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Peter

@biotechpedro.bsky.social
386 followers 535 following 119 posts

PhD student at Fraticelli lab @irbbarcelona.org‬ I try to convert coffee into code and ideas to uncover biological mysteries. I enjoy creativity more than productivity. Single-cell, lineage tracing, computational biology, cellular variability, [...]

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Reposted by Peter
Marvin Tanenbaum @marvintanenbaum.bsky.social · 08/10/2026
Did you ever want to sequence that one interesting cell you observed in your microscopy experiment? We have a new pre-print out today that describes a genetic barcoding method, Waldo, to perform live-cell imaging and single-cell sequencing on the same single cells. www.biorxiv.org/content/10.6...
biorxiv.org
Linking live-cell imaging to single-cell sequencing using genetic barcoding
Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures gen...
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Steve Huntsman @stevehuntsman.bsky.social · 09/10/2026
arxiv.org/abs/2610.10072
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Peter @biotechpedro.bsky.social · 07/10/2026
Hi Jeff, very cool work! Do you think Power-Seek (t.co/9F03HJ4l3D) could benefit from your coupled dataset and therefore infer memory proteins forgotten at the RNA level?
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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Erik van Nimwegen @erikvannimwegen.bsky.social · 01/10/2026
Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right? TLDR: No. #methodsmatter Not even close. On realistic synthetic data MILK performs worse than UMAP.
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Peter @biotechpedro.bsky.social · 05/10/2026
nf-co.re/tumourevo/1....
nf-co.re
tumourevo: Introduction
Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
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Victor Maull Miquel @vmaull.bsky.social · 04/10/2026
Hace 200 años, Darwin y Hooker se preguntaron si era posible cambiar el clima de una isla construyendo un ecosistema de novo. Demostraron que sí. Ahora he viajado a Ascension con @nastassiakn.bsky.social para entender cómo ocurrió y cómo podemos exportarlo. Gracias @pflis.bsky.social por contarlo.
elpais.com
Ascensión, la isla desértica que se hizo selva
Este remoto paraje en medio del Atlántico podría esconder la fórmula para combatir la desertificación en otros lugares del planeta. Un científico español ha decidido investigarlo. Viajamos hasta allí ...
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Nicolas Robine 🇪🇺🇫🇷🇺🇸 @nicorobine.bsky.social · 30/09/2026
"Written in development and lost in ageing: the grammar of cellular identity". Review in @nature.com www.nature.com/articles/s41...
nature.com
Written in development and lost in ageing: the grammar of cellular identity - Nature
Ageing reflects progressive decanalization of mammalian cell identity, driven by erosion of a regulatory grammar written during development.
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IRB Barcelona @irbbarcelona.org · 28/09/2026
📢 The 𝗜𝗥𝗕 𝗕𝗮𝗿𝗰𝗲𝗹𝗼𝗻𝗮 𝗜𝗻𝘁𝗲𝗿𝗻𝗮𝘁𝗶𝗼𝗻𝗮𝗹 #𝗣𝗵𝗗 #𝗙𝗲𝗹𝗹𝗼𝘄𝘀𝗵𝗶𝗽𝘀 – 𝗘𝘅𝘁𝗿𝗮𝗼𝗿𝗱𝗶𝗻𝗮𝗿𝘆 𝗖𝗮𝗹𝗹 𝟮𝟬𝟮𝟲 is now open, offering up to 8 PhD fellowships in #Biomedicine or #OrganicChemistry. Explore the participating groups, check the application requirements and apply 👉 shorturl.at/7iSOa 🧪
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Emma R Andersson @anderssonlab.bsky.social · 23/09/2026
🧬 Preprint! 🧵 Our goal is to genetically manipulate every embryonic germ layer to enable high throughput in vivo studies. We previously showed mouse ectoderm can be targeted by amniotic injection, enabling cell-specific manipulation, lineage tracing, and knockouts. But how to reach mesoderm?
