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Marco Podobnik

@mpodobnik.bsky.social
426 followers 465 following 42 posts

Walter Benjamin Fellow at @armilabs.bsky.social‬ Melbourne interested in all things developmental, regenerative, and evolutionary biology. @mpi-bio-fml.bsky.social alumnus. marcopodobnik.wordpress.com

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Reposted by Marco Podobnik
Nature Reviews Genetics @natrevgenet.nature.com · 17/09/2026
ICYMI: New online! Zebrafish relatives as models for functional comparative genetics and genomics
dlvr.it
Zebrafish relatives as models for functional comparative genetics and genomics
Nature Reviews Genetics, Published online: 10 September 2026; doi:10.1038/s41576-026-01007-4Comparative functional genetics and genomics across Danio, Devario and Danionella species reveal molecular and cellular bases of phenotypic divergence, establishing danionin fishes as powerful model systems for understanding a wide range of evolutionary innovations.
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Marco Podobnik @mpodobnik.bsky.social · 17/09/2026
Analyse your teleost skeletal muscle section with fishROI - Now published: link.springer.com/article/10.1...
link.springer.com
fishROI: a specialized workflow for semi-automated muscle morphometry analysis in teleosts - Skeletal Muscle
Background Quantitative histological analysis of skeletal muscle morphometry provides critical insights into muscle physiology but remains labor-intensive and technically demanding. While recent devel...
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Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Marco Podobnik @mpodobnik.bsky.social · 10/09/2026
Our @natrevgenet.nature.com article out now. This is a hymn to danionin fishes, with sections on phylogeny, reproduction, immunity, morphology, regeneration and behaviour. rdcu.be/CntbxvfZsUba
rdcu.be
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Nature Reviews Genetics @natrevgenet.nature.com · 10/09/2026
New online! Zebrafish relatives as models for functional comparative genetics and genomics
dlvr.it
Zebrafish relatives as models for functional comparative genetics and genomics
Nature Reviews Genetics, Published online: 10 September 2026; doi:10.1038/s41576-026-01007-4Comparative functional genetics and genomics across Danio, Devario and Danionella species reveal molecular and cellular bases of phenotypic divergence, establishing danionin fishes as powerful model systems for understanding a wide range of evolutionary innovations.
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Marco Podobnik @mpodobnik.bsky.social · 10/09/2026
Our @natrevgenet.nature.com article out now. This is a hymn to danionin fishes, with sections on phylogeny, reproduction, immunity, morphology, regeneration and behaviour. rdcu.be/CntbxvfZsUba
rdcu.be
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Sepand Rastegar @rastapopolus.bsky.social · 10/09/2026
🐟 1st German Fish Model Research Meeting | Sept 16–18, 2026, Heidelberg. ~200 participants, 40 talks, 75 posters. Keynotes: Tilly Mommersteeg, Laure Bally-Cuif, Ferenc Müller. germanfishmeeting.org #Zebrafish #FishModels
germanfishmeeting.org
1st German Fish Model Research Meeting | German Fish Model Research Meeting
Discover the 1st German Fish Model Research Meeting—uniting global experts on zebrafish, cavefish, killifish, medaka & more. Join us to collaborate, share breakthroughs, and advance fish biology resea...
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Reposted by Marco Podobnik
Alex Schier @schierlab.bsky.social · 08/09/2026
The first Danionella paper from the lab. Danionella cerebrum is transparent, so you can see all of the internal organs. But what sensory information are the organs sending to the brain? In our new preprint, Emily Bayer wanted to find out. 1/4 www.biorxiv.org/content/10.6...
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Misha Ahrens @mishaahrens.bsky.social · 09/09/2026
Whole-body cellular activity imaging in zebrafish, headed by Virginie Ruetten @vmsruetten.bsky.social - new paper is out: www.nature.com/articles/s41...
nature.com
Imaging cellular activity across all organs reveals body-wide circuits - Nature
An imaging system developed to record cellular activity throughout the whole body of zebrafish captures cellular organ dynamics and identifies multiple distributed circuits.
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Reposted by Marco Podobnik
EMBL Australia @emblaustralia.org · 28/08/2026
Ready to take the next step in your research career? 👨‍🔬 We're seeking an outstanding researcher to establish an independent research program as an EMBL Australia Group Leader at the Australian Regenerative Medicine Institute (ARMI) @monashuniversity.bsky.social 🗓️ Apply by 2 October 🔗 bit.ly/4qHYtjb
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Raphaël Clément @raphclement.bsky.social · 27/08/2026
A developmental biologist's guide to mechanics, just out in Development! In which we learn about the three pillars of any mechanical model: forces, mechanical properties, and boundary conditions. @pflenne.bsky.social @alessandrochppr.bsky.social @caojialing1002.bsky.social @dev-journal.bsky.social
journals.biologists.com
A developmental biologist's guide to mechanics
Summary: A guide to mechanics in development: unlock how forces, material properties and geometry shape the forms of life.
