control”, George Stephanopoulos, Orhan Karsligil and Matthew Dyer, in Nonlinear Model-Based Control, R. Berber and C. Kravaris (editors), Kluwer (1998) | ||
“Multi-Scale Model-Predictive Control”, Orhan Karsligil, Matthew Dyer and George Stephanopoulos, Proceedings of DYCOPS-5, Kerkyra, Greece (1998) | * “Multi-Scale Model-Predictive Control”, Orhan Karsligil, Matthew Dyer and George Stephanopoulos, Proceedings of DYCOPS-5, Kerkyra, Greece (1998) | ||
* “Multi-scale Aspects in Model-Predictive Control”, George Stephanopoulos, Orhan Karsligil, and Matthew Dyer, Journal of Process Control, Vol: 10, Issue: 2-3, pp. 275-282 (2000) | |||
==Video Collection== | |||
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===The Inner Life of the Cell=== | |||
Developed for Harvard Biology Classes. A very nice introduction of the inner workings of a cell... | |||
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<param name="movie" value="http://www.youtube.com/v/5NDI0lojaeI"></param> | |||
<param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/5NDI0lojaeI" type="application/x-shockwave-flash" wmode="transparent" width="425" height="350"></embed></object></p></html></center> | |||
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===Protein Synthesis=== | |||
A video from 1971, done at UCSD... I believe this cannot be done anymore.. Nobody would participate... 35 years later I am curious what initiator one is doing... | |||
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<param name="movie" value="http://www.youtube.com/v/u9dhO0iCLww"></param><param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/u9dhO0iCLww" type="application/x-shockwave-flash" wmode="transparent" width="425" height="350"></embed></object></p></html></center> | |||
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Latest revision as of 15:15, 2 November 2006
About Me
I am a research scholar working in Prof. Gregory Stephanopoulos' lab. I am mostly interested in complex networks and pattern discovery. You can read more on my background and previous research at my online resume
For now you can visit my blog at: Orhan's Blog for more information. I will update this site with my current research and research resources.
ResourcesIn this section I plan to collect some useful online resources. My Paper CollectionI am using a site called CiteULike to keep track of all the papers I am reading or planning to read. One can tag papers, create bibliographies automatically and one can also upload the PDFs so that they can be retrieved anytime one desires. You can find my collection of papers (only the user can access the PDFs because of the copyright issues) at Orhan's Paper Collection Biology NewsBiology News Net is a very useful Biology News collection site. SoftwareThis site (http://bioinformatics.org/software/index.php3) has a long list of links to Bioinformatics software. Online DatabasesHere I will add the online Gene, Protein, Metabolite databases AlgorithmsHere I will add algorithm sites that might be useful for bioinformatics type of computations. Research GroupsResearch groups that I follow for interesting research. Online CoursesHere I am planning to add links to some online course materials that I find very useful. |
My Simple Blog11/03/06
<showhide>
__HIDER__ My Research Ideas
|
My Publications and Presentations
Current Work
- Group Presentation, Literature Review on "Multidimensional Signatures in Antimicrobial Peptides". You can get the pdf for the presentation from here.
- Review of Elementary Mode Analysis. A short summary. You can get the pdf for the summary from here
- More detailed information for the presentation [[1]]
- Multiscale Data Smoothing Algorithm (Draft). A multiscale thresholding strategy followed with an optimization step to minimize jumps in the data. You can find the description of the algorithm in the following PDF presentation
Process Design and Control Days
- Thesis under Prof. George Stephanopoulos on “Multiscale Modeling, Identification, and Model Predictive Control of Processing Systems.” (May 2000)
- “Multi-Scale Modeling, Estimation and Control of Processing Systems”, George Stephanopoulos, Matthew Dyer, and Orhan Karsligil, Computers and Chemical Engineering, 21, p. S797-S803 (1997)
- “Multi-Scale Considerations in Linear and Nonlinear Estimation and Control”, George Stephanopoulos, Orhan Karsligil and Matthew Dyer, in Nonlinear Model-Based Control, R. Berber and C. Kravaris (editors), Kluwer (1998)
- “Multi-Scale Model-Predictive Control”, Orhan Karsligil, Matthew Dyer and George Stephanopoulos, Proceedings of DYCOPS-5, Kerkyra, Greece (1998)
- “Multi-scale Aspects in Model-Predictive Control”, George Stephanopoulos, Orhan Karsligil, and Matthew Dyer, Journal of Process Control, Vol: 10, Issue: 2-3, pp. 275-282 (2000)
Video Collection
The Inner Life of the CellDeveloped for Harvard Biology Classes. A very nice introduction of the inner workings of a cell... <param name="movie" value="http://www.youtube.com/v/5NDI0lojaeI"></param> <param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/5NDI0lojaeI" type="application/x-shockwave-flash" wmode="transparent" width="425" height="350"></embed></object></p></html> |
Protein SynthesisA video from 1971, done at UCSD... I believe this cannot be done anymore.. Nobody would participate... 35 years later I am curious what initiator one is doing... <html><p><object width="425" height="350"><br /> <param name="movie" value="http://www.youtube.com/v/u9dhO0iCLww"></param><param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/u9dhO0iCLww" type="application/x-shockwave-flash" wmode="transparent" width="425" height="350"></embed></object></p></html> |