Schematic of method developed and application. At embryonic day 7.5, a lentiviral library carrying unique 30-nucleotide barcodes and a fluorescent reporter is injected into the mouse exocoelomic cavity. An E8 embryo cross-section shows that this cavity is continuous with the intraembryonic coelomic cavity, allowing the virus to reach and barcode mesodermal progenitors, including lateral plate and paraxial mesoderm.
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Greg Egan @gregegansf.bsky.social · 27/07/2026
While the Fields Medal celebrates the under-40s, the mathematician Joan Birman has, at the age of 99, solved a major open problem in representations of the Braid groups, a topic she has worked on for more than 60 years.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026
A single-cell RNA-seq catalog of ground truth gene coregulation www.biorxiv.org/content/10.64898/20…
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Peter @biotechpedro.bsky.social · 17/09/2026
Would like to heat thoughts of the community on this. Looking forward to the version after peer reviewing!
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Jase Gehring @skyjase.bsky.social · 14/09/2026
Must be crazy to be David Baker and have your scientific dreams come true in your lifetime in your lab
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Peter @biotechpedro.bsky.social · 17/09/2026
I remember the first time I read it, when it was preprinted. I just said: "oh, finally!!!"
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Pierre-Paul Axisa @ppaxisa.bsky.social · 14/09/2026
Already several mentions of uses in bioinformatics like transcriptomics. little doubt that it’s useful but still a universal problem of how many. If you give several analyst the same data I think there could be a 10 fold variation on the # clusters "identified". This paper nicely asks "how many?"
doi.org
CHOIR improves significance-based detection of cell types and states from single-cell data - Nature Genetics
Cluster hierarchy optimization by iterative random forests (CHOIR) offers a robust and accurate method to identify cell clusters across a variety of single-cell resolution data with statistical suppor...
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Mann Lab @mannlab.bsky.social · 15/09/2026
Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native. doi.org/10.64898/202...
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Lars Velten @larsplus.bsky.social · 04/09/2026
It's been preprint week! Joe's great Perturb-seq story "back-to-back" with our single cell AML atlas (led by @simonhaas.bsky.social). 🤒: www.biorxiv.org/content/10.6... 🧬: www.biorxiv.org/content/10.6... These two apparently very different stories were posted back to back because of a surprise 😮🧵:
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Peter @biotechpedro.bsky.social · 03/09/2026
Congratulations Michael!!! 🥳
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Inigo Martincorena @imartincorena.bsky.social · 03/09/2026
Big paper alert! This project has been years in the making. A comprehensive description of somatic mutation rates and signatures across 53 tissues or cell types using NanoSeq. A large collective effort led by Mimy Pham, Mike Stratton and @r-rahbari.bsky.social. www.biorxiv.org/content/10.6...
biorxiv.org
A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells
Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune syst...
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Joe Bowness @joebowness.bsky.social · 01/09/2026
Very happy to share the first pre-print from my postdoc work with @larsplus.bsky.social (which we also presented at the excellent @isehsociety.bsky.social Annual Meeting last weekend). Here we performed a CRISPRi Perturb-seq screen targeting >500 transcriptional regulators in ex vivo mouse HSPCs.
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Pierre-Luc Germain @plger.bsky.social · 26/08/2026
Sharing a new preprint about technical variation in (bulk/ #SingleCell ) #ATACseq and motif accessibility analyses, and methods to correct for them www.biorxiv.org/content/10.6...
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Dani León-Periñán @danilexn.bsky.social · 26/08/2026
The paper is here: www.nature.com/articles/s41...
nature.com
Ultrafast and reference-free sequence discovery in single-cell data - Nature
Malva enables ultrafast, reference-free searching of raw single-cell sequences across millions of cells, transforming static transcriptomic atlases into dynamic resources for understanding the functio...
