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Neuro David

@neuro-david.bsky.social
112 followers 219 following 5 posts

Geneticist in love with RNAs and neurons.

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Reposted by Neuro David
Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Craig Kaplan @triggerloop.bsky.social · 29/06/2026
The Kaplan Lab at the University of Pittsburgh has received funds to recruit a postdoctoral fellow to establish a multiplexed assay of variant effect for a disease gene. This relates to our studies on RNA Polymerase II. This project requires experience with human cell lines and genomics 1/
cfopitt.taleo.net
Post Doctoral Associate
Click the link provided to see the complete job description.
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Nature Reviews Genetics @natrevgenet.nature.com · 01/05/2026
Free to read here: rdcu.be/efBjP
rdcu.be
Transcriptomics in the era of long-read sequencing
Nature Reviews Genetics - Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read...
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Reposted by Neuro David
EMBO Reports @emboreports.org · 28/04/2026
Second April issue is live! link.springer.com/journal/4431... Cover features work by Hwei-Jan Hsu and co-workers, Institute of Cellular and Organismic Biology, Academia Sinica, showing that Wdr4 regulates ribosome biogenesis and intestinal homeostasis via let-7. link.springer.com/article/10.1...
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Nature Reviews Genetics @natrevgenet.nature.com · 31/03/2026
FYI: New online! Gene regulatory networks: from correlative models to causal explanations
dlvr.it
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics, Published online: 09 March 2026; doi:10.1038/s41576-026-00939-1In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without compromising explanatory power.
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Hao Yin @haoyin.bsky.social · 31/03/2026
FGF8-expressing embryonic body Organizer fusion induced rostral-caudal arealization of elongated hPSC-derived cortical assembloids (15-mm long😎) Modeling FGFR3-related temporal lobe dysgenesis #NatMeth 2024 www.nature.com/articles/s41...
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Reposted by Neuro David
Fabien Burki @fburki.bsky.social · 29/03/2026
www.nature.com/articles/s41... #protistsonsky
nature.com
Transient molecular chimerism for exploiting xenogeneic organelles - Nature Communications
Kleptoplasty, the transient integration of foreign organelles, could illuminate organellogenesis. Here, using the flagellate, Rapaza viridis, the authors show that host nuclear proteins are imported i...
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Reposted by Neuro David
Hao Yin @haoyin.bsky.social · 25/03/2026
Hao's Preprint Reading List March 25 2026 Pericyte loss in🧠small vessel disease Single-cell atlas of postnatal👤🫁development Substrate microtrench confers Endothelial cell resilience to >200 dyn/cm2 shear SuperFocus Single-cell spatial multi-omics Zebrafish ZMAP docs.google.com/document/d/e...
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Yasin Dagdas @plantophagy.bsky.social · 25/03/2026
Congrats Milica @alessandrick.bsky.social & everyone @gekaragoz.bsky.social lab. Glad we could contribute to this awesome story on #UFMylation & #RQC crosstalk @embojournal.org link.springer.com/article/10.1...
link.springer.com
The coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER - The EMBO Journal
Clearance of arrested nascent polypeptides resulting from ribosomal stalling is essential for proteostasis. Stalled endoplasmic reticulum (ER)-bound ribosomes are marked by ubiquitin-fold modifier 1 (...
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Nature Reviews Genetics @natrevgenet.nature.com · 23/03/2026
New online! Genetic influences on haematopoiesis
dlvr.it
Genetic influences on haematopoiesis
Nature Reviews Genetics, Published online: 23 March 2026; doi:10.1038/s41576-026-00947-1Haematopoiesis is a classic process for understanding the genetic basis of human health and disease. In this Review, Poeschla and Sankaran discuss this history and more recent advances in our understanding of the roles of rare variants in monogenic blood diseases, germline and somatic variants in population-level variation, as well as emerging therapeutic applications.
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Reposted by Neuro David
Ben Steventon @bensteventon.bsky.social · 23/03/2026
Happy to share this work from @alexneaverson.bsky.social where she has dissected the timing and relative contribution of the organiser and its derivates to multiple aspects of early neural development: www.biorxiv.org/content/10.6...
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James Briscoe @jamesbriscoe.bsky.social · 23/03/2026
New work by @sagnera.bsky.social & co A conserved sequence of TFs: OC2 → Pou2f2 → Pou3f1 drives chronological diversification of spinal neuron subtypes across multiple cardinal domains Spinal neuron diversity is generated by integrating spatial & temporal programs www.science.org/doi/10.1126/...
science.org
Evidence for chronological diversification of spinal neuron subtypes by a shared sequence of transcription factors
Molecular and functional diversification of spinal cord output neurons by a conserved sequence of transcription factors.
