User: emekdemir

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emekdemir100
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Posts by emekdemir

<prev • 9 results • page 1 of 1 • next >
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Job: Pack your bags and move to Portland!! Multiple network biology/pathway informatics positions at OHSU
... Do you think that biology needs better models and better software tools? Are you interested in computational approaches to medicine? If your answer is yes, we might have a great position for you! We are looking for individuals who are passionate about making a positive impact to medicine through co ...
pathways system biology jobs networks omics written 3.5 years ago by emekdemir100
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Job: Software Engineer in MSKCC Computational Biology
... Join a computational and systems biology group, collaborate with a creative team of scientists and engineers, facilitate basic research and potential innovation in cancer therapy. Design and build solutions to turn complex data into knowledge and to turn knowledge into clinical decision support. Sei ...
bioinformatics job network biology written 4.3 years ago by emekdemir100
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Answer: A: What is your opinion on the network score of IPA (Ingenuity Pathway Analysis) an
... Unfortunately IPA has been completely opaque about its algorithms and their multiple hypothesis testing seems to be iffy at best... use with extreme caution.. ...
written 4.4 years ago by emekdemir100
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Answer: A: A question about rBiopaxParser
... Hi Nafiseh, If you can post the owl files I might guess what the problem might be. I am suspecting nested pathways. But I don't develop/use rBioPAXParser so they would be at best guesses. I also want to point out that there is another R library for acessing Pathways in BioPAX form - it is called P ...
written 4.4 years ago by emekdemir100
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Answer: A: How do we browse different data from the same sample from TCGA ?
... You also might want to look at the cbioportal.org ...
written 4.6 years ago by emekdemir100
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Answer: A: Is there any resource annotating protein function within a pathway?
... What you are exploring is a simplified view, geared toward mostly genomic use-cases - PC contains detailed information about the actual reactions between proteins. You can use Chibe to fully explore them: http://www.biomedcentral.com/1471-2164/15/642 As with the protein structure properties I am no ...
written 4.6 years ago by emekdemir100
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Answer: A: Is there any resource annotating protein function within a pathway?
... Hi, Would pathwaycommmons.org webservices would help? Also would you elaborate a bit more on your use case? What do you expect in terms of the  "role annotation" ? A controlled vocabulary term? What would be some example terms?   Best, ED     ...
written 4.6 years ago by emekdemir100
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Answer: A: How to find genes that are involved in particular pathway ?
... If you have the uniprot identifiers try this PathwayCommons webservice: http://www.pathwaycommons.org/pc2/traverse?uri=http://identifiers.org/uniprot/P38398&path=ProteinReference/entityReferenceOf:Protein/participantOf/pathwayComponentOf/name If you play with the url you will find out that the ...
written 4.6 years ago by emekdemir100
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Answer: A: Is There A Web-Server Or Software That Can Create A Network Between Given Signal
... Yes there is .. You can use PathwayCommons graph searches. http://www.pathwaycommons.org/pc2/#graph You can seed the paths-between search with the pathway members of 2 pathways. I'd suggest limiting yourself to a distance of 1 or 2 as chances are you will get a huge network back. For more quest ...
written 5.2 years ago by emekdemir100

Latest awards to emekdemir

Appreciated 4.3 years ago, created a post with more than 5 votes. For Software Engineer in MSKCC Computational Biology
Scholar 4.4 years ago, created an answer that has been accepted. For A: A question about rBiopaxParser

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