Reposted by Neuro DavidSergey Ovchinnikov @sokrypton.org · 14/09/2026Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr) 727698
Reposted by Neuro DavidArnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026Happy 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 belownature.comDiversity and evolution of chromatin regulatory states across eukaryotes - Nature GeneticsThis study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar... 1018481
Reposted by Neuro DavidCraig Kaplan @triggerloop.bsky.social · 29/06/2026The 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.netPost Doctoral AssociateClick the link provided to see the complete job description. 23341
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 01/05/2026Free to read here: rdcu.be/efBjPrdcu.beTranscriptomics in the era of long-read sequencingNature 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... 072
Reposted by Neuro DavidEMBO Reports @emboreports.org · 28/04/2026Second 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... 022
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 31/03/2026FYI: New online! Gene regulatory networks: from correlative models to causal explanationsdlvr.itGene regulatory networks: from correlative models to causal explanationsNature 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. 0188
Reposted by Neuro DavidHao Yin @haoyin.bsky.social · 31/03/2026FGF8-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... 031
Reposted by Neuro DavidFabien Burki @fburki.bsky.social · 29/03/2026www.nature.com/articles/s41... #protistsonskynature.comTransient molecular chimerism for exploiting xenogeneic organelles - Nature CommunicationsKleptoplasty, 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... 0219
Reposted by Neuro DavidHao Yin @haoyin.bsky.social · 25/03/2026Hao'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... 0123
Reposted by Neuro DavidYasin Dagdas @plantophagy.bsky.social · 25/03/2026Congrats 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.comThe coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER - The EMBO JournalClearance 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 (... 15417
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 23/03/2026New online! Genetic influences on haematopoiesisdlvr.itGenetic influences on haematopoiesisNature 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. 031
Reposted by Neuro DavidBen Steventon @bensteventon.bsky.social · 23/03/2026Happy 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... 14613
Reposted by Neuro DavidJames Briscoe @jamesbriscoe.bsky.social · 23/03/2026New 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.orgEvidence for chronological diversification of spinal neuron subtypes by a shared sequence of transcription factorsMolecular and functional diversification of spinal cord output neurons by a conserved sequence of transcription factors. 04111
Reposted by Neuro DavidDebby Silver @debbysilver.bsky.social · 19/03/2026Delighted 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.comSpecies-specific chromatin architecture and neurogenesis mediated by a human enhancerHow 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... 35020
Reposted by Neuro DavidDi Jiang @dijiang319.bsky.social · 19/03/2026Unstructured transcription factor interactions enable emergent specificity | @science.org www.science.org/doi/10.1126/...science.orgUnstructured transcription factor interactions enable emergent specificityHow intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), ... 05015
Reposted by Neuro DavidScience Magazine @science.org · 19/03/2026Wild 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 08136
Reposted by Neuro DavidHao 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... 152
Reposted by Neuro DavidNucleic 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 082
Reposted by Neuro DavidJames Briscoe @jamesbriscoe.bsky.social · 17/03/2026If 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.orgnf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasetsHodgetts 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... 0165
Reposted by Neuro DavidHHMI @hhmi-science.bsky.social · 16/03/2026New 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 043
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 12/03/2026Seb 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. Bauerrdcu.beCRISPR-based therapeutic genome editing for inherited blood disordersNature 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... 051
Reposted by Neuro DavidJames Briscoe @jamesbriscoe.bsky.social · 09/03/2026New 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/e7zx7rdcu.beGene regulatory networks: from correlative models to causal explanationsNature 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... 212446
Reposted by Neuro DavidGladfelter Lab @gladfelterlab.bsky.social · 08/03/2026Condensates 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.comRNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell BiologyGeisterfer, 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... 111243
Reposted by Neuro DavidPáll Melsted @pmelsted.bsky.social · 06/03/2026Excited 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 618887
Reposted by Neuro DavidFocalPlane @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.comImaging spotlight: the axonal membrane-associated periodic skeleton - FocalPlaneImaging spotlight: the axonal membrane-associated periodic skeleton - News 054
Reposted by Neuro DavidScience Magazine @science.org · 28/02/2026In 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.agKeeping cells fitFragments of aberrant cytoplasmic mRNA pair with nuclear RNAs to augment transcription 06313