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Debby Silver @debbysilver.bsky.social · 19/03/2026
Delighted to share that our study is now out @cp-cellstemcell.bsky.social www.cell.com/cell-stem-ce... Congrats to Dr. @federicamosti.bsky.social for the culmination of a beautiful thesis!
cell.com
Species-specific chromatin architecture and neurogenesis mediated by a human enhancer
How human-specific DNA changes shape brain development is poorly understood. Mosti et al. discover a human enhancer, HAR1984, which drives ETV5 and TRA2B expression via human-enriched chromatin intera...
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Di Jiang @dijiang319.bsky.social · 19/03/2026
Unstructured transcription factor interactions enable emergent specificity | @science.org www.science.org/doi/10.1126/...
science.org
Unstructured transcription factor interactions enable emergent specificity
How intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), ...
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Reposted by Neuro David
Science Magazine @science.org · 19/03/2026
Wild rice is a perennial, creeping plant. The secret to its perennial growth habit lies in a developmental reversal directed by small RNAs. This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice. Learn more: scim.ag/40GOjDb
This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.
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Hao Yin @haoyin.bsky.social · 18/03/2026
🤵Artery Super-enhancer (H3K27ac ChIPseq) analysis (127 TFs)▶️ PRDM16 as a positive regulator of Injury-induced (not developmental) Proliferation of Vascular Smooth Muscle Cell😎 Any role in SMC-to-brown adipocyte conversion?😁 @jiliang-zhou.bsky.social #JMCC 2026 www.sciencedirect.com/science/arti...
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Nucleic Acids Research @narjournal.bsky.social · 18/03/2026
⭐NAR Breakthrough! ⭐ Back-to-back NAR studies show #Palbociclib binds #HIV TAR RNA with low affinity & striking specificity. Induced-fit RNA refolding creates a #druggable pocket, blocking #SEC recruitment.📖 Read the articles here: doi.org/10.1093/nar/... doi.org/10.1093/nar/... #DrugDiscovery
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James Briscoe @jamesbriscoe.bsky.social · 17/03/2026
If you're analysing Cut&Run or Cut&Tag data here's a nf-core NextFlow pipeline to simplify and standardise data processing joss.theoj.org/papers/10.21...
joss.theoj.org
nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets
Hodgetts et al., (2026). nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets. Journal of Open Source Software, 11(119), 9672, https://doi.org/10.21...
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HHMI @hhmi-science.bsky.social · 16/03/2026
New work from #HHMIInvestigator Huda Zoghbi & colleagues points to a promising new treatment strategy for Rett syndrome, a rare disorder that affects brain development in infants & children, primarily girls: bit.ly/3Np4Ng9. @bcmhouston.bsky.social | Texas Children’s Hospital
Huda Zoghbi in her lab in Houston talking with another researcher
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 14/03/2026
ICYMI
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Nature Reviews Genetics @natrevgenet.nature.com · 12/03/2026
Seb will be giving a talk this afternoon @ #KSGenomeEng26 Check out his recent review in @natrevdrugdiscov.nature.com on CRISPR-based therapeutic genome editing for inherited blood disorders rdcu.be/e70WP #Review by Sébastien Levesque & Daniel E. Bauer
rdcu.be
CRISPR-based therapeutic genome editing for inherited blood disorders
Nature Reviews Drug Discovery - CRISPR-based technologies provide a diverse set of tools to correct pathogenic mutations. This Review describes the promise and the challenges of genome editing...
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Reposted by Neuro David
James Briscoe @jamesbriscoe.bsky.social · 09/03/2026
New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations" Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations? rdcu.be/e7zx7
rdcu.be
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...
