User: Arnaud Ceol

gravatar for Arnaud Ceol
Arnaud Ceol730
Reputation:
730
Status:
Trusted
Location:
Milan, Italy
Website:
http://arnaudceol.word...
Twitter:
arnaudceolpro
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
5 years, 10 months ago
Email:
a**************@gmail.com

With a degree in computer sciences and a specialization in bioinformatics, I developed during a PhD in Molecular and Cellular Biology several databases and tools for the storage and manipulation of Molecular Interaction (MI) data (MINT, Domino, HomoMINT, etc.). This has been possible through an active participation in International consortium like the Protein Standard Initative (PSI-MI) and the International Molecular Exchange consortium (imex).

In the Structural Bioinformatics and Network Biology group, I used this experience in the field of network biology, for instance to identify novel drug targets in Gram-negative bacteria.

At the Italian Institute of Technology, I'm now focusing on the development of tools and servers for the analyses of genomic data.

Posts by Arnaud Ceol

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Mutation processing by cbioportal
... Thanks, I found the post you mention https://www.biostars.org/p/220922/. My question is therefore some king of duplicate. I had also seen the doc in the cbioportal's faq, but unfortunately it doesn't say a lot about how the data is processed. My guess is that cbioportal shows all mutations identif ...
written 17 hours ago by Arnaud Ceol730
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Answer: A: miRNA and mRNA
... If you are interested in cancer, you can check the GDC portal: it contains both. https://portal.gdc.cancer.gov/search/s?facetTab=files ...
written 1 day ago by Arnaud Ceol730
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Mutation processing by cbioportal
... Hi, I got lost with the mutations from TCGA made available from cbioportal (http://www.cbioportal.org/) and from the gdc portal (http://gdc-portal.nci.nih.gov/), and I've the feeling I'm missing something. My problem is that I found different number of mutations, although the source should be the s ...
cbioportab maf tcga gdc written 1 day ago by Arnaud Ceol730 • updated 1 day ago by igor3.9k
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Answer: A: subcellular localization human / Mouse / Rat
... You may check the Compartment database: http://compartments.jensenlab.org/ (this is a Stringdb's style database for sub cellular compartments). ...
written 1 day ago by Arnaud Ceol730
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Answer: A: How to reorder dendrogram (R)?
... I've used a few time dendosort ([https://f1000research.com/articles/3-177/v1][1] and [https://cran.r-project.org/web/packages/dendsort/index.html][2]), this is a nice library to sort your dendograms. You should have a look. [1]: https://f1000research.com/articles/3-177/v1 [2]: https://cran.r-p ...
written 6 days ago by Arnaud Ceol730
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Answer: A: adv of RPKM for gene expression profile
... I found this useful post about this topic some time ago: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ , it should answer your question. ...
written 5 weeks ago by Arnaud Ceol730
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Answer: A: database for enhancer sequences in human/mammal genomes
... You may start with the results of ChromHMM (http://compbio.mit.edu/ChromHMM/) or Segway (http://noble.gs.washington.edu/proj/encyclopedia/). In both cases, we are talking about prediction (by machine learning), rather than a proper knowledge base. ...
written 5 weeks ago by Arnaud Ceol730
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Comment: C: Bioinformatics software distribution
... "web/whatever application to use straight forward": I'm justing meaning any application (either desktop or web based), that can be used out of the box (as opposite to a library that should be integrated into other software). As far as I know, it is not possible to create plugins for Samtool and Fa ...
written 5 weeks ago by Arnaud Ceol730
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DAS 2 interface: is it used?
... Hello, A few years ago there was an attempt to create a new enhanced version of the DAS protocol to **share genomic data**, called DAS/2 ([http://www.das2.org/][1]). I know at least one implementation of a **DAS/2** server (**Genopub**: [some documentation here][2]), with a flash based web interfa ...
das/2 genopub igb das written 6 weeks ago by Arnaud Ceol730
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Answer: A: Bioinformatics software distribution
... > UPDATE: two more questions: > > 1) What do you think about having access for your tool as a library or > a package for python, ruby, perl, R, other languages? Is this > important and needed? > This is often at least really useful. It means that you can integrate it in your own ...
written 6 weeks ago by Arnaud Ceol730

Latest awards to Arnaud Ceol

Scholar 25 days ago, created an answer that has been accepted. For A: Bioinformatics software distribution
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Happened To The Bind (Biological Interaction Network) Database And Is Acces
Popular Question 10 months ago, created a question with more than 1,000 views. For Asking The Developers Before Asking Biostars
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Go Enrichment From Protein Id
Appreciated 3.0 years ago, created a post with more than 5 votes. For Asking The Developers Before Asking Biostars
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: What Happened To The Bind (Biological Interaction Network) Database And Is Acces
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Asking The Developers Before Asking Biostars
Supporter 3.0 years ago, voted at least 25 times.
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Go Enrichment From Protein Id
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Gene Disease (Cancer) Association
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Protein-Protein Interaction Prediction
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: How To Know Percentage Of Identity Between Every Pair Of Orthologous Genes In Se
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What Happened To The Bind (Biological Interaction Network) Database And Is Acces
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Converting A Set Of Protein Ids To Gene Ids
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

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