iiinova — where your digital self keeps evolving

Reposted by Mari Sepp

allen institute @alleninstitute.org · 26/09/2026

Twenty years ago, on this day in 2006, Allen Institute for Brain Science announced the completion of our inaugural project: a web-based, 3D map of gene expression in the mouse brain providing scientists with a level of data previously not available. #openscience

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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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Justus Kebschull @justuskebschull.bsky.social · 21/09/2026

NEW PREPRINT! An evo-devo look at how new cerebellar nuclei are made. Spoiler: it’s all driven by region-specific excitatory progenitors in the early rhombic lip; inhibitory neurons fill in later. If you care about brain evolution or cerebellar development, check it out: tinyurl.com/CNdevelopment

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Fernando Garcia-Moreno @phylobrain.bsky.social · 18/09/2026

The cerebral cortex that is reading this sentence (yours, to be explicit) did not come out of nowhere. It has evolved over hundreds of millions of years... To study this evolutionary process, we decided to focus on non-avian reptiles for our new paper in Cerebral Cortex 🐢🦎🧠 🧵

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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026

Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...

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Riley Mangan @rimangan.bsky.social · 28/08/2026

I'm very excited to share the preprint of the central project of my postdoc, titled "Sequence-to-function deep learning decodes human cis-regulatory evolution" available today on BioRxiv. Preprint: www.biorxiv.org/content/10.6...

Figure 1: Sequence-based deep learning prediction of lineage-specific cis-regulatory elements in human evolution (a) Identification of lineage-specific cis-regulatory elements (linCREs). We generated diploid personalized genomes across 17 hominin and great ape short read sequencing libraries through reference-guided assembly. We used Enformer22 to predict genome-wide chromatin accessibility profiles across 100 epigenomic contexts across all 34 haplotypes. We compared chromatin accessibility at open chromatin elements to identify linCREs. (b) Six classes of linCREs, defined by the lineage and direction of differential accessibility. Schematics at top illustrate accessibility profiles defining each class. Total linCRE instances and the number of distinct loci are reported for each class. Predicted accessibility across all 34 haplotypes in a 3kb window centered on a representative example element of each class are shown below, colored by lineage.

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Mari Sepp @marisepp.bsky.social · 01/08/2026

Excited to see this preprint out! New work on the development of the enigmatic unipolar brush cells from the lab of @lenakutscher.bsky.social

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Mari Sepp @marisepp.bsky.social · 31/07/2026

Congratulations to all the F2F fellows! Wishing you all the very best on the exciting journey ahead.

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Mari Sepp @marisepp.bsky.social · 30/07/2026

Co-option of certain transposable elements as regulatory elements in specific cerebellar cell states, e.g. HERVL in rhombic lip–derived neuroblasts. Led by awesome Tetsuya @tyamadat.bsky.social, together with @ioansarr.bsky.social and @kaessmannlab.bsky.social

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Maria Antonietta Tosches @matosches.bsky.social · 29/06/2026

Better late than never... an update on the recent work from the lab. First of all, the Foundation: @astridd93.bsky.social phenomenal paper on the evolution of layering in the cerebral cortex 🧵1/7 www.biorxiv.org/content/10.1...

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Alex Schier @schierlab.bsky.social · 17/06/2026

Might cerebellar disinhibition underlie Restless Legs Syndrome symptoms? Will Joo found that loss of the RLS-associated gene meis1b perturbs locomotion in zebrafish by disinhibiting cerebellar output. www.sciencedirect.com/science/arti...

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The Transmitter @thetransmitter.bsky.social · 10/06/2026

According to @edvardmoser.bsky.social, director of the Kavli Institute for Systems Neuroscience, the four recipients of the Kavli Prize in Neuroscience challenged what had long been regarded as a central dogma in neuroscience. By Alissa de Chassey www.thetransmitter.org/awards/four-...

thetransmitter.org

Protein synthesis pioneers garner Kavli neuroscience prize

Their research revealed how neurons synthesize proteins in previously unrecognized places.

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Lili Milani @lilimilani.bsky.social · 27/05/2026

🧬 Join us at the 25th International Gene Forum – with stellar speakers from around the world (again)! Register now to secure your spot! 📅 August 25–26, 2026 📍 Estonian National Museum, Tartu, Estonia 🌐 Information & registration: www.geneforum.ee #Geneforum2026 #Geneforum

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Mari Sepp @marisepp.bsky.social · 27/05/2026

“By comparing gene activity across many species - from early vertebrates to humans - we can understand how we became who we are.” (hopefully precise enough) Prof. Dr. Henrik Kaessmann, evolutionary geneticist Recipient of the Ernst Schering Prize 2026 ❤️ Thrilled to see this, Henrik - congrats!

