iiinova — where your digital self keeps evolving

Micha Müller @michamuller.bsky.social · 09/10/2026

And thank you @marvintanenbaum.bsky.social, who was a great mentor throughout my PhD, which came to an end yesterday. I’ll miss you and all the other lab members sorely!

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Micha Müller @michamuller.bsky.social · 09/10/2026

I had such a great time working with so many people at the Hubrecht on this, and learned an enormous amount about single-cell genomics, DNA damage and chromosome missegregation from the @jopkind.bsky.social kind.bsky.social and @kopslab.bsky.social

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Micha Müller @michamuller.bsky.social · 09/10/2026

For more details, here's the link to the preprint: www.biorxiv.org/content/10.6...

biorxiv.org

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Micha Müller @michamuller.bsky.social · 09/10/2026

As a proof of principle, we induced chromosome missegregation in RPE-1 cells with an Mps1 inhibitor, then used Waldo to link the live-cell phenotypes (e.g. micronuclei, nuclear deformation) to the karyotype and transcriptome of the same cell (scKaryoSeq + scRNA-seq).

Two example cells followed by imaging and then sequenced. Top: time-lapse example images from 0 to 18 hours. Cell 1 goes through mitosis at 4.5 hours and forms a micronucleus, marked by dashed boxes; Cell 2 never divides. Bottom left: an scRNA-seq UMAP coloured by inferred cell-cycle phase, with both cells located on it. Bottom right: single-cell karyotypes, showing Cell 1 with one copy of chromosome 13 and three copies of chromosome 17, while Cell 2 is diploid throughout.

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Micha Müller @michamuller.bsky.social · 09/10/2026

For single-cell sequencing, barcodes can be read out either from the mRNAs that encode the Waldo receptors, or from the same probes used for imaging, coupled to a DNA barcode instead of a fluorescent dye. Both can be captured in one library, but either also works on its own.

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Micha Müller @michamuller.bsky.social · 09/10/2026

Staining and destaining take only a few minutes, because the probe is small and a ssDNase rapidly cleaves the linker between peptide and dye. Each barcode round therefore fits between imaging time-points, and since it uses a single channel, phenotyping can be continued alongside it.

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Micha Müller @michamuller.bsky.social · 09/10/2026

Waldo barcodes are made of synthetic receptor-probe pairs displayed at the cell surface, so they can be read out in live cells. To get barcodes complex enough to label many cells uniquely, we read the receptors iteratively, so diversity is not capped by the number of fluorophores.

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Micha Müller @michamuller.bsky.social · 09/10/2026

Very excited to share Waldo: a genetic single-cell barcode that can be read out in both live-cell imaging and single-cell sequencing, so both measurements can be made for the same cells. ⬇️

Schematic of Waldo barcoding. Two cartoon cells each display a different combination of coloured synthetic receptors on their surface, giving each cell a distinct barcode shown below it as a row of numbered coloured and black squares. Three boxes at the top show the same receptor detected three ways: by a fluorescent peptide probe, by a peptide probe carrying a DNA barcode, and as barcoded receptor mRNA.

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Reposted by Micha Müller

Peter Ly @peterlylab.bsky.social · 19/05/2026

Excited to share our latest paper! We found that large pieces of the human genome can transfer between cells upon direct contact, endowing recipient cells with heritable phenotypic changes. @cp-cell.bsky.social (1/7) www.cell.com/cell/fulltex...