Reposted by Neuro DavidTrends 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... 183
Reposted by Neuro DavidZebrafish Rock! 🎃 @zebrafishrock.bsky.social · 25/02/2026Good representation from teleosts 👍 051
Reposted by Neuro DavidMiguel Ramalho-Santos @mrsantos.bsky.social · 25/02/2026Discussed @mrsantosny.bsky.social lit review: Stress controls heterochromatin inheritance via histone H3 ubiquitylation. www.nature.com/articles/s41...nature.comStress controls heterochromatin inheritance via histone H3 ubiquitylation - NatureA histone ubiquitin-dependent regulatory hub governs stimulus-dependent heterochromatin propagation, with important implications for understanding mechanisms governing rapid changes in the epigen... 102
Reposted by Neuro DavidMichael Bok @mikebok.bsky.social · 24/02/2026From 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? 111740
Reposted by Neuro DavidJulius Brennecke @juliusbrennecke.bsky.social · 23/02/2026LINE-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? 2124
Reposted by Neuro DavidStella Hurtley @smhsci.bsky.social · 20/02/2026Out now in @science.org Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...science.orgRibosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomesCells 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... 05822
Reposted by Neuro DavidNature @nature.com · 21/02/2026Nature research paper: Single-cell and isoform-specific translational profiling of the mouse brain go.nature.com/4aYPQu7go.nature.comSingle-cell and isoform-specific translational profiling of the mouse brain - NaturePost-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. 0224
Reposted by Neuro DavidNature @nature.com · 19/02/2026Nature research paper: Accurate predictions of disordered protein ensembles with STARLING go.nature.com/4cyskFwgo.nature.comAccurate predictions of disordered protein ensembles with STARLING - NatureThe deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input. 0121
Reposted by Neuro DavidHarvard Med Cell Biology @harvardcellbio.bsky.social · 18/02/2026New 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.comGiant DNA viruses encode a hallmark translation initiation complex of eukaryotic lifeIn contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral t… 072
Reposted by Neuro DavidRNA Society Journal @rnajournal.bsky.social · 17/02/2026Advances 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 01911
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 18/02/2026FYI: New online! Emergence and evolution of protein-coding de novo genesdlvr.itEmergence and evolution of protein-coding de novo genesNature 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. 043
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 17/02/2026New online! Annotating genomes at increased scale and resolutiondlvr.itAnnotating genomes at increased scale and resolutionNature 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. 084
Reposted by Neuro DavidMiguel Ramalho-Santos @mrsantos.bsky.social · 18/02/2026Discussed @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.comCell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivoChovatiya 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 ... 151
Reposted by Neuro DavidMax Haase @maxhaase.bsky.social · 18/02/2026Our 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. 1/14nature.comAncient co-option of LTR retrotransposons as yeast centromeres - NatureEvolutionarily 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... 9236119
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 16/02/2026New online! Evolutionary causes and consequences of gene duplicationdlvr.itEvolutionary causes and consequences of gene duplicationNature 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. 01610
Reposted by Neuro DavidNature Reviews Genetics @natrevgenet.nature.com · 16/02/2026New online! Bridging technical innovation and computational advances in studies of RNA–protein assembliesdlvr.itBridging technical innovation and computational advances in studies of RNA–protein assembliesNature 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. 042
Reposted by Neuro DavidbioRxiv Neuroscience @biorxiv-neursci.bsky.social · 29/01/2026Dynamical Aβ-Tau-Neurodegeneration Model Predicts Alzheimer's Disease Mechanisms and Biomarker Progression www.biorxiv.org/content/10.64898/20… 021
Reposted by Neuro DavidHao 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... 075
Reposted by Neuro DavidAlex Pollen @brainevodevo.bsky.social · 23/01/20261/ 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.comDissecting gene regulatory networks governing human cortical cell fate - NatureSystematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti... 76828
Reposted by Neuro Davideric lai @lucksmith.bsky.social · 23/01/2026new 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.orgSeparable 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 12611
Reposted by Neuro DavidEdda 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.comAntisense transcription can induce expression memory via stable promoter repression - Genome BiologyBackground 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... 15623
Reposted by Neuro DavidNicolas Panayotis @npanayotis.bsky.social · 20/01/2026Very 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.orgSubcellular depletion of importin β1 impairs presynaptic local translation and spatial memoryAxonal localization of importin β1 is required for presynaptic functions that support spatial memory tasks. 24718
Reposted by Neuro DavidNature 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 233