Orhan Karsligil

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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]]]
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==Bioinformatics News==
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==About Me==
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Following are news that I saw on internet on bioinformatics topics. I will try to keep this page up to date. If you find interesting things please let me know by [mailto://okarsligil@gmail.com email]
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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]
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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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----
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<table>
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<tr>
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<table><tr>
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<td width=600px bgcolor=#DEE8B8>
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 +
==Resources==
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In this section I plan to collect some useful online resources.
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===My Paper Collection===
 +
I am using a site called [http://www.citeulike.org/ 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 [http://www.citeulike.org/user/okarsligil Orhan's Paper Collection]
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===Biology News===
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[http://www.biologynews.net/ Biology News Net] is a very useful Biology News collection site.
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===Software===
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[http://bioinformatics.org/software/index.php3 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.
 +
</td>
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<td valign=top bgcolor=#CDDE95>
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==My Simple Blog==
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11/03/06
 +
*Done a presentation on Elementary Flux Modes
 +
*Starting on the code for Unsupervised Multiresolution Smoother (UMS)
<showhide>
<showhide>
__HIDER__<br>
__HIDER__<br>
<hide>
<hide>
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===April 25, 2006===
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Old days will go here
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====Scientists design potent anthrax toxin inhibitor====
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</hide>
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Scientists funded by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), have engineered a powerful inhibitor of anthrax toxin that worked well in small-scale animal tests.
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</showhide>
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[http://www.biologynews.net/archives/2006/04/24/scientists_design_potent_anthrax_toxin_inhibitor.html More on this story]
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===April 24, 2006===
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==My Research Ideas==
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====Anthrax inhibitor counteracts toxin, may lead to new therapeutics====
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#Motif Search
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Researchers from Rensselaer Polytechnic Institute and the University of Toronto have designed a nanoscale assembly of molecules that successfully counteracts and inhibits anthrax toxin in animal and laboratory experiments. The novel approach used to neutralize anthrax toxin could be applied in designing potent therapeutics for a variety of pathogens and toxins, according to the researchers.
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##Motifs with gaps
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[http://www.biologynews.net/archives/2006/04/24/anthrax_inhibitor_counteracts_toxin_may_lead_to_new_therapeutics.html More on this story]
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##Motif search covering reversed sequences
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===April 23, 2006===
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##Multiresolution Motif Search Algorithms
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====A new and very potent antimicrobial compound has been discovered====
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#3D structure and motifs
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Scientists have discovered a bacteria-fighting compound 100 times more effective than penicillin - in wallaby milk.
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##Not shape but proximity motifs
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[http://www.smh.com.au/news/National/New-penicillin-found-in-wallaby-milk/2006/04/23/1145730796727.html More on this story]
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##3D motifs with gaps
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===April 22, 2006===
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#Specialized Clustering Algorithms
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====Newly discovered protein kills anthrax bacteria by exploding their cell walls====
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#Multiscale Analysis of signals
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Not all biological weapons are created equal. They are separated into categories A through C, category A biological agents being the scariest: They are easy to spread, kill effectively and call for special actions by the pubic health system. One of these worrisome organisms is anthrax, which has already received its fair share of media attention. But work in Vince Fischetti’s laboratory at Rockefeller University suggests that
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##Thresholding
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##Clustering
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##Trend analysis
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##Motif searches</td>
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</tr></table>
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<td>
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==My Publications and Presentations==
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===Current Work===
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* 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]
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** More detailed information for the presentation [[http://www.openwetware.org/wiki/Orhan_Karsligil:ElementaryModes]]
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* 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]
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===Process Design and Control Days===
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* 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)
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* “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)                   
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* “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)
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* “Multi-Scale Model-Predictive Control”, Orhan Karsligil, Matthew Dyer and George Stephanopoulos, Proceedings of DYCOPS-5, Kerkyra, Greece (1998)
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A bacterium's final gasp. A bacillus bacterium, a close relative of anthrax, begins to explode after being treated with PlyPH. The PlyPH protein, discovered by Rockefeller scientists, offers several advantages over existing anthrax treatments.
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* “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)
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a newly discovered protein could be used to fight anthrax infections and even decontaminate areas in which anthrax spores have been released.
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[http://newswire.rockefeller.edu/?page=engine&id=497 More on this story]
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===March 30, 2006===
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====Minimal genome should be twice the size, study shows====
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The simplest bacteria need almost twice as many genes to survive than scientists first believed, according to new research published in Nature (30 March 2006).
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[http://www.biologynews.net/archives/2006/03/29/minimal_genome_should_be_twice_the_size_study_shows.html More on this story]
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==Video Collection==
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===March 28, 2006===
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<table>
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===="Accelerated Evolution" Converts RNA Enzyme to DNA Enzyme In Vitro====
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<tr>
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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.
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<table><tr>
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<td bgcolor=#DEE8B8>
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[http://www.scripps.edu/newsandviews/e_20060327/evo.html More on this story]
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===The Inner Life of the Cell===
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===March 27, 2006===
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Developed for Harvard Biology Classes. A very nice introduction of the inner workings of a cell...
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====New RNAi tools enable systematic studies of gene function====
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<center><html><p><object width="425" height="350"><br />
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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.
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<param name="movie" value="http://www.youtube.com/v/5NDI0lojaeI"></param>
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<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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</td>
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<td valign=top bgcolor=#CDDE95>
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[http:/
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===Protein Synthesis===
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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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<center>
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<html><p><object width="425" height="350"><br />
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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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</td></tr></table>

Current revision

Dr. Orhan Karsligil Orhan's email
Dr. Orhan Karsligil Orhan's email

Contents

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

  1. Motif Search
    1. Motifs with gaps
    2. Motif search covering reversed sequences
    3. Multiresolution Motif Search Algorithms
  2. 3D structure and motifs
    1. Not shape but proximity motifs
    2. 3D motifs with gaps
  3. Specialized Clustering Algorithms
  4. 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

  • “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...


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