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Franzi Lorbeer @florbeer.bsky.social · 21/08/2026
0/ New preprint from the Stark and Grün labs! @reyna-rosales.bsky.social @dominicgrun.bsky.social @alex-stark.bsky.social We developed BARe-seq to ask what in the DNA controls transcriptional bursting - key findings for anyone working on transcription, gene regulation, or cis-regulatory elements 🧵
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Peter @biotechpedro.bsky.social · 21/08/2026
I've tried Bonsai in various datasets through the web server. It has always added some insights to my understanding of the data. Totally recommended, especially seeing the new additions 🤩
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Can Bonsai also identify clusters/cell types in the data? Yes, Bonsai has both an unsupervised method for finding clearly distinct clades of cells in the tree, and a supervised method that finds the clades that best match a given reference annotation. 4/n
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Marco Grillo @mgrillo.bsky.social · 19/08/2026
Latest from our lab: highly multiplexed spatial miRNA profiling, with @agustinrobles.bsky.social, @augjensen.bsky.social, @nilssonlab.org and others! www.biorxiv.org/content/10.6...
biorxiv.org
Spatial microRNA profiling at single-cell resolution by in situ barcoded extension
The spatial organization of post-transcriptional regulation is a fundamental yet difficult to access layer of tissue biology. MicroRNAs (miRNAs) are small RNAs with a key role in post-transcriptional ...
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Sung Kim @sungkim.bsky.social · 19/08/2026
Mathematics in the age of AI by Terence Tao An essay on how the mathematical community might respond to the arrival of AI tools that are capable of performing research-level mathematical tasks. arxiv.org/abs/2608.16753
arxiv.org
Mathematics in the age of AI
An essay, based on a public lecture delivered at the 2026 International Congress of Mathematicians, on how the mathematical community might respond to the arrival of artificial intelligence tools that...
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Waggoner Lab @labwaggoner.bsky.social · 19/08/2026
@nature.com Matters Arising @caleblareau.bsky.social @leifludwig.bsky.social Artefacts in single-cell mtDNA analyses misinform phylogenies www.nature.com/articles/s41... on www.nature.com/articles/s41... response @bloodgenes.bsky.social www.nature.com/articles/s41...
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EMBL Events @events.embl.org · 31/07/2026
Get your calendars, because the new 2027 EMBL Annual Poster has arrived: s.embl.org/2027-poster Whether you'd like to enhance your skills in a practical course or engage with the latest research at one of our conferences, we've got you covered. See you at EMBL in 2027! 🙌 #LifeSciences #EMBL
The image depicts the 2027 EMBL Annual Poster featuring the new events programme for 2027. On the left side is a colorful banner, on the right is the list of events sorted by month
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Rita Mateus @ritamateus.bsky.social · 03/08/2026
New preprint alert!!! Super proud to finally share an authentic 'tour-de-force' from the amazing PhD students Shivani Gunnan @shivanigunnan.bsky.social, Max Kotz and Lucas Ribas, in collaboration with @friedrich-group.bsky.social 👇a small thread www.biorxiv.org/content/10.6...
biorxiv.org
Developmental growth rates adapt to enable self-correction of organ morphology after injury.
Proportional organ growth requires tissue-level control of cell behavior. Yet the cues that adapt growth rates, especially after organ injury, remain unclear. Here, we uncover that developing organs a...
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Nature Biotechnology @natbiotech.nature.com · 12/08/2026
Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming - @institutcurie.bsky.social www.nature.com/articles/s41...
nature.com
Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming - Nature Biotechnology
OneCell CUT&Tag enables multiomic analysis of a single cell without computation.
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Junhong Choi @choijunhong.bsky.social · 11/08/2026
Excited to share the first preprint from our lab! We combined a DNA Typewriter lineage recorder with clone-resolved founder profiling to find what makes metastatic potential heritable in lung cancer xenografts. 1/13 www.biorxiv.org/content/10.6...
biorxiv.org
Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential
Metastasis causes most cancer deaths, yet no recurrent mutation specifically drives it, raising the possibility that metastatic potential is a non-genetic yet heritable cell state. Classic experiments...