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Marvin Tanenbaum @marvintanenbaum.bsky.social · 13/05/2026

For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...

biorxiv.org

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Reposted by Micha Müller

Bram Verhagen @bramverhagen.bsky.social · 13/05/2026

Happy to share our preprint! Using massively parallel reporter assays, single-molecule imaging, deep learning and cryo-EM, we decode the sequence requirements for translation initiation and describe the “extended translation initiation sequence” (eTIS) that modulates start codon recognition. 🧵👇

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Reposted by Micha Müller

Hubrecht Institute @hubrechtinstitute.bsky.social · 16/02/2026

For the first time, scientists watched the flu virus live as it infected human airway cells. The group from @marvintanenbaum.bsky.social developed a new imaging technique, VISUN, and observed a large variation in infection success. See www.hubrecht.eu/flu-virus/. Video by @janinschoko.bsky.social

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Micha Müller @michamuller.bsky.social · 12/02/2026

Our paper on visualising influenza A virus in live cells with single viral RNA resolution is now out in Cell Systems 🥳 For more details about what we did, see the thread about the preprint below ⬇️

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Marvin Tanenbaum @marvintanenbaum.bsky.social · 28/01/2026

Now out in Nature! We visualize infection of the RNA virus RSV in real-time with single-vRNP resolution to understand how RSV establishes viral factories, biomolecular condensates that act as sites of viral replication. A huge collaborative effort led by Dhanushika Ratnayake! rdcu.be/e1bBW

rdcu.be

Pre-assembly of biomolecular condensate seeds drives RSV replication

Nature - Viral ribonucleoprotein–viral protein networks form pre-replication centres that nucleate viral factories and drive respiratory syncytial virus replication.

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Reposted by Micha Müller

Maximilian Madern @maxmadern.bsky.social · 20/01/2026

Excited to share our new paper! We developed a method to visualize proteasomal degradation at the single–molecule level in live cells, enabling us to dissect distinct modes of substrate engagement, probe co-factor dependence, and study proteasome–ribosome collisions. www.biorxiv.org/content/10.6...

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Reposted by Micha Müller

Arjun Raj @arjunraj.bsky.social · 14/11/2025

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

cell.com

Single-cell susceptibility to viral infection is driven by variable cell states

Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

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Reposted by Micha Müller

Hubrecht Institute @hubrechtinstitute.bsky.social · 28/04/2025

It's possible to apply for the Hubrecht Talent Program again! The HTP aims to promote scientific excellence in the Netherlands by supporting talented minority students in pursuing a career in scientific research. Read more in the flyer and on www.hubrecht.eu/about-us/hub...

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Reposted by Micha Müller

Ina Sonnen @sonnenlab.bsky.social · 11/03/2025

How do embryos ensure precise tissue patterning? It’s all about timing cell divisions! Our new preprint reveals how cell proliferation syncs with signaling oscillations to regulate precision of somite formation and growth. Check the full story: www.biorxiv.org/content/10.1...

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Reposted by Micha Müller

Maximilian Madern @maxmadern.bsky.social · 03/02/2025

Our paper is out! We delevoped a method to follow individual translating ribosomes for hours in living cells, and discovered that ribosomes are great friends and help each other in problematic situations: www.cell.com/cell/fulltex...

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Reposted by Micha Müller

Marvin Tanenbaum @marvintanenbaum.bsky.social · 03/02/2025

Our paper on Stopless-ORF Circular RNAs (socRNAs) is now out in Cell. By high-res tracking and comparing translation by either single or multiple ribosomes, we find that ribosomes cooperate to overcome pausing to ensure fast and efficient translation www.cell.com/cell/fulltex...

cell.com

Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation

Ribosomes cooperate through transient collisions to ensure efficient translation.

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Reposted by Micha Müller

Marvin Tanenbaum @marvintanenbaum.bsky.social · 21/01/2025

Our new paper is out: "Mapping the complete influenza A virus infection cycle through single vRNP imaging". Combining newly-developed single-molecule imaging approaches with in situ viral transcriptomics, we identify numerous non-canonical infection pathways. www.biorxiv.org/content/10.1...

biorxiv.org

Mapping the complete influenza A virus infection cycle through single vRNP imaging

Cell-to-cell heterogeneity is a common feature of viral infection that can generate enormous complexity, complicating understanding of infection progression and interpretation of differences between v...

