Ramon Massoni Badosa
@rmassonix.bsky.social
Postdoc at NYGC and WCM in love with single-cell multiomics, immunology, hematology, data science. I care about open science and education
Reposted by Ramon Massoni Badosa
Come learn the tricks of giving a BAD talk: begin the process by organizing your slides - the more, the better, try to impress, run over your time, embrace distractions, and treat questions as threats!
Join us tomorrow at Weill Cornell for this month's Postdoc Night Science NYC!
Join us tomorrow at Weill Cornell for this month's Postdoc Night Science NYC!
October 14, 2025 at 12:28 PM
Come learn the tricks of giving a BAD talk: begin the process by organizing your slides - the more, the better, try to impress, run over your time, embrace distractions, and treat questions as threats!
Join us tomorrow at Weill Cornell for this month's Postdoc Night Science NYC!
Join us tomorrow at Weill Cornell for this month's Postdoc Night Science NYC!
Dear Postdocs of New York: Next Wednesday, we’re closing out an amazing year of NYC Postdoc Night Science Club sessions at our very own @weillcornell.bsky.social !
If you’re interested in giving engaging, memorable talks, you cannot miss this one.
Details below, hope to see you all there!
If you’re interested in giving engaging, memorable talks, you cannot miss this one.
Details below, hope to see you all there!
Interested in learning how to be a good speaker and give effective talks? Season 2 of the NYC Postdoc Night Science Club begins October 15th. Join us NYC Postdocs for a 2hr workshop and maybe also a drink at a bar! Free registration (usually ~100 come): docs.google.com/forms/d/1dII...
October 7, 2025 at 10:22 PM
Dear Postdocs of New York: Next Wednesday, we’re closing out an amazing year of NYC Postdoc Night Science Club sessions at our very own @weillcornell.bsky.social !
If you’re interested in giving engaging, memorable talks, you cannot miss this one.
Details below, hope to see you all there!
If you’re interested in giving engaging, memorable talks, you cannot miss this one.
Details below, hope to see you all there!
Reposted by 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!).
May 13, 2025 at 7:42 PM
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!).
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!
Let's dive into the art of asking the right questions, then network with fellow postdocs & find new science buddies 😊
Register below!
May 29, 2025 at 2:28 AM
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!
Let's dive into the art of asking the right questions, then network with fellow postdocs & find new science buddies 😊
Register below!
Reposted by Ramon Massoni Badosa
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
@stearnslab.bsky.social @kelseymonson.bsky.social @rmassonix.bsky.social
May 14, 2025 at 9:30 PM
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
@stearnslab.bsky.social @kelseymonson.bsky.social @rmassonix.bsky.social
Reposted by Ramon Massoni Badosa
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/
January 24, 2025 at 7:36 PM
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/
Reposted by Ramon Massoni Badosa
@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.
Our original biorxiv submission of the ChromBPNet preprint had issues with supp. methods & file links not working (even though we they were uploaded). This updated version has fixed those issues. Everything shud be available now. Thanks for your patience.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 13, 2025 at 6:23 PM
@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.
Reposted by Ramon Massoni Badosa
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...
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…
www.sciencedirect.com
January 13, 2025 at 3:00 AM
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...
Cant wait to read it😍
Felicitats Pau!!
Felicitats Pau!!
The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
January 4, 2025 at 12:51 AM
Cant wait to read it😍
Felicitats Pau!!
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..
This morning, the FICA taxes kicked in..
January 3, 2025 at 6:55 PM
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..
This morning, the FICA taxes kicked in..
Reposted by Ramon Massoni Badosa
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/
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/
December 25, 2024 at 11:48 PM
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/
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/
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
Many academics point to bioRxiv as “the one thing improving science publishing”.
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
December 23, 2024 at 4:25 AM
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.
Reposted by Ramon Massoni Badosa
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
Many academics point to bioRxiv as “the one thing improving science publishing”.
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
December 22, 2024 at 10:21 PM
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.
December 18, 2024 at 5:00 PM
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.
Hello, world!
November 25, 2024 at 2:28 AM
Hello, world!