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Guido Barzaghi @guidobarzaghi.bsky.social · 11/08/2026
📄 That's a wrap 📄 we're excited to share that the latest from @arnaudkr.bsky.social 's lab and Judith Zaugg's lab is at last online at doi.org/10.1038/s415.... Many thanks to my co-first @valentinabaderna.bsky.social and to @embl.org for the wonderful research environment.
doi.org
Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency - Nature Genetics
This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...
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Nozomu Yachie @nzmyachie.bsky.social · 10/08/2026
We just posted a new preprint on a microRNA (miRNA)-responsive CRISPR guide RNA: the cuffed guide RNA (cgRNA).   Here’s what we did 🧵 www.biorxiv.org/content/10.6...
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Peter @biotechpedro.bsky.social · 11/08/2026
"we should [...] aim for systematic comparisons with simpler representations, dynamical analysis, and explicit model hierarchies..." 🤩
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Peter @biotechpedro.bsky.social · 07/08/2026
Very much needed work 🤩 www.nature.com/articles/s41...
nature.com
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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bioRxivpreprint @biorxivpreprint.bsky.social · 07/08/2026
The Phantom of the PCR: detection and consequences of spurious UMIs in mainstream RNA sequencing www.biorxiv.org/content/10.64898/20…
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Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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Paper Skygest Team @paper-feed.bsky.social · 19/08/2025
**Please repost** If you're enjoying Paper Skygest -- our personalized feed of academic content on Bluesky -- we'd appreciate you reposting this! We’ve found that the most effective way for us to reach new users and communities is through users sharing it with their network
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Stirling Churchman @stirlingchurchman.bsky.social · 28/07/2026
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...
biorxiv.org
Analog intrinsic recoding measures RNA dynamics without chemical conversion
Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...
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Amy D Willis @amydwillis.bsky.social · 20/07/2026
Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/
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Lars Velten @larsplus.bsky.social · 16/07/2026
@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity link.springer.com/article/10.1186/s13059-026-04186-9 Julia achieved three cool things with this work...🧵
link.springer.com
Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity - Genome Biology
Background Cell state-specific gene expression programs emerge from the interplay between cis-regulatory elements (CREs), such as enhancers, and transcription factors (TFs). Massively parallel reporte...
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Itai Yanai @itaiyanai.bsky.social · 14/07/2026
1906 Nobel Prize winner Santiago Ramón y Cajal's 'Advice for a Young Investigator' makes important points: 1. The only thing in your power is your preparation 2. Be suspicious of “brilliance” 3. Be appropriately respectful of authority, but no more 4. Balance concentration and relaxation 🔽
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Alfonso Martinez Arias @amartinezarias.bsky.social · 14/07/2026
In the midst of foundational models of the cell (or should I say pseudocell), seen as an “bag”, this www.cell.com/cell/fulltex... is a great antidote, and one that anyone who knows that a cell is more than its genes, can relate to and understand #RealCellsRUs #NotInTheGenes
cell.com
Establishing a conceptual framework for holistic cell states and state transitions
Technological advances have brought “big data” to the cellular level. Rafelski and Theriot share their vision of defining a cell's state in a holistic way that reflects all molecular, organizational, ...
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Saez-Rodriguez Group @saezlab.bsky.social · 09/07/2026
🧵 ParTIpy, our Python package for Pareto Task Inference just got published in Molecular Systems Biology (Peer reviewed at Review Commons) 🔗 Manuscript: link.springer.com/article/10.1... 💻 Code: github.com/saezlab/part... 📚 Docs: partipy.readthedocs.io/en/latest/
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Maxim Greenberg @maxvcg.bsky.social · 06/07/2026
I had an (honestly) really fun time writing up an "In Preprints" piece on the two fantastic studies from @grandlab.bsky.social and @schubelerlab.bsky.social. Check it out here. I have also put the original threads from the authors below. journals.biologists.com/dev/article/...
journals.biologists.com
In preprints – housekeeping the housekeeping genes
The term ‘housekeeping gene’ evokes a sense of banality. These are the boring genes that hum in the background, impervious to cell state or stress. For a developmental biologist captivated by the impa...
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