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Justus Kebschull @justuskebschull.bsky.social · 24/05/2026

For all cerebellum and cerebellar nuclei aficionados: A cre line specifically tagging the large, excitatory B-cells in the mouse cerebellar nuclei: www.biorxiv.org/content/10.6... Lmk if you want to use it!

biorxiv.org

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Justus Kebschull @justuskebschull.bsky.social · 17/05/2026

New from the lab: BARseq3! Barcodes + high efficiency spatial transcriptomics and translatomics in the same cells, or just a nice spatial transcriptomics assay. All in a modular, expandable system to enable truly multimodal measurements. Check it out: www.biorxiv.org/content/10.6...

biorxiv.org

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Kaessmann Lab @kaessmannlab.bsky.social · 08/05/2026

Huge congrats from our whole lab to Sir David Attenborough on his 100th birthday!!! 🎉🥳❤️ I had the honor of meeting him - and being interviewed by him - in 2013 for his BBC documentary "Rise of Animals: Triumph of the Vertebrates", which featured part of our work.

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Johanna Joyce @johannajoyce.bsky.social · 22/04/2026

What should Europe do when demand for #ERC funding keeps rising? Restrict access or invest in excellence? Please read our open letter calling for reconsideration of the ERC 2027 resubmission restrictions & for constructive alternatives that preserve openness Consider to share & sign - see below 🧪

linkedin.com

#erc | Johanna Joyce

What should Europe do when demand for its most successful frontier research programme keeps rising? Restrict access, or invest in the excellence it has created? A new open letter, spearheaded by Sara...

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Idoia Quintana-Urzainqui @idoiaeu.bsky.social · 21/04/2026

🦈🧠2 JOB OFFERS in the brand-new Neuroshark group starting at the Institute of Neuroscience Paris-Saclay (NeuroPSI)? Lab manager: www.linkedin.com/posts/idoia-... Bioinformatician: www.linkedin.com/posts/idoia-... Curious about the lab but not your profile? Feel free to contact me

linkedin.com

Lab manager job | Idoia Quintana Urzainqui

JOB OPPORTUNITY 🦈 🧠 🔬. We are looking for a Lab Manager to help establish a new group studying shark embryos to understand the origin of the vertebrate brain. Reach out if this motivates you. We’re ba...

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Mari Sepp @marisepp.bsky.social · 20/04/2026

By applying for an MSCA Postdoctoral Fellowship with the University of Tartu, you can access 3 funding pathways: MSCA, ERA Fellowships, and national funding schemes. Get in touch if interested in brain development, autism spectrum disorders, and single-cell genomics. ut.ee/en/content/p...

ut.ee

Postdoctoral research at the University of Tartu

Estonia, a hub of innovation and cutting-edge research, offers a vibrant ecosystem for postdoctoral researchers.

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Manuel Irimia @mirimiam.bsky.social · 20/04/2026

Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬 Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15 www.biorxiv.org/content/10.6...

biorxiv.org

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Stein Aerts @steinaerts.bsky.social · 16/04/2026

Very proud of this and so cool that enhancer-level models can predict the effect of genetic variation. There is so much personal variation in terms of gene regulation in the human brain, it is fantastic to uncover this thanks to technology (whole-genome sequencing and single-cell multiomics) and AI

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Mari Sepp @marisepp.bsky.social · 31/03/2026

Exciting study by @lenakutscher.bsky.social and @doctorpauln77.bsky.social on male bias in medulloblastoma: “testosterone and the XY genotype cooperate to increase the abundance of specific cerebellar progenitor populations” Elegant use of Four Core Genotypes mice + recapitulation in organoids

ky.social

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Mari Sepp @marisepp.bsky.social · 30/03/2026

Amazing Margarida and her amazing research. Curiosity and enthusiasm in action 💙

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Jörn Diedrichsen @diedrichsenjorn.bsky.social · 24/03/2026

Also out today - A quick intro piece on the role of the cerebellum in cognition. What does it do? How will we find out? This is what @actlab.bsky.social and I think the critical questions are right now. It was fun to write - especially the section on evolution.... journals.plos.org/plosbiology/...

journals.plos.org

How does the cerebellum contribute to cognitive functions?

The role of the cerebellum in motor functions is well understood. But why is the same circuitry engaged in functions such as working memory, language, and social cognition? This Unsolved Mystery looks...

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Lena Kutscher @handle.invalid · 24/03/2026

interested in working on sex differences during development and in tumor initiation! come join our lab via the MSCA MasterClass

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Dario Tommasini @dariotommasini.bsky.social · 10/03/2026

Inhibitory neurons are among the most transcriptomically diverse class of neurons in the CNS, with some brain regions having 60+ distinct cell types. Do humans share the same repertoire as rodents? Birds? Fish? 1/13

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The Brain Prize @brainprize.org · 05/03/2026

Warm congratulations to The Brain Prize winners 2026, Professor David Ginty and Professor Patrik Ernfors, for their pioneering work on how the nervous system detects and processes touch and pain. Karolinska Institutet HHMI #Neuroscience #BrainPrize2026

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Mari Sepp @marisepp.bsky.social · 03/03/2026

A beautiful 😍 review on vertebrate organ evolution - from molecular basis and evolutionary forces to the emergence of novel forms and functions.

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Mari Sepp @marisepp.bsky.social · 12/02/2026

How have concerted and mosaic evolutionary mechanisms shaped the expansion of the human cerebellum? Our review with @tyamadat.bsky.social and @ioansarr.bsky.social available free till March 29: authors.elsevier.com/a/1ma2wFzn7a...