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Kate Cavanaugh @katecavanaugh.bsky.social · 25/08/2026
🧵 What if one reason fertility declines with age isn’t just genetic-but mechanical? Thrilled to share our new paper in @NatureCellBio : Elevated contractility drives implantation failure in mouse embryos from aged females… here’s what we found 👇 www.nature.com/articles/s41... 1/11
nature.com
Elevated contractility drives implantation failure in mouse embryos from aged females - Nature Cell Biology
Cavanaugh et al. show that embryos from aged mice have increased contractility and tissue viscosity on embryonic day 4.5, which leads to poor spreading and attachment. Similar age-associated mechanica...
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Stefano Di Talia @ditalialab.bsky.social · 24/08/2026
Happy to see Ashley's paper out @natphys.nature.com www.nature.com/articles/s41...
nature.com
Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration
Nature Physics - Zebrafish can regenerate amputated fins back to their original size. It is now shown that gradients in extracellular signal-regulated kinase activity act as rulers during fin bone...
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Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
biorxiv.org
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
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The Company of Biologists @biologists.bsky.social · 11/08/2026
We are gathering feedback from our readers, authors and reviewers about the use of AI tools in scholarly publishing. Have your say at: www.surveymonkey.com/r/ZBFC663
Community survey: The role of AI tools in scholarly publishing — announcement from The Company of Biologists, showing five stylized people and three speech bubbles to represent community discussion.
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Nature Reviews Genetics @natrevgenet.nature.com · 11/08/2026
New online! Genetics and genomics of hybridization
dlvr.it
Genetics and genomics of hybridization
Nature Reviews Genetics, Published online: 11 August 2026; doi:10.1038/s41576-026-00995-7Hybridization, the exchange of genes between divergent lineages, is now recognized as widespread across eukaryotes and essential to understanding genome evolution. In this Review, Schumer and Rieseberg overview methodological advances facilitating recent progress, reassess the frequency, causes and consequences of hybridization, and highlight key open questions.
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Tom Baden @neurofishh.bsky.social · 18/08/2026
New primer on Danionella cerebrum, with @xinwei-wang.bsky.social . What a fun little fish :) Free access here: authors.elsevier.com/a/1ndEe_LsQS...
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Bob Wong @bbmwong.bsky.social · 11/08/2026
Are you an ecologist/evolutionary biologist looking for an ongoing academic position? Monash University’s School of Biological Sciences is hiring! Come join us in Melbourne, Australia! Details here: careers.pageuppeople.com/513/cw/en/jo...
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Ensembl @ensembl.org · 10/08/2026
Ensembl is moving this week! 🧬 Links will point you to the new Ensembl. The default site will be ensembl.org for all species from across the tree of life. We’re starting with the Ensembl Genomes sites, and we’ll end with the Ensembl 116 site.
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International Zebrafish Society @izfs.bsky.social · 04/08/2026
NEW GRANT OPPORTUNITY! Ever wanted to travel to a different lab to learn more? Or expand your knowledge and experience in the field? #IZFS has a new grant opportunity for you! Read more about the Knowledge Exchange Grant here: www.izfs.org/awards/knowl... #ZebrafishGrant
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Zebrafish Rock! @zebrafishrock.bsky.social · 25/07/2026
"The importance of a model is choosing one that allows you to address the question that you’re setting out to address." Sage advice from Prof. Judith Eisen (University of Oregon), Pioneer of Zebrafish Research & 2024 George Streisinger Award Winner. #ZebrafishFunFacts 🧪
Image of Professor Judith Eisen.
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Nicholas Bellono @nbellono.bsky.social · 09/07/2026
How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...
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Steffen Scholpp @scholpplab.bsky.social · 08/07/2026
No better way to head to #EZM2026 than with a freshly published success! Our eLife paper is now out: elifesciences.org/articles/107.... We show optimised prime editing in zebrafish for precise DNA substitutions and insertions. Huge thanks to the fantastic team #Zebrafish #GenomeEditing #eLife
elifesciences.org
Optimised genome editing for precise DNA insertion and substitution using prime editors in zebrafish
Nickase and nuclease Prime Editors offer complementary routes for precise zebrafish genome editing, balancing accuracy for substitutions with efficiency for short insertions.
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Austin Seroka @austinseroka1.bsky.social · 06/07/2026
We're excited to present a single-cell atlas of vertebrate cranial motor neuron development, the first story from my postdoctoral work in the Moens lab, up now on bioRxiv!
