iiinova — where your digital self keeps evolving

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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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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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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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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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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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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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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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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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Mònica Sánchez-Guixé @guixe-m.bsky.social · 06/07/2026

I would like to announce that I have recently started my own research group, the Pediatric Cancer Genomics Laboratory, at Institut de Recerca Sant Joan de Déu (IRSJD) - Fundació de Recerca Sant Joan de Déu.

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Alfonso Martinez Arias @amartinezarias.bsky.social · 26/06/2026

It is important to be alarmed when there is something to be alarmed about. But this is NOT the case. NO, serious scientists don’t do that, and these are serious scientists. Importantly, if you read the paper -not the blurb- you will find in it a proper ethical statement with approval. 🧵

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MwahahahahahadScientist @mads100tist.bsky.social · 25/06/2026

As a scientist, I find it troubling we first do the experiments and *then* we talk about the ethics of it (but first we publish it high ofc)🧪

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Nikolai Slavov @slavov-n.bsky.social · 24/06/2026

Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 25/06/2026

fastQpick: scalable bootstrap and subsampling of FASTQ reads www.biorxiv.org/content/10.64898/20…

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Sinem Saka @sinemsaka.bsky.social · 21/06/2026

If you’ve built DNA-barcoded antibody panels, you know the pain: every barcode means another conjugation. In our new preprint we introduce UnO, which transforms antibody conjugation problem into a universal barcode conversion workflow, enabling rapid panel generation. www.biorxiv.org/content/10.6...

biorxiv.org

Universal oligo adapters for high-efficiency DNA-barcoded antibody panel generation

DNA-barcoded antibodies are central to a broad range of spatial and dissociative assays and applications, including multiplexed imaging, single-cell profiling, and proximity detection. Direct modifica...

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Dan Sarni @dansarni.bsky.social · 18/06/2026

What if DNA methylation changes aren’t just ticking of our biological clock but rather the rust breaking the gears? Very excited to share our work - how DNA methylation contributes to stem cell dysfunction and aging, published in @natgenet.nature.com doi.org/10.1038/s415... #epigenetics #aging 1/11

doi.org

A progeria syndrome links DNA hypermethylation to age-related pathology - Nature Genetics

This study investigates the consequences of hypermethylation in a progeria syndrome caused by gain-of-function DNMT3A mutations, finding effects on adult stem cell function.

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Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Mick Milsom @milsommick.bsky.social · 16/06/2026

Following some amazing discussions with colleagues at EHA about our recent publication in @natcellbio.nature.com, here are some important points showing why considering HSC reconstitution kinetics will make you re-think the concept of lineage biases rdcu.be/fkASJ 1/9

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Federico Gaiti @fgaiti.bsky.social · 11/06/2026

Happy to share our new review in Blood, led by Jiaoyi Chen & Benson Wu! We explore how DNA methylation can help retrace a cancer’s history and reveal how tumours evolve and respond to treatment. www.sciencedirect.com/science/arti...

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