Orhan Karsligil

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)

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... <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>

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.... <html><object width="425" height="350"><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></html>