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EnriquezLab @enriquezlab.bsky.social · 02/07/2026
How do dozens of distinct muscles emerge from the same pool of precursor cells? Our new Science Advances paper uncovers the developmental logic that coordinates myoblast identities to build diverse muscles. 📄 www.science.org/doi/10.1126/... #DevelopmentalBiology #Drosophila #Muscle
science.org
Spatiotemporal control of myoblast identity drives muscle diversity in the Drosophila leg
This study reveals how muscle diversity arises in flies, enabling the complex movements that drive animal behavior.
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Emre Yaksi @emreyaksi.bsky.social · 02/07/2026
I am excited to announce the latest paper from our lab, published in Science ! In this study, we show that thalamocortical-like circuits in the zebrafish brain process sensory information hierarchically across topographically organized forebrain circuits.
science.org
Hierarchical sensory processing in zebrafish thalamocortical-like circuits
Thalamocortical projections shape the functional regionalization and parallel sensory computations across the mammalian cortex. However, the principles of thalamocortical computations in non-mammalian...
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Igor Adameyko @adameykolab.bsky.social · 02/07/2026
Dear Friends, I just published an insightful review on neural crest evolutionary origin and later transformations. “Co-option and innovation in neural crest evolution”: www.science.org/doi/10.1126/...
science.org
Co-option and innovation in neural crest evolution
Neural crest evolution reassembled ancient programs in pigment cell lineage, resulting in vertebrate innovations.
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Syd Sattler @sydsat.bsky.social · 29/06/2026
What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵
biorxiv.org
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
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Phil Abitua @ohnolog.bsky.social · 30/06/2026
Annual killifish continue to surprise us: they make neutrophils before almost every other cell type, even before gastrulation. Neutrophils usually arise from the lateral plate mesoderm (forming in cyan), but in killifish they are already patrolling around the embryo in gold. tinyurl.com/killiphil
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Project Gutenberg @gutenberg.org · 27/06/2026
We read an entire scroll — without ever opening it PHerc. 1667, sealed since the eruption of Vesuvius in 79 AD, has been virtually unwrapped and read from beginning to end scrollprize.org/firstscroll The Herculaneum Papyrus Scrolls project www2.cs.uky.edu/dri/herculan... #books #old_Manuscripts
Part of Herculaneum Papyrus 1005 (P.Herc. 1005), col. 5. Contains Epicurean tetrapharmakos from Philodemus' Adversus sapientes ex libris. Original from 1st century(?). Handwritten copy by Giuseppe (?) Casanova 1803-1806.

https://en.wikipedia.org/wiki/Herculaneum_papyri#/media/File:Tetrapharmakos_PHerc_1005_col_5.png
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Itai Yanai @itaiyanai.bsky.social · 24/06/2026
🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92
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M. Brent Hawkins @homeobox.bsky.social · 22/06/2026
Excited to share the final published version of our work on the evolution of dorsal-ventral patterning in fins and limbs, now up on @currentbiology.bsky.social In review we added new single LARM element deletions to assess their impact on dorsality. Take a look! 🔬🧪🐟🐁 www.cell.com/current-biol...
A scientific figure showing the phenotypic effects of removing individual enhancer elements from the LARM. On the left side of the image are schematic diagrams of the targeted deletions and on the right are fin skeletons showing altered anatomy.
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Alfonso Martinez Arias @amartinezarias.bsky.social · 21/06/2026
IMPORTANT study from @hocinerekaik.bsky.social @denisduboule.bsky.social and a significant validation of SCBEMs, #gastruloids in particular, as a discovery tool www.biorxiv.org/content/10.6... 🧵
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James Briscoe @jamesbriscoe.bsky.social · 18/06/2026
As Editor of @dev-journal.bsky.social I get asked "What are you doing about your impact factor?" In our new editorial we say: Ask not what Dev can do for the impact factor. Ask what you can do for Dev's IF The IF is about how we all cite, review & assess each other's work doi.org/10.1242/dev....
doi.org
The elephant in the room: impact factor
Summary: This Editorial offers an honest look at impact factor trends in developmental biology, explains how Development serves its community, and makes the case that sustaining developmental biology ...
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Braasch Lab @ Michigan State University @fishevodevogeno.bsky.social · 13/06/2026
In memory of David Hockney: Your Outer Fish #FishArt
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Ben Hogan @benjhogan.bsky.social · 09/06/2026
Just a few months to IVBM in Australia! Come down and enjoy great science, food, beaches, wine and company. Time to register now at ivbm2026.com
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Marco Podobnik @mpodobnik.bsky.social · 08/06/2026
Dear all, please join my @isrbio.bsky.social webinar on how danionin fishes grow skeletal muscle. Tomorrow via Zoom. Details here: isrbio.org/webinars
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Tschopp Lab @tschopplab.bsky.social · 14/05/2026
One of my dream projects, ever since joining here in Basel, out now in @nature.com : single-cells 🤝 eco-morphological proxies rdcu.be/fiyso How cells and tissues adapt to dietary niches... Thanks and congrats to Antoine, Walter, and all the other co-authors for this great collaboration!! 🙏🥳
rdcu.be
Adaptive cellular evolution in the intestine of hyperdiverse cichlid fishes
Nature - Single-cell transcriptomics combined with morphological and ecological data show that the rapid evolutionary radiation of cichlid fishes in Lake Tanganyika was accompanied by dietary...