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Micha Müller @michamuller.bsky.social · 21/01/2025

This was a big team effort by the bsky-less @Huib, @janinschoko.bsky.social, @baarsmatthijs.bsky.social and Jakob in @marvintanenbaum.bsky.social lab. Also, a great collaboration with @RonFouchier and @antonelladost.bsky.social & @hansclevers.bsky.social on the patient samples and airway organoids!

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Micha Müller @michamuller.bsky.social · 21/01/2025

We envision that the tools described in this manuscript open up new avenues to study IAV biology in unprecedented detail. Conceptually, with virus-specific modifications our imaging systems are even broadly applicable to many different (-)RNA viruses.

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Micha Müller @michamuller.bsky.social · 21/01/2025

(3) Finally, we found that even when vRNPs are present, they often lack transcriptional activity. As a result, most infected cells only transcribe very few vRNPs. We conclude that viral transcription itself is a highly limiting factor in determining the successful outcome of IAV infections.

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Micha Müller @michamuller.bsky.social · 21/01/2025

(2) Mitosis causes vRNPs to be distributed over two separate sister cells. Therefore, these sister-cells often end up having incomplete sets of genome segments. We termed this “viral aneuploidy”, akin to chromosome segregation errors occurring during host cell division.

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Micha Müller @michamuller.bsky.social · 21/01/2025

(1) As previously reported, due to the segmented nature of the IAV genome, virions can lack one or multiple genome segments. We confirmed this both by using live-cell imaging of incoming vRNPs and by performing smFISH on viral particles.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Finally, we wondered what the underlying reason for the observed defects in viral gene expression could be and found three mechanisms:

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Micha Müller @michamuller.bsky.social · 21/01/2025

We analyzed naturally occurring single-gene KOs (cells expressing all but one viral gene) - which are otherwise hard to generate because most viral genes are essential - to study viral protein function and gained insights into which proteins are important for viral replication and nuclear export.

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Micha Müller @michamuller.bsky.social · 21/01/2025

We wondered why so many infections fail to progress through all life-cycle stages. We combined our live-cell imaging technologies with multiplexed smFISH and found that many viruses fail to transcribe one or multiple genes.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Using single-cell traces of many hundreds of cells, we constructed a kinetic map of IAV infections, revealing large heterogeneity in the timing and success rates of the individual steps in the viral life cycle. Infections are very unsuccessful, with only ~4% of them resulting in progeny production.

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Micha Müller @michamuller.bsky.social · 21/01/2025

To capture the late-stage event of new virions budding off, we developed a second, orthogonal technique that visualizes the build-up of HA-protein on the cell surface of infected cells and even labels budding virions.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Further we can follow IAV over time and observed vRNPs replicating and later getting exported from the nucleus to allow assembly of new virions.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Using this technology we show for the first time the moment that virions fuse with the endosomal membrane and release vRNPs step-by-step into the host cell

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Micha Müller @michamuller.bsky.social · 21/01/2025

The NP nanobody recognizes a broad range of IAV strains, including swine, avian, and human strains, and even viruses directly isolated from patient samples! Since there is no need to genetically modify the viruses, it is very easy to do experiments with new strains and isolates.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Influenza viruses are segmented, negative-sense RNA viruses that, like other (-)RNA viruses, have their genomes encapsidated by nucleoproteins (NP). We exploited this characteristic to visualize single, unmodified IAV genomes by expressing a fluorescently labelled nanobody that binds to NP.

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Micha Müller @michamuller.bsky.social · 21/01/2025

Very happy to share our preprint on visualizing the life cycle of Influenza viruses using single-molecule imaging! 🥳 We developed two techniques to visualize infections of unmodified influenza viruses in live cells from endosomal release to budding of new viruses. For more details&videos see below ⬇️

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Jop Kind @jopkind.bsky.social · 29/11/2024

I am really happy to announce the first Hubrecht Symposium on March 13th 2025! We will organize these yearly events on a specific topic in molecular and developmental biology to emphasize the importance of fundamental research for Dutch science. Free of charge! www.hubrecht.eu/hubrecht-sym...

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