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Reposted by Neuro David
Gladfelter Lab @gladfelterlab.bsky.social · 08/03/2026
Condensates are powerful ways to break symmetry and cells do remarkable things with them. Here we show that in a multinucleate fungus, a condensate regulates translation of a cyclin and a formin in distinct locations. www.nature.com/articles/s41...
nature.com
RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology
Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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FocalPlane @focalplane.bsky.social · 05/03/2026
🔬🔦In our latest Imaging spotlight, Nicholas Boyer takes us through the key results, & offers some top technical tips, from their research on the axonal membrane-associated periodic skeleton with Rohan Sharma, Christophe Leterrier @christlet.bsky.social, Subhojit Roy @roylab-ucsd.bsky.social & team.
focalplane.biologists.com
Imaging spotlight: the axonal membrane-associated periodic skeleton - FocalPlane
Imaging spotlight: the axonal membrane-associated periodic skeleton - News
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Science Magazine @science.org · 28/02/2026
In a new Science study, researchers report on transcriptional adaptation, a dual feedback and feedforward mechanism that uses genetic redundancy to compensate for mutations in protein-coding genes. Learn more in a new #SciencePerspective: scim.ag/4ryeXtN
scim.ag
Keeping cells fit
Fragments of aberrant cytoplasmic mRNA pair with nuclear RNAs to augment transcription
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Trends in Neurosciences @cp-trendsneuro.bsky.social · 26/02/2026
'Making of BDNF: role of promoters, enhancers, and untranslated regions' by Eli-Eelika Esvald, Annela Avarlaid, Indrek Koppel, Jürgen Tuvikene & Tõnis Timmusk www.cell.com/trends/neuro...
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 25/02/2026
Good representation from teleosts 👍
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Miguel Ramalho-Santos @mrsantos.bsky.social · 25/02/2026
Discussed @mrsantosny.bsky.social lit review: Stress controls heterochromatin inheritance via histone H3 ubiquitylation. www.nature.com/articles/s41...
nature.com
Stress controls heterochromatin inheritance via histone H3 ubiquitylation - Nature
A histone ubiquitin-dependent regulatory hub governs stimulus-dependent heterochromatin propagation, with important implications for understanding mechanisms governing rapid changes in the epigen...
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Michael Bok @mikebok.bsky.social · 24/02/2026
From our new paper out now in @currentbiology.bsky.social: www.cell.com/current-biol... w/ @neurofishh.bsky.social @gkafetzis.bsky.social @denilsson.bsky.social Looking across animals, the vertebrate eye is an obvious outlier. Why is it so different that other highly visual animals?
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Julius Brennecke @juliusbrennecke.bsky.social · 23/02/2026
LINE-L1, HIV, Ty3 retrotransposons in insects. several of these genomes are > 40% adenosine! What is the molecular origin & evolutionary pressure resulting in A-rich genomes of retrotransposons & some retroviruses? it must be so hardwired that hosts exploit this bias for genome defense any ideas?
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Stella Hurtley @smhsci.bsky.social · 20/02/2026
Out now in @science.org Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...
science.org
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes
Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...
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Nature @nature.com · 21/02/2026
Nature research paper: Single-cell and isoform-specific translational profiling of the mouse brain go.nature.com/4aYPQu7
go.nature.com
Single-cell and isoform-specific translational profiling of the mouse brain - Nature
Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hippocampal neuronal and non-neuronal cell types, highlighting functional differences between CA1 and CA3.
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Nature @nature.com · 19/02/2026
Nature research paper: Accurate predictions of disordered protein ensembles with STARLING go.nature.com/4cyskFw
go.nature.com
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.
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Harvard Med Cell Biology @harvardcellbio.bsky.social · 18/02/2026
New work from @harvardcellbio.bsky.social faculty Amy Lee uncovered fundamental aspects of protein translation initiation by a giant DNA virus. www.sciencedirect.com/science/arti...
sciencedirect.com
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral t…
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RNA Society Journal @rnajournal.bsky.social · 17/02/2026
Advances in CLIP-derived methods have enabled high-resolution mapping of individual RNA binding protein-RNA interactions as well as RNA binding protein-associated RNA–RNA interactions #RNA #CLIP @evannostrandlab.bsky.social bit.ly/4bYjAsg
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Nature Reviews Genetics @natrevgenet.nature.com · 18/02/2026
FYI: New online! Emergence and evolution of protein-coding de novo genes
dlvr.it
Emergence and evolution of protein-coding de novo genes
Nature Reviews Genetics, Published online: 28 January 2026; doi:10.1038/s41576-025-00929-9De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanistic and evolutionary processes underlying their emergence and evolution, and the patterns in their encoded protein structures.
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Nature Reviews Genetics @natrevgenet.nature.com · 17/02/2026
New online! Annotating genomes at increased scale and resolution
dlvr.it
Annotating genomes at increased scale and resolution
Nature Reviews Genetics, Published online: 17 February 2026; doi:10.1038/s41576-026-00937-3In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and function, providing researchers with genome annotation resources of unprecedented scale and resolution.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 18/02/2026
Discussed @mrsantos.bsky.social lit review: Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo. www.cell.com/developmenta...
cell.com
Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo
Chovatiya et al. developed PReCIS-seq, an in vivo approach that maps transcriptionally engaged RNA polymerase II in Cre-targeted cells within intact mouse tissues, without cell isolation. They report ...
