Moderator: Chris Evelo

gravatar for Chris Evelo
Chris Evelo9.9k
Reputation:
9,890
Status:
Trusted
Location:
Maastricht, The Netherlands
Website:
http://www.bigcat.unim...
Last seen:
2 years ago
Joined:
6 years, 6 months ago
Email:
c**********@gmail.com

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

<prev • 575 results • page 1 of 58 • next >
1
vote
2
answers
775
views
2
answers
Answer: A: Is there or why isn't there or when is there a glossary database including all b
... Well the problem with standards is in general that there are too many of them. But we do of course have resources for biological terms that try to combine the various controlled vocabulary and ontology initiatives. The two main ones are NCBO (the US center for Biomedical ontologies) at http://www.bi ...
written 2.1 years ago by Chris Evelo9.9k
1
vote
4
answers
902
views
4
answers
Comment: C: Protein location by gene name
... I am not sure about Protein Atlas. We actually downloaded some of the data they use for our own TissueAnalyzer on WIkiPathways. So you definitely download the data and use it locally and do your own queries, but they might support online queries too.  NeXtProt definitely offers a SPARQL endpoint (t ...
written 2.1 years ago by Chris Evelo9.9k
3
votes
4
answers
902
views
4
answers
Answer: A: Protein location by gene name
... You could use data from the human protein atlas or neXtProt for this.   ...
written 2.1 years ago by Chris Evelo9.9k
1
vote
2
answers
789
views
2
answers
Answer: A: How to handle the problem of one probe set ID mapping to several genes in HG-U1
... Yes there is. The common way to solve this is to use alternative probeset annotations. These are available as custom .cdf files from the brain array website. These custom cdf files solve a number of other problems with bad probes too.   One easy way to use these is via our arrayanalysis.org service ...
written 2.1 years ago by Chris Evelo9.9k
0
votes
1
answer
623
views
1
answers
Answer: A: In a probe cell ,the probe IDs are all the same?
... I think your questions is about probe sets on Affymetrix microarrays, right? And the question is whether all probes in a probeset are the same? No they are not. The trick is that every probe targets a different part of the RNA and has different specific binding properties  (and sometimes different s ...
written 2.1 years ago by Chris Evelo9.9k
0
votes
2
answers
759
views
2
answers
Answer: A: identification of single pathway from microarray data
... This  is the inverse of this question: How To Find The Pathways In Which A Given Gene Or Protein Is Involved?  You are looking for genes in a pathway while there the question was to find pathways for a gene. Since most tools that can do one of these things also can do the other you might want to ch ...
written 2.1 years ago by Chris Evelo9.9k
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Strand Specificity of Arrays and RNAseq
... Especially for older microarrays @seidel's answer is correct in principle but in practice often translates to "should be strand-specific". Microarray reporters were often found to be less well targeted than intended; hitting the wrong gene, hitting multiple genes and indeed sometimes targeting the w ...
written 2.1 years ago by Chris Evelo9.9k
0
votes
6
answers
9.1k
views
6
answers
Comment: C: How To Find The Pathways In Which A Given Gene Or Protein Is Involved?
... It is a good idea to check the latest update date of DAVID before you use that. Currently that is from January 2010. ...
written 2.1 years ago by Chris Evelo9.9k
2
votes
2
answers
1.5k
views
2
answers
Answer: A: Biological Pathways And Drug Designing
... While @Giovanni's answer is correct I can add a bit more information about what we were actually asked to do around WikiPathways by pharma. By making WikiPathways content available as RDF we were able to load in the Open PHACTS linked data resource. In this way you can immediately look for things ...
written 2.2 years ago by Chris Evelo9.9k
0
votes
2
answers
1.4k
views
2
answers
Answer: A: Illumina Sentrix Beads Arrays
... We have combined different Bioconductor packages for QC, normalisation, statistics of Illumina bead arrays with a pathway analysis approach in PathVisio using RPC access to that. That pipeline now is part of arrayanalysis.org. We recently described it in this paper. ...
written 2.2 years ago by Chris Evelo9.9k

Latest awards to Chris Evelo

Teacher 2.1 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 2.1 years ago, created an answer that has been accepted. For A: What happened with miRecords mirna database website ?
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: How To Pronounce "De Bruijn"?
Teacher 2.7 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 2.7 years ago, created an answer that has been accepted. For A: What happened with miRecords mirna database website ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For What Was The Best April Fools Joke Related To Bioinformatics You Saw?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Do You Know Any People Doing Bioinformatics For Microbial Ecology Studies?
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: Why Should I Use Galaxy ?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Will A Masters In Bioinformatics Help Me In Getting A Job?
Cylon 3.1 years ago, received 1,000 up votes.
Scholar 3.1 years ago, created an answer that has been accepted. For A: What happened with miRecords mirna database website ?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Which programming language to integrate several open source software into one wo
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Appreciated 3.3 years ago, created a post with more than 5 votes. For Any Experiences/Solutions For Problems With The Last R Update?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For What Was The Best April Fools Joke Related To Bioinformatics You Saw?
Centurion 4.7 years ago, created 100 posts.
Supporter 4.7 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1474 users visited in the last hour