Ramon Massoni Badosa

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).

RAAAAAAHHH!!

Dear NYC postdocs: the Postdoc Night Science is coming to our very own New York Genome Center on June 2, 5:30-7:30 pm!

Let's dive into the art of asking the right questions, then network with fellow postdocs & find new science buddies 😊

Register below!

NYC Postdocs! Join us for Night Science at the New York Genome Center on June 2nd for a discussion on the creative process of finding novel questions. This time we hit the bar after! Register: docs.google.com/forms/d/1s9W...
@stearnslab.bsky.social @kelseymonson.bsky.social @rmassonix.bsky.social

... which may impact downstream analysis such as GRN modeling.

Thank you so much for putting this together! This will help us design our next experiments. I'd be very curious to see how GEM-X compares to Flex head-to-head. I foresee that Flex will better detect lowly expressed genes (such as TF),...

I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/

@anusri.bsky.social first author & developer of ChromBPNet is looking for opportunities in industry in ML for bio/genomics. She is an excellent rigorous scientist (as u can see from the paper). Very strongly recommend her. Plz reach out to her if u have openings. Plz forward.

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, he…

There is a huge difference between biochemically defined motifs and real life chromatin sites. In our 2016 paper we found all sorts of TFBS variants that would have never showed up in any database www.sciencedirect.com/science/arti...

Another day, another #HRHorrorStory

Cant wait to read it😍

Felicitats Pau!!

One thing I didn't expect in the US is that I'd pay almost a third of my salary in taxes :(

This morning, the FICA taxes kicked in..

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

Totally agree, but in practical terms that's what's gonna drive change

Of course, the main push back against this is: "if I publish my data I'll get scooped". And I totally sympathize with that, especially when people's careers are on the line. So we need to think as a community of ways of tackling this

Agreed! Not only that, pushing yourself to share code and data with the preprint ensures that it's properly done and not as an after thought or because "reviewers forced me too". What the latter accomplishes is GitHub repos that are impossible to navigate and data that is improperly annotated

Sharing code and data should also be required in the preprint. People are starting to use preprints as a way of advertising their science before it's published, sometimes with half-baked results. We should subject preprints to a higher level of rigor, with fully reusable, transparent and open data.

Some of the best ways to take advantage of preprints: share broadly that you posted one but also to send your preprint directly to colleagues who might care and may have missed it. Just as you like to be alerted to research you care about and may not have seen yet, so does everyone else

Still in 2024, I see way too many papers that don't share their data openly. I understand that in some cases the raw genomic reads need to have restricted access, but there's no excuse not to share any count matrix or processed object openly in repositories such as FigShare or Zenodo.

Felicitats Pau!! Molt bona feina!!

Hello, world!