Peter
@biotechpedro.bsky.social
PhD student at Fraticelli lab @irbbarcelona.org
I try to convert coffee into code and ideas for uncovering biological mysteries.
Some interests: single-cell, lineage tracing, computational biology, cellular variability, premalignancy, resistance...
I try to convert coffee into code and ideas for uncovering biological mysteries.
Some interests: single-cell, lineage tracing, computational biology, cellular variability, premalignancy, resistance...
Related with my last post, I entered X and found this bioRxiv preprint: doi.org/10.1101/2025...
I'm going to say some consciously exaggerated comments below.
I'm going to say some consciously exaggerated comments below.
December 3, 2025 at 10:43 AM
Related with my last post, I entered X and found this bioRxiv preprint: doi.org/10.1101/2025...
I'm going to say some consciously exaggerated comments below.
I'm going to say some consciously exaggerated comments below.
I'm lately liking Bluesky. These ~2 months has been full of interesting papers & discussions (thanks Paper Skygest @paper-feed.bsky.social). Not crypto-bros, not so many AI-bros - just like in Twitter/X
December 3, 2025 at 10:29 AM
I'm lately liking Bluesky. These ~2 months has been full of interesting papers & discussions (thanks Paper Skygest @paper-feed.bsky.social). Not crypto-bros, not so many AI-bros - just like in Twitter/X
Reposted by Peter
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
Feng et al. present the first genome-scale CRISPR interference perturbation map with
scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering
population-scale CRISPR pe...
www.cell.com
December 3, 2025 at 9:17 AM
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
Reposted by Peter
Congratulations to the new cohort of 28 EMBO Young Investigators! They are joining an international network of more than 800 life scientists – Welcome!
Read the press release here:
https://www.embo.org/press-releases/twenty-eight-group-leaders-become-embo-young-investigators/
Read the press release here:
https://www.embo.org/press-releases/twenty-eight-group-leaders-become-embo-young-investigators/
December 2, 2025 at 1:06 PM
Congratulations to the new cohort of 28 EMBO Young Investigators! They are joining an international network of more than 800 life scientists – Welcome!
Read the press release here:
https://www.embo.org/press-releases/twenty-eight-group-leaders-become-embo-young-investigators/
Read the press release here:
https://www.embo.org/press-releases/twenty-eight-group-leaders-become-embo-young-investigators/
We've been using this for years - I'm still surprised how Xist alone is so good for sex classification at single-cell level.
Credit where should be given: original idea by Daniel Fernández-Pérez (a.k.a the best postdoc!)
Credit where should be given: original idea by Daniel Fernández-Pérez (a.k.a the best postdoc!)
Excited to share that our article on accurate sample deconvolution of pooled snRNA-seq data using sex-dependent gene expression patterns is live on NAR Genomics and Bioinformatics! 🎉
Check it out here: doi.org/10.1093/narg...
#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics
Check it out here: doi.org/10.1093/narg...
#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics
Validate User
doi.org
December 1, 2025 at 12:01 PM
We've been using this for years - I'm still surprised how Xist alone is so good for sex classification at single-cell level.
Credit where should be given: original idea by Daniel Fernández-Pérez (a.k.a the best postdoc!)
Credit where should be given: original idea by Daniel Fernández-Pérez (a.k.a the best postdoc!)
Reposted by Peter
Sample-level modeling of single-cell data at scale with tinydenseR https://www.biorxiv.org/content/10.1101/2025.11.26.690752v1
December 1, 2025 at 3:46 AM
Sample-level modeling of single-cell data at scale with tinydenseR https://www.biorxiv.org/content/10.1101/2025.11.26.690752v1
Reposted by Peter
"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...
Bulk RNA-seq to the rescue of differential expression analysis i...
Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is…
doi.org
December 1, 2025 at 8:30 AM
"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...
Reposted by Peter
Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.
· #AcademicSky ·
The European Research Council is launching €7m Plus Grants for ambitious, long‑term research — open to researchers at any career stage but limited to about 30 awards; current ERC grantees and applicants are ineligible, reports @clanicholson.bsky.social.
The European Research Council is launching €7m Plus Grants for ambitious, long‑term research — open to researchers at any career stage but limited to about 30 awards; current ERC grantees and applicants are ineligible, reports @clanicholson.bsky.social.
ERC’s new €7m Plus Grants open to researchers at any career stage - Research Professional News
European Research Council president describes scheme as part attempt to lure US talent
www.researchprofessionalnews.com
November 29, 2025 at 10:53 AM
Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.
Reposted by Peter
🧬 New preprint out on bioRxiv!
Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years.
📄 doi.org/10.1101/2025...
🙏 Huge thanks to all co-authors
Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years.
📄 doi.org/10.1101/2025...