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Molly Schumer @mollyschumer.bsky.social · 12/05/2026
Excited to share this new pre-print from the fantastic @kelsiehunnicutt.bsky.social! Kelsie put together a thoughtful and thorough review on hybridization in animal evolution: ecoevorxiv.org/repository/v.... She tracks notable shifts in perspectives on the study of hybridization through time.
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Shawn Burgess @burgesslab.bsky.social · 04/05/2026
Some great news, Ensembl has released the GRCz12tu and the GRCz12ab annotations on their beta release site, so now the genes can be looked at in a genome browser. You can load up either one (plus a second TU genome) here: beta.ensembl.org/species-sele... #zebrafish
beta.ensembl.org
Species selector — Ensembl
Select one or more species to start using Ensembl
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James Gagnon @james-gagnon.bsky.social · 28/04/2026
Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...
A cartoon showing how a caged guide RNA poises CRISPR cleavage until release by light. Below, a cartoon of injection of "light-activated CRISPR" into the embryo, followed by activation.
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Zebrafish Rock! @zebrafishrock.bsky.social · 28/04/2026
New tool from the Currie Lab @armilabs.bsky.social 🐟
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Eric Topol @erictopol.bsky.social · 27/04/2026
This NYT magazine article on longevity science, reversing aging with cellular reprogramming, is over the top. We have no proof that rejuvenation of a human organ is possible, no less the whole body, and there is risk of inducing cancer. gift link www.nytimes.com/2026/04/27/m...
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Michalis Averof @michalis-averof.bsky.social · 19/04/2026
These images show live embryos of animals (jellyfish, crustacean, worm, sea urchin, sea squirt, beetle) and one of animals closest single-celled relatives. They were captured taking advantage of fluorescent proteins localised on the outer membrane of cells, allowing us to observe cell outlines. 1/9
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Melanie D. White @melaniedwhite.bsky.social · 01/04/2026
I'm so pleased to see this work on neural crest development out in Nature today! This was a truly fantastic collaboration with @gleesonlab.bsky.social, Keng loi (Harry) Vong and @xiaoxuyang.bsky.social. Huge thanks to everyone involved 👏 🧪🐣 #devbio www.nature.com/articles/s41...
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MadScientist @mads100tist.bsky.social · 16/03/2026
It's out! Happy to present ITEC, a semi supervised algorithm with an extremely low error rate that can track cells in files of any size (think Terabytes!). We used it in many organisms, including zebrafish, to study how organs form and linked it to gene expression www.biorxiv.org/content/10.6... +🧪
biorxiv.org
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Alex Schier @schierlab.bsky.social · 12/03/2026
Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Margarida Cardoso Moreira @margaridamcm.bsky.social · 25/02/2026
Our internal organs are evolutionary marvels. New technologies are transforming our understanding of the evolution of vertebrate organs. You can find more by reading here: rdcu.be/e5EgU #EvoBio #EvoDevo 🐟🦎🐢🦇🐊🦜
rdcu.be
The molecular evolution of vertebrate organs
Nature Ecology & Evolution - This Review discusses recent advances in the molecular evolution of vertebrate organs, including rates of evolution of organs and cell types, molecular mechanisms...
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Marco Podobnik @mpodobnik.bsky.social · 25/02/2026
Beautiful work led by Yansong (Kevin) Lu on skeletal muscle growth in zebrafish, giant danio, Danionella cerebrum, and killifish. HCR, new image analysis tool, scRNA-seq, and CRISPR. New international collaborations between Uni Melbourne, NCVC/Osaka, Stanford & ARMI www.biorxiv.org/content/10.6...
New morphometric analysis tool developed by Lu et al. applied to skeletal muscle cross-sections of four different juvenile teleost fish species. Main finding: Mosaic hyperplasia, i.e., the addition of new myofibers in the deep myotome, is near-zero in the small Danionella but dramatically enhanced in the giant danio relative to the intermediate grower zebrafish, establishing this mode of hyperplasia as a main driver of skeletal muscle growth in differently sized fishes.
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Parichy Lab | Dave Parichy @dparichy.bsky.social · 23/02/2026
We have a postdoc position available. Please forward to anyone who may be interested.
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