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Lena Kutscher @handle.invalid · 11/02/2026

Ramsey Najm and I have a joint postdoc position advertised through the @hlsalliance.bsky.social Interinstitutional Postdoc call! Our project proposes to generate better posterior cerebellar organoids to improve fidelity of pediatric medulloblastoma models. www.health-life-sciences.de/opportunitie...

health-life-sciences.de

HEALTH + LIFE SCIENCE ALLIANCE | Interinstitutional Postdocs

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Urmo Võsa @urmovosa.bsky.social · 09/02/2026

Hiring a PhD student! 🎓 Looking for a PhD student to work on the prediction of complex diseases by integrating genetics, multi-omics, and electronic health records. Details: genomics.ut.ee/sites/defaul... Please share with anyone interested!

genomics.ut.ee

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Lena Kutscher @handle.invalid · 08/02/2026

Some friends and I wrote a review with @biologists.bsky.social !! Together with Esther Becker and Simone Mayer, we explore the state of the cerebellum organoid field and offer practical guidance on getting this model system started in your own lab. journals.biologists.com/dmm/article/...

journals.biologists.com

Generating cerebellar organoids from pluripotent stem cells

Summary: This Special Article provides a comprehensive overview of the methods, applications and considerations for the generation of cerebellar organoids.

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Mari Sepp @marisepp.bsky.social · 08/02/2026

Congrats to @urmovosa.bsky.social and the international research team behind this achievement, including colleagues at @estbiobank.bsky.social!

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Mari Sepp @marisepp.bsky.social · 29/01/2026

This paper marks the end of a long but rewarding project - and the start of something new (more below👇). Massive thanks to @kaessmannlab.bsky.social, @ioansarr.bsky.social, @tyamadat.bsky.social, our amazing collaborators @steinaerts.bsky.social, Stefan Pfister, Rüdiger Behr and the entire team! 💙

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Mari Sepp @marisepp.bsky.social · 20/01/2026

Big congrats to @kmatlik.bsky.social and all the EMBO Installation Grantees 2026! 👏🎉

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Stein Aerts @steinaerts.bsky.social · 15/01/2026

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

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Fena Ochs @fenaochs.bsky.social · 02/01/2026

We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...

nature.com

Postdocs at Center for Gene Expression in Department of Cellular and Molecular Medicine - Copenhagen, Hovedstaden (DK) job with University of Copenhagen | 12849488

We are looking for 2 or more highly motivated postdocs interested in ribosome biology, 3D chromatin organisation, or regulation of protein turnove...

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Idoia Quintana-Urzainqui @idoiaeu.bsky.social · 22/12/2025

Really happy to join NeuroPSI at Paris Saclay to lead a research group funded by an ERC Consolidator grant #ERCCoG . We'll study the origins of the vertebrate brain using shark embryos. 🦈 🧠 Reach out if you are interested in joining the team 🤍

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Margarida Cardoso Moreira @margaridamcm.bsky.social · 17/12/2025

Join us at SMBE26! We are in a golden period for understanding the evolution of gene regulation.

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Simons Foundation @simonsfoundation.org · 11/12/2025

In 2018, Tomasz Nowakowski received our Fellows-to-Faculty Award to jumpstart his new lab. We spoke with him about his research and the Fellows-to-Faculty program, which is open for apps: www.simonsfoundation.org/fellows-to…

simonsfoundation.org

Fellows-to-Faculty Alum Tomasz Nowakowski Studies Human Cortical Development

Simons Foundation Fellows-to-Faculty alumnus Tomasz Nowakowski spoke with the foundation about his experiences with the program.

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Idoia Quintana-Urzainqui @idoiaeu.bsky.social · 09/12/2025

#ERCCogG granted!!! Immensely grateful for this opportunity. Thanks @erc.europa.eu . Many news coming soon. New lab opening and will be posting positions. 🦈🧠🤍 Go sharkies!

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Reza Shadmehr @rezashadmehr.bsky.social · 08/12/2025

We tend to think of neurons as either excitatory or inhibitory, but some neurons chemically inhibit their downstream targets while electrically exciting their neighbors. What is gained by having an inhibitory neuron excite its neighbor? www.biorxiv.org/content/10.6...

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Damir Baranasic @da-bar.bsky.social · 03/12/2025

JASPAR 2026 is out 🎉 The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models. Database: jaspar.elixir.no Paper (NAR): doi.org/10.1093/nar/... 🧵1/2

jaspar.elixir.no

JASPAR: An open-access database of transcription factor binding profiles

JASPAR is the largest open-access database of curated and non-redundant transcription factor (TF) binding profiles from six different taxonomic groups.

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Leopold Parts @leopoldparts.bsky.social · 03/12/2025

Claudia Feng's Ph.D work is now out, co-led with @brittavelten.bsky.social and @steglelab.bsky.social . Large-scale CRISPRi perturbations in genetically heterogenous iPSC lines, with single cell readout - enjoy :)

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