🙏 Huge thanks to all co-authors
Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions
Single-cell whole-genome sequencing of 335 cells from seven colorectal cancers, coupled with Bayesian phylodynamic modeling, revealed tumors often originate decades before diagnosis, remain indolent, ...
doi.org
November 28, 2025 at 7:54 AM
🧬 New preprint out on bioRxiv!
Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years.
📄 doi.org/10.1101/2025...
🙏 Huge thanks to all co-authors
Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years.
📄 doi.org/10.1101/2025...
🙏 Huge thanks to all co-authors
Reposted by Peter
k-spaces: Mixtures of Gaussian latent variable models https://www.biorxiv.org/content/10.1101/2025.11.24.690254v1
November 28, 2025 at 10:46 AM
k-spaces: Mixtures of Gaussian latent variable models https://www.biorxiv.org/content/10.1101/2025.11.24.690254v1
November 22, 2025 at 4:28 PM
Reposted by Peter
This is important for 🧪🔬
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Fluorescent protein and peptide tags alter condensate formation and dynamics in vivo and in vitro | EMBO reports
imageimageProtein and peptide tags can profoundly alter condensation in a tag- and protein-specific
manner, both in cells and in vitro, highlighting the need for careful validation in
condensate studi...
www.embopress.org
November 22, 2025 at 7:16 AM
This is important for 🧪🔬
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted by Peter
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
This seems AMAZING: CRIPSR-All!
A preprint out today from Arc Innovation Investigator Theo Roth, Austin Hartman, Oliver Takacsi-Nagy, and colleagues introduces CRISPR All–a unified programming language for editing human cells across all major genetic perturbation types at once.
November 22, 2025 at 11:06 AM
This seems AMAZING: CRIPSR-All!
Reposted by Peter
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
November 20, 2025 at 9:36 AM
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
Reposted by Peter
Would you like to model and analyze sample-specific regulatory networks? Check out our latest BioRxiv pre-print in which we present 𝐒𝐢𝐒𝐚𝐍𝐀, a command line workflow that makes modeling and analysis of single-sample networks really easy, transparent, and reproducible 🪄: www.biorxiv.org/content/10.1...
November 13, 2025 at 9:24 AM
Would you like to model and analyze sample-specific regulatory networks? Check out our latest BioRxiv pre-print in which we present 𝐒𝐢𝐒𝐚𝐍𝐀, a command line workflow that makes modeling and analysis of single-sample networks really easy, transparent, and reproducible 🪄: www.biorxiv.org/content/10.1...
Reposted by Peter
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 7, 2025 at 10:29 AM
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
Reposted by Peter
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Peter
Big New! @elife.bsky.social @genetics-gsa.bsky.social #G3journal are joining editorial forces with @reviewcommons.org - bringing not just field-specific expertise to the process but also making #PreprintPeerReview a truly collaborative effort!🎉👏
Read more to find out👇
www.embo.org/features/pub...
Read more to find out👇
www.embo.org/features/pub...
Publishers join the Review Commons peer review process – Features – EMBO
Editors from eLife, Genetics, G3 and Journal of Cell Biology will contribute to the EMBO preprint peer review platform
www.embo.org
November 3, 2025 at 9:33 AM
Big New! @elife.bsky.social @genetics-gsa.bsky.social #G3journal are joining editorial forces with @reviewcommons.org - bringing not just field-specific expertise to the process but also making #PreprintPeerReview a truly collaborative effort!🎉👏
Read more to find out👇
www.embo.org/features/pub...
Read more to find out👇
www.embo.org/features/pub...
Reposted by Peter
1/ @reviewcommons.org, @embo.org's preprint peer review platform, is taking an important step forward. Multiple publishers, including eLife, are now jointly running the peer-review process on behalf of the platform.
🔗 buff.ly/Rm1XotK
🔗 buff.ly/Rm1XotK
October 30, 2025 at 2:45 PM
1/ @reviewcommons.org, @embo.org's preprint peer review platform, is taking an important step forward. Multiple publishers, including eLife, are now jointly running the peer-review process on behalf of the platform.
🔗 buff.ly/Rm1XotK
🔗 buff.ly/Rm1XotK
Reposted by Peter
Training other methods on the same data may not be feasible due to compute limitations. Training on other much smaller data won’t be the same task. Training your implementation or with your compute limitations is not representative of the original method.
October 26, 2025 at 10:51 PM
Training other methods on the same data may not be feasible due to compute limitations. Training on other much smaller data won’t be the same task. Training your implementation or with your compute limitations is not representative of the original method.
Reposted by Peter
Academics also can be driven and intelligent, but the driver is often personal curiosity and understanding, with a fair bit of showing off (academic egos are something else; I am self aware enough to realise I am not immune to this though I do try to tame it).
October 26, 2025 at 7:48 AM
Academics also can be driven and intelligent, but the driver is often personal curiosity and understanding, with a fair bit of showing off (academic egos are something else; I am self aware enough to realise I am not immune to this though I do try to tame it).