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...
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).
Reposted by Peter
Thread on the intellectual landscape around LLMs 👇
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I am genuinely impressed by large language models - they can absorb disparate components of text into some consolidated view, they can produce extremely good language and - with the right model - translate pretty well between languages and they are an excellent text based UI for humans to use. But..
October 26, 2025 at 8:30 AM
Thread on the intellectual landscape around LLMs 👇
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
Reposted by Peter
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Reposted by Peter
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:47 PM
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Reposted by Peter
Are professors who don’t teach or mentor, just academic executives who raise money and market other people’s work? When did teaching stop being an important part of this job?
October 25, 2025 at 5:26 AM
Are professors who don’t teach or mentor, just academic executives who raise money and market other people’s work? When did teaching stop being an important part of this job?
Reposted by Peter
How can we scale subcellular spatial proteomics across many experiments and conditions?
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
October 23, 2025 at 1:40 PM
How can we scale subcellular spatial proteomics across many experiments and conditions?
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Reposted by Peter
Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE
Discovery and engineering of retrons for precise genome editing - Nature Biotechnology
A metagenomic screen identifies retron reverse transcriptases for precise genome-editing applications.
go.nature.com
October 23, 2025 at 2:59 PM
Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE
Reposted by Peter
Correlation isn’t causation, as the mantra goes—but statistical noise in correlational data can reveal causal information. When X and Y are causally linked, their noise tends to be asymmetric & this can guide #CausalInference. Check out our 📃👇 doi.org/10.1111/nous... #philsky #philsci #StatsSky #HPS
October 21, 2025 at 9:20 AM
Correlation isn’t causation, as the mantra goes—but statistical noise in correlational data can reveal causal information. When X and Y are causally linked, their noise tends to be asymmetric & this can guide #CausalInference. Check out our 📃👇 doi.org/10.1111/nous... #philsky #philsci #StatsSky #HPS
Reposted by Peter
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
A plastic EMP1⁺ to LGR5⁺ cell state conversion as a bypass to KRAS-G12D pharmacological inhibition in metastatic colorectal cancer
Abstract. Inhibitors of the oncogene KRAS hold promise for treating metastatic CRC (mCRC). Here we show that a selective, covalent small molecule inhibitor of the active (ON) conformation of RAS-G12D,...
aacrjournals.org
October 23, 2025 at 6:07 PM
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
Reposted by Peter
New “discrete state” model of hematopoiesis published in Nature Immunology. rdcu.be/eL8oO
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice
Nature Immunology - Grimes and colleagues integrate multiomic features to create a framework that allows the isolation of discrete cell states across hematopoiesis and exploit the underlying gene...
rdcu.be
October 22, 2025 at 1:10 PM
New “discrete state” model of hematopoiesis published in Nature Immunology. rdcu.be/eL8oO
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
Reposted by Peter
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 6:23 AM
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Reposted by Peter
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 15, 2025 at 12:22 PM
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
Reposted by Peter
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
October 10, 2025 at 4:47 PM
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
Reposted by Peter
I read and write, I explore and I question, I design and script and analyse, I interpret and communicate. I do this to train my mind in the hopes of one day generating new knowledge. New knowledge that might even be useful, and that no algorithm can yet be trained on.
Y'all. I just got ChatGPT to do everything in R for this manuscript. I mean EVERYTHING. And it's all legit and reproducible. I'm shook.
How are we mentoring our trainees in statistics now? Who needs to learn coding in R line by line, and who doesn't?
scienceforeveryone.science/statistics-i...
How are we mentoring our trainees in statistics now? Who needs to learn coding in R line by line, and who doesn't?
scienceforeveryone.science/statistics-i...
Statistics in the era of AI
How do we mentor, teach, and do stats when AI can do so much of the work?
scienceforeveryone.science
October 12, 2025 at 8:07 AM
I read and write, I explore and I question, I design and script and analyse, I interpret and communicate. I do this to train my mind in the hopes of one day generating new knowledge. New knowledge that might even be useful, and that no algorithm can yet be trained on.
Reposted by Peter
Our benchmark + guidelines for atlas-level differential gene expression of single cells is online:
academic.oup.com/bib/article/...
Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.
Collab w/ @leonhafner.bsky.social @itisalist.bsky.social
academic.oup.com/bib/article/...
Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.
Collab w/ @leonhafner.bsky.social @itisalist.bsky.social
August 13, 2025 at 5:51 AM
Our benchmark + guidelines for atlas-level differential gene expression of single cells is online:
academic.oup.com/bib/article/...
Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.
Collab w/ @leonhafner.bsky.social @itisalist.bsky.social
academic.oup.com/bib/article/...
Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.
Collab w/ @leonhafner.bsky.social @itisalist.bsky.social
Reposted by Peter
October 12, 2025 at 9:25 AM
Reposted by Peter
Fantastic review on the importance of rigorous experimental design. Amen. 😊
"'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher"
@manuelkleiner.bsky.social
"'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher"
@manuelkleiner.bsky.social
How thoughtful experimental design can empower biologists in the omics era - Nature Communications
Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...
www.nature.com
August 7, 2025 at 10:38 PM
Fantastic review on the importance of rigorous experimental design. Amen. 😊
"'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher"
@manuelkleiner.bsky.social
"'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher"
@manuelkleiner.bsky.social
Reposted by Peter
How can mitophagy be an effective quality control mechanism if mtDNA mutations reach high enough levels to cause disease?
This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility.
www.science.org/doi/10.1126/...
This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility.
www.science.org/doi/10.1126/...
Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations
Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as...
www.science.org
October 10, 2025 at 8:45 AM
How can mitophagy be an effective quality control mechanism if mtDNA mutations reach high enough levels to cause disease?
This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility.
www.science.org/doi/10.1126/...
This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility.
www.science.org/doi/10.1126/...