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Max Haase @maxhaase.bsky.social · 18/02/2026
Our paper is now out in Nature: “Ancient co-option of LTR retrotransposons as yeast centromeres” www.nature.com/articles/s41... A short thread on how retrotransposons helped give rise to yeast point centromeres. 1/14
nature.com
Ancient co-option of LTR retrotransposons as yeast centromeres - Nature
Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...
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Nature Reviews Genetics @natrevgenet.nature.com · 16/02/2026
New online! Evolutionary causes and consequences of gene duplication
dlvr.it
Evolutionary causes and consequences of gene duplication
Nature Reviews Genetics, Published online: 16 February 2026; doi:10.1038/s41576-026-00935-5Gene duplication is a key evolutionary mechanism, as initially redundant paralogues diverge over time. The authors review how adaptive and non-adaptive forces influence the evolutionary fates of gene duplicates, highlighting the importance of function–fitness relationships and gene expression dynamics.
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Nature Reviews Genetics @natrevgenet.nature.com · 16/02/2026
New online! Bridging technical innovation and computational advances in studies of RNA–protein assemblies
dlvr.it
Bridging technical innovation and computational advances in studies of RNA–protein assemblies
Nature Reviews Genetics, Published online: 16 February 2026; doi:10.1038/s41576-026-00931-9Empirical and artificial intelligence-based approaches are redefining how RNA-dependent protein assemblies are mapped, modelled and targeted, revealing their dynamic roles in health and disease and outlining closed-loop strategies for predictive functional RNA and ribonucleoprotein design.
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 29/01/2026
Dynamical Aβ-Tau-Neurodegeneration Model Predicts Alzheimer's Disease Mechanisms and Biomarker Progression www.biorxiv.org/content/10.64898/20…
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Hao Yin @haoyin.bsky.social · 24/01/2026
#AlternativeSplicing analysis pipeline MAJIQ v2 - VOILA v2 modulizer 👉Build gene splicegraph including unannotated, complex elements (e.g. de novo intron retention) 👉Quantify AS events & modules 👉Comparative analysis of GTEx v8 all 53 tissues #NatComm 2023 www.nature.com/articles/s41...
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Alex Pollen @brainevodevo.bsky.social · 23/01/2026
1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...
nature.com
Dissecting gene regulatory networks governing human cortical cell fate - Nature
Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...
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eric lai @lucksmith.bsky.social · 23/01/2026
new paper from the Lai lab! Renfu Shang performs careful mechanistic dissection of miRNA cluster assistance and reveals many insights and surprises to this enigmatic regulatory strategy that gives suboptimal miRNAs a boost. if you love Northerns, you'll ♥️ this! 🧬 genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Edda Schulz @eddaschulz.bsky.social · 20/01/2026
⚠️ The final work of two former PhD students Till @tschwammle.bsky.social and Verena @verenamutzel.bsky.social is out! ➡️⬅️ They dissect how memory can arise from antisense transcription using mathematical modelling 💻, genomics 🧬 and synthetic biology ⚒️! link.springer.com/article/10.1...
link.springer.com
Antisense transcription can induce expression memory via stable promoter repression - Genome Biology
Background The capacity of cells to retain a memory of previous signals enables acquisition of unique fates and adaptation to their environment. The underlying gene expression memory can arise from mu...
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Nicolas Panayotis @npanayotis.bsky.social · 20/01/2026
Very happy to share our new paper in #ScienceSignaling revealing that importin β1 isn’t just important for nuclear transport or neuronal growth. We now show it is key for presynaptic plasticity in the hippocampus, local translation, and memory! www.science.org/doi/10.1126/...
science.org
Subcellular depletion of importin β1 impairs presynaptic local translation and spatial memory
Axonal localization of importin β1 is required for presynaptic functions that support spatial memory tasks.
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Nature Reviews Genetics @natrevgenet.nature.com · 21/01/2026
📢 Our February issue is live! go.nature.com/4jTt2z5 Reviewed topics include: how spatial omics has reshaped our understanding of human development and disease; multiplexed assays of variant effect (MAVEs); haplotype phasing and genotype imputation; forensic genetics in the omics era
Illustrated night sky with planets (cells), a shooting star, and star constellations against a blue grid background reminiscent of architectural drawings.
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