Orhan Karsligil: Difference between revisions

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.

Resources

In this section I plan to collect some useful online resources.

My Paper Collection

I 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 News

Biology News Net is a very useful Biology News collection site.

Software

This site (http://bioinformatics.org/software/index.php3) has a long list of links to Bioinformatics software.

Online Databases

Here I will add the online Gene, Protein, Metabolite databases

Algorithms

Here I will add algorithm sites that might be useful for bioinformatics type of computations.

Research Groups

Research groups that I follow for interesting research.

Online Courses

Here I am planning to add links to some online course materials that I find very useful.

My Simple Blog

11/03/06

Done a presentation on Elementary Flux Modes
Starting on the code for Unsupervised Multiresolution Smoother (UMS)

<showhide> __HIDER__
<hide> Old days will go here </hide> </showhide>

My Research Ideas

Motif Search
1. Motifs with gaps
2. Motif search covering reversed sequences
3. Multiresolution Motif Search Algorithms
3D structure and motifs
1. Not shape but proximity motifs
2. 3D motifs with gaps
Specialized Clustering Algorithms
Multiscale Analysis of signals
1. Thresholding
2. Clustering
3. Trend analysis
4. Motif searches

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 Cell

Developed for Harvard Biology Classes. A very nice introduction of the inner workings of a cell...

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...

@@ Line 1: / Line 1: @@
 [[Image:orhan.jpg|frame|Dr. Orhan Karsligil [mailto://orhan@karsligil.com Orhan's email]]]
-==Bioinformatics News==
+==About Me==
-Following are news that I saw on internet on bioinformatics topics. I will try to keep this page uptodate. If you find interesting things please let me know by [mailto://okarsligil@gmail.com email]
-===March 28, 2006===
-===="Accelerated Evolution" Converts RNA Enzyme to DNA Enzyme In Vitro====
-Scientists at The Scripps Research Institute have successfully converted an RNA enzyme (ribozyme) into a DNA enzyme (deoxyribozyme) through a process of accelerated in vitro evolution. The molecular conversion or transfer of both genetic information and catalytic function between these two different genetic systems, which are both based on nucleic acid-like molecules, is exactly what many scientists believe occurred during the very earliest period of earth's existence.
-[http://www.scripps.edu/newsandviews/e_20060327/evo.html More on this story]
-===March 27, 2006===
-====New RNAi tools enable systematic studies of gene function====
-An international public-private research team led by scientists at the Broad Institute of MIT and Harvard announced today the construction and availability of an extensive library of molecular reagents to silence most human and mouse genes.
-[http://www.biologynews.net/archives/2006/03/24/new_rnai_tools_enable_systematic_studies_of_gene_function.html   More on this story]
-====Junk DNA may not be so junky after all====
-Researchers at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins have invented a cost-effective and highly efficient way of analyzing what many have termed "junk" DNA and identified regions critical for controlling gene function. And they have found that these control regions from different species don't have to look alike to work alike.
-[http://www.biologynews.net/archives/2006/03/24/junk_dna_may_not_be_so_junky_after_all.html More on this story]
-I created a page where I collect interesting (for me at least) bioinformatics information. The page can be found [http://openwetware.org/wiki/Okarsligil_news here].
-==Introduction==
 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.
+----
 <table>
 <tr>
@@ Line 53: / Line 36: @@
 </td>
 <td valign=top bgcolor=#CDDE95>
+==My Simple Blog==
+/03/06
+*Done a presentation on Elementary Flux Modes
+*Starting on the code for Unsupervised Multiresolution Smoother (UMS)
+<showhide>
+__HIDER__<br>
+<hide>
+Old days will go here
+</hide>
+</showhide>
 ==My Research Ideas==
-# test</td>
+#Motif Search
+##Motifs with gaps
+##Motif search covering reversed sequences
+##Multiresolution Motif Search Algorithms
+#3D structure and motifs
+##Not shape but proximity motifs
+##3D motifs with gaps
+#Specialized Clustering Algorithms
+#Multiscale Analysis of signals
+##Thresholding
+##Clustering
+##Trend analysis
+##Motif searches</td>
 </tr></table>
-</tr>
-<tr>
 <td>
 ==My Publications and Presentations==
 ===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===
-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==
+<table>
+<tr>
+<table><tr>
+<td bgcolor=#DEE8B8>
+===The Inner Life of the Cell===
+Developed for Harvard Biology Classes. A very nice introduction of the inner workings of a cell...
+<center><html><p><object width="425" height="350"><br />
+<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>
+</td>
+<td valign=top bgcolor=#CDDE95>
-“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)
+===Protein Synthesis===
- </td>
+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...
-</tr>
+<center>
-</table>
+<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></center>
+</td></tr></table>