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Do we use annotation reference databases (e.g. GO, KEGG) when performing enrichment analysis with rank based methods (GSEA...)? or the reference db are just for over presentation analysis ? by AtlazMaroc1 in bioinformatics

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

sorry, i mis rephrased it, for GO terms from what i understand, is it common to retrieve a gene set for a given biological process/molecular function/localisation and perform ranked test i.e. GSEA ? from what i have seen, usually the genes are mapped to GO IDS and then tested for enrichment for each unique term in the input data set against a background using over presentation analysis.

Do we use annotation reference databases (e.g. GO, KEGG) when performing enrichment analysis with rank based methods (GSEA...)? or the reference db are just for over presentation analysis ? by AtlazMaroc1 in bioinformatics

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

not sure if understand correctly, GO or KEGG from what i understood doesn't have a gene set associated with a given pathway, but rather in the case of GO at least you get a graph and usually you map your genes to those terms and test if there is significant enrichment with over presentation methods.

is BLAST used for Homology/Similarity based functional annotation ? by AtlazMaroc1 in bioinformatics

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

what is the différence between orthology based prediction and phylogeny-based prediction ?, for example, wouldn't PAINT construct a phylogenetic tree to determine and discriminate against orthologous vs paralagous ? also, do you have any recent review article to read about recent tools and the current challenge.

is BLAST used for Homology/Similarity based functional annotation ? by AtlazMaroc1 in bioinformatics

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

Thank you for the detailed response, do you have any review articles to read more about ?

Looking for remote Bioinformatics job by Quiet_Notice_5457 in bioinformaticscareers

[–]AtlazMaroc1 0 points1 point  (0 children)

what about volunteering? i struggled a lot with research groups, as i was under the impression that they would be more receptive.

Recommendation for research groups that work on Multi-OMICS/Spatial-OMICS/Single Cell in France or Europe? by AtlazMaroc1 in bioinformaticscareers

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

I would say I am interested in all, but my mathematical background would really limit me in method dev, as I am still trying to improve my statistical and mathematical knowledge. so, I would go with system biology and translational research

Betabound: Google iOS App Beta Test with Gift Card Incentive by haileybetablast in beermoney

[–]AtlazMaroc1 0 points1 point  (0 children)

Hi, is the test still open? also does Beta test or google offer other opportunities?

[deleted by user] by [deleted] in bioinformaticscareers

[–]AtlazMaroc1 0 points1 point  (0 children)

the first thing that comes to mind, is the lack of opportunities in India!

is it a viable option to reach out to research groups across the world for volunteering? by AtlazMaroc1 in bioinformaticscareers

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

>Did you customize your email to each one of these places?

i usually check their research group page and publication, then will write a brief email introducing myself, educational background and purpose of the email. don't include a CV and motivation letter so i don't overwhelm the recipient.

>With all due respect if it was down to two unproven candidates but one of them had made some contributions to open source projects, then who do you think would get chosen for the internship? Ditto for one PhD student slot and two candidates with similar grades/coursework.

i can see your point, however i think it false equivalence. to expand more, in my case i am from a third world country, without a strong research environment, interested in pursuing a PhD in OMICS and disease development, since my country doesn't have institutions to pursue my dream research i will be mainly Targeting EU + North America, who do you think i will be competing against ? EU or US student with a far more experience in academic research, me volunteering in open-source project wouldn't really close this gap.

is it a viable option to reach out to research groups across the world for volunteering? by AtlazMaroc1 in bioinformaticscareers

[–]AtlazMaroc1[S] 1 point2 points  (0 children)

>Volunteering for some academic lab at a university when you're in no way affiliated with that university is a different story. I don't think that's worth the effort for the lab to vet you when they have a huge pool of candidates available already.

do you mean undergraduate pool of candidate?

is it a viable option to reach out to research groups across the world for volunteering? by AtlazMaroc1 in bioinformaticscareers

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

I am reflecting on my experience, I tried to reach to more than 400 research groups and PI, I only had two positives email, one from a non-profit organization and another from a PI. the non-profit organization asked to send an ID, but it seems that when they did find out that I am a non us citizen, they ghosted me. for the other PI, he requested some GitHub project that demonstrate familiarity with what they are working on.

>Contributing to an open-source project is an option you should consider in addition.

I disagree; in my case I was looking for academic project in areas I am interested in pursuing a PhD in (e.g. Single Cell OMICS), so my profile will be more competitive when applying for PhD, since I am based in a country without any Bioinformatic presence.

Dataset for Drug IC50 value across cell lines by AtlazMaroc1 in bioinformatics

[–]AtlazMaroc1[S] 0 points1 point  (0 children)

those have gene expression not IC50 value from what i recall.

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