Frederic Bastian

Frederic Bastian

@fred_bstn

Followers65
Following60

@Bgeedb project manager, bioinformatician @marc_rr's lab, @ISBSIB @DEE_UNIL. Driven by studying gene expression, hoping to help to do so with our bioinfo tools

Joined on June 15, 2018
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We looked inside some of the tweets by @fred_bstn and here's what we found interesting.

Inside 100 Tweets

Time between tweets:
20 days
Average replies
3
Average retweets
73
Average likes
55
Tweets with photos
5 / 100
Tweets with videos
0 / 100
Tweets with links
0 / 100

Damn, this is overly long. This paper represents just the "ground" work for @Bgeedb IMO ðŸĪŠ. Now, if future allows, we can build on top of it and have fun. Add new datatypes (hello scRNA-Seq). New tools that we'd like to be useful for biological discoveries. See you soon I hope!

And many many more... @antifreezeprot for the BgeeDB package. @aechchiki, will spend a summer on dev. stage ontology with you again :p @ljljolin, @TinaBegum27, @GiuliaZancolli, damn, all members and alumni of @marc_rr's lab, thank you, for all the good times and help and advices.

Many more allowing the @Bgeedb team to be as fun and great. @JulienWollbrett for the pipeline/R/Java development. @essepf for the pipeline and analyses of #SingleCell RNA-seq. Tarcisio Mendes de Farias for the #ontology #SPARQL work. Do you allow me to say that I love you all? :p

@marc_rr has ben supervising the project from the start. The good thing with Marc is that he knows everything about everything :p Thus I could always rely on him for... everything. He supported me even in the darkest times. Thanks for mentoring and allowing me to do what I want.

You'll find more in the paper of course! Our pipeline, our @Bioconductor @RPackages to retrieve @Bgeedb #transcriptomics data, or reproduce analyses on your own data. E.g., generate present/absent expression calls from your #RNASeq data, thanks to the work of @JulienWollbrett

These tools are usable mostly thanks to Valentine Rech de Laval, as she cares about user experience. She's a great web and Java developer, and I have to shut up and listen when she tells me about web development :p Thanks Valentine, also for having been capable of bearing me 😅🙏

The Expression Comparison tool allows comparative #transcriptomics, to find the conditions with the most conserved and highest expression of a gene list, within or between species. E.g., brain regions for the brain-specific genes SRRM4 in Tetrapoda: https://t.co/2ufhlaY54x

You'll also find TopAnat, performing Enrichment Analyses on expression data. It tells you what are the conditions where the expression of your gene set is over-representated. E.g., specific brain regions when you enter a list of genes related to autism: https://t.co/JaMc5lLBTD

All of that so that @Bgeedb can tell you where and when your genes are expressed, and do automated comparative #transcriptomics. Among the tools described in the paper, you'll find the Gene Page, ranking conditions for a gene per expression levels, e.g. https://t.co/GURLfRBIye

To store and analyze TB of data is quite a challenge. We burn the @ISBSIB @unil clusters, pull all data from MODs @alliancegenome, all of that thanks to @seb_moretti. Seb, always present and on top of scientific watch for new tools, I hope you still enjoy when we crash servers :p

All #transcriptomics data in @Bgeedb are analyzed to produce present/absent expression calls, which allows integration/comparison over all datasets and species. @_julien_roux has been instrumental to set up these analyses. Thanks Julien, for all the work and out-of-work time :p

Which leads to... biomedical #ontology! @chrismungall, my guru! 🙏 Without @uberanat we could never integrate and compare data in 29 species in @Bgeedb, soon 60+. Thank you, and @ontowonka, for what I learned about ontologies. And the @OBOFoundry community for the great resources

So, we describe the data to retrieve in @Bgeedb: #RNAseq, #affymetrix, #insituhybridization, EST. Quality filtered, curated healthy wild-type samples, annotated to anatomy (@uberanat), life stages, sex, strain/ethnicity, in 29 animal species. We went through 12,000 #GTEx samples!

Tons of #transcriptomics data in Bgee, annotated by @ANiknejad @accomte et al. The work that @ANiknejad does, it's incredible. Spotting any inconsistency, knowing all resources by heart, became anatomy expert, it's crazy seriously. Thank you so much Anne, for always being there.

Now, should I tell you about the results in the paper, or the adventure that it has been for me over the years to work on @Bgeedb and in its team? I'm gonna try to mix both. Let's go, and let's start with... #biocuration!

First, why it took us so long to publish a thorough description of Bgee. Well, to make it short: damn, my bad! "hey, let's wait just for this tiny extra feature before publishing!" - 6 months later... "Oh yeah, and this little one!". 6 months later - ... worst decisions ever :p

With the publication of the preprint about @Bgeedb in @biorxiv_bioinfo, I'll allow myself to make a thread. It's gonna be long and out of control. But there'll be some stuff about the content of the paper, I promise! https://t.co/cEJIMF4vou

Finally, after all these years, a paper describing all the data, #biocuration and tools in the Bgee database of gene expression! Read, enjoy, and give us feedback (and cite). @fred_bstn et al 😀 https://t.co/rUVyzRNtFB #rnaseq #bioinformatics #database

If you are a scientist in any discipline and you want to contribute to the fight against COVID-19, we have created a platform to help you do so: https://t.co/QzcCRLcEfw And if you're already working on COVID-19, this is also for you! More details in the thread 👇

SIB
a year ago
The ISB Intnl Society for #Biocuration @biocurator provides 2 travel fellowships to ISB members to attend @BC2Conference. Students, junior curators, curators from low-income countries or countries suffering from natural disasters are encouraged to apply: https://t.co/QaRuL5sKNq https://t.co/Fb5OYp4GqT

The ISB Intnl Society for #Biocuration @biocurator provides 2 travel fellowships to ISB members to attend @BC2Conference. Students, junior curators, curators from low-income countries or countries suffering from natural disasters are encouraged to apply: https://t.co/QaRuL5sKNq https://t.co/Fb5OYp4GqT

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