Moderator: Chris Evelo

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Chris Evelo10.0k
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Location:
Maastricht, The Netherlands
Website:
http://www.bigcat.unim...
Last seen:
3 years, 11 months ago
Joined:
8 years, 5 months ago
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Herding big cats at the department of Bioinformatics - BiGCaT at Maastricht University.

See my short CV at Academia.edu, my publication list is the best maintained one. Check twitter for my latest thoughts. My group's main services are all open source. They are here:

Posts by Chris Evelo

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Answer: A: Currency Metabolites in KEGG Metabolic Pathway Database
... I don't really know about how KEGG does it, but on WikiPathways it usually works the other way around. People add the main reactions and main metabolites simply because that is easier and gives a better overview. They can however add any metabolite they wish which indeed sometimes lead to inconsiste ...
written 4.1 years ago by Chris Evelo10.0k
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
... Note that the really stupid mistake here is a bit hidden "important files without backups" ...
written 4.1 years ago by Chris Evelo10.0k
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Answer: A: How to Normalize the Microarray Data Obtained from ncbi?
... If I understand you correctly you look at this study: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1739 For that study you can download the originally submitted data as "SOFT formatted family file(s)". That will normally contain raw data. Since this is Affymetrix that should include .cel fi ...
written 4.3 years ago by Chris Evelo10.0k
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Comment: C: what is applications of gene ranking except GSEA?
... Actually I would not say that that is what GSEA is. GSEA (gene set enrichment analysis) ranks sets of genes (typically from pathways or ontology classes) based on the (expression change) values of the genes in these sets.  So it ranks the sets not the genes, although it uses the gene ranks to derive ...
written 4.3 years ago by Chris Evelo10.0k
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Job: PhD student position: obesity related pathway and network biology at Maastricht University
... We are looking for a PhD student to understand disease development in obese persons using network biology approaches. 4 Year position at Maastricht University in the Netherlands. https://www.academictransfer.com/employer/UM/vacancy/27320/lang/en/#.VTS5EtSa4c8 ...
bioinformatics job network biology pathways written 4.3 years ago by Chris Evelo10.0k
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Comment: C: several gene names for a probeID in affymetrix annotation file
... Different things indeed. But the custom annotation from brainarray that I mentioned in my answer should solve both. ...
written 4.4 years ago by Chris Evelo10.0k
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Answer: A: several gene names for a probeID in affymetrix annotation file
... Yes, that is a common problem with Affymetrix probesets. They can often hit multiple genes that either share sequences covered by specific genes or probesets just turned out not to be as consistent as intended. Affymetrix is aware of that problem and documents it. You can even see a problem directly ...
written 4.4 years ago by Chris Evelo10.0k
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Answer: A: Pathway analysis for transcriptome profiles
... Our approach is unfortunately not in the article that seninp mentioned. But you can use PathVisio to analyse and visualise expression data on the WikiPathways curated pathway collection, the Reactome pathway set in WikiPathways format or a combination of both. ...
written 4.6 years ago by Chris Evelo10.0k
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Answer: A: Assigning Pathway Type to MSigDB gene sets
... At WikiPathways we use the Pathway Ontology to classify pathway. Since WikiPathways pathways are included in the MSigDB sets (or are at least they were last time I checked) that might be useful to you. Some other resources like Reactome do the same thing, or they use a mixture of the pathway ontolog ...
written 4.7 years ago by Chris Evelo10.0k
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Job: Various positions available for PhD students and postdocs in Maastricht (The Netherlands)
... The new Maastricht Centre for Systems Biology (MaCSBio) in the Netherlands has several positions available for PhD students and postdocs related to systems biology in general, biostatistics, network biology and modelling. The different positions and have different individual skill needs (and one PhD ...
systems biology modelling job network biology written 4.9 years ago by Chris Evelo10.0k

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Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Microarray Data Without Replicates. Any Hope To Get Something Out Of It?
Scholar 4.0 years ago, created an answer that has been accepted. For A: What happened with miRecords mirna database website ?
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Scholar 4.6 years ago, created an answer that has been accepted. For A: What happened with miRecords mirna database website ?
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Microarray Data Without Replicates. Any Hope To Get Something Out Of It?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For What Was The Best April Fools Joke Related To Bioinformatics You Saw?
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