Mauricio Oliveira

A genetically encoded device for transcriptome storage in mammalian cells Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and s...

So cool - someone finally hacked 'the vault'.
www.science.org/doi/10.1126/...

The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation https://www.biorxiv.org/content/10.64898/2026.01.05.697729v1

Life before getting stuck at the junction. Nice paper from @karlaneugebauer.bsky.social lab about roles of EJC components in splicing.

genesdev.cshlp.org/content/40/1...

Proteoform medicine: characterizing and targeting protein forms in human disease Nature Reviews Genetics, Published online: 05 January 2026; doi:10.1038/s41576-025-00915-1Proteoforms are the diverse protein molecules produced from a single gene whose primary sequence and composition can be diversified by genetic, transcriptomic, translational and post-translational variation. This Review synthesizes technologies and network approaches to map, quantify and functionally characterize proteoforms, outlining routes to proteoform-guided biomarkers and therapeutics

New online! Proteoform medicine: characterizing and targeting protein forms in human disease

David's AlphaFold WorkShop 2026 YouTube video by David Fay

Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2

www.youtube.com/watch?v=u63o...

Simultaneous single-cell proteomics and epigenetic analysis of histone deacetylase inhibition in human cells - Communications Biology A focused analysis of the histone proteins and post-translational modifications in single cell proteomics provides insight into the heterogeneity of histone deacetylase inhibition.

After 2 years in peer review, this paper is finally published and it features figures from a completely unrelated paper rather than crappy ones I made! www.nature.com/articles/s42...

How heterogeneity shapes dynamics and computation in the brain Much effort has been spent clustering neurons into transcriptomic or functional cell types and characterizing the differences between them. Beyond sub…

"My New Year's Resolution is to find a principled way to think about all those cell types in the brain"

Why friend, you are in luck, because @rgast.bsky.social has just the perspective for you: www.sciencedirect.com/science/arti...

#ER_literature

8 links to BETTER understand principal component analysis (PCA) 🧵 👇

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...

Transcriptomics in the era of long-read sequencing
#Review by @carolinamonzo.bsky.social, Tianyuan Liu & @anaconesa.bsky.social @conesalab.bsky.social @csic.es
Free to read here: rdcu.be/efBjP

AI-assisted coding: 10 simple rules to maintain scientific rigor These guidelines can help researchers ensure the integrity of their work while accelerating progress on important scientific questions.

@russpoldrack.org's guidelines for AI-assisted coding can help researchers ensure the integrity of their work while accelerating progress on important scientific questions.

#neuroskyence

www.thetransmitter.org/artificial-i...

Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues - Nature Cell Biology Yuan et al. present S2-omics, an end-to-end workflow that automatically identifies regions of interest in histology images to maximize molecular information capture in spatial omics experiments.

☕@drmingyaoli.bsky.social & co present S2-omics, an end-to-end workflow that automatically identifies regions of interest in histology images to maximize molecular information capture in spatial omics experiments.
bit.ly/4j2rIcG

The vault associates with membranes in situ The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...

Vaults. They are cell biology's greatest puzzle! This preprint from Martin Beck's lab shows them docked on ER membranes with a ribosome inside. What on earth is going on there??

#CellBiology #WTFology

www.biorxiv.org/content/10.6...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

Congrats @marceljuengling.bsky.social and @erin-schuman.bsky.social, beautiful work!!

Brain-wide synaptosome profiling reveals localized mRNAs that diversify synapses Chemical synapses are the principal communication nodes of the brain, defined by their specialization and plasticity. Their diversity spans multiple levels, from the polarity and magnitude of electrop...

Cool!

www.biorxiv.org/content/10.6...

solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html

Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1 - PubMed GTP-binding protein 1 (GTPBP1) is a widespread translational GTPase closely related to elongation factor eEF1A. The loss of GTPBP1 leads to neurodevelopmental and neurodegenerative disorders in animals....

Hot off the press from the RTI: Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1
buff.ly/UCQRlnd #RNA #RNATherapeutics

How distributed is the brain-wide network that is recruited for cognition? - Nature Reviews Neuroscience Both localized and distributed views on the functional organization of the brain have been put forward. In this Perspective, Rosen and Freedman examine the degree to which these two views account for ...

How distributed is the brain-wide network that is recruited for cognition?
www.nature.com/articles/s41...
#neuroscience

Conservation of mRNA operon formation in control of the heat shock response in mammalian cells Eukaryotes coordinate their response to heat shock through an evolutionarily conserved mechanism involving mRNA operon expression.

Eukaryotes from yeasts to mammals use mRNA operons to coordinate their heat shock response, indicating the RNA operon mechanism that regulates gene coexpression is conserved in evolution.

Learn more in #ScienceAdvances: https://scim.ag/4av1cpR

👇See our newest study:
What was supposed to be a control experiment uncovered a new function of mTOR: 3’mediated translation control in primary human T cells, mediated through DDX21. AU-rich elements are required for this effect. Happy reading!
authors.elsevier.com/a/1mDFf3vVUP...

Development's Pathway to Independence Programme Our grants support and encourage the sharing of knowledge throughout the community by facilitating international collaboration, event attendance and the organisation of scientific meetings, conference...

Applications are open for @dev-journal.bsky.social 2026 Pathway to Independence (PI) programme, supporting postdocs applying for group leader positions:

Mentoring
Profile raising
Leadership training
Network building

Spread the word...

www.biologists.com/grants/devel...

Proteomic Analysis in Alzheimer's Disease with Psychosis Reveals Separate Molecular Signatures for Core AD Proteinopathy and Postsynaptic Density Disruption https://www.biorxiv.org/content/10.1101/2025.11.26.690872v1

Neuronal APOE4 alone is sufficient to drive tau pathology, neurodegeneration, and neuroinflammation in an Alzheimer’s disease mouse model Apolipoprotein E4 (APOE4), the strongest genetic risk factor for late-onset Alzheimer’s disease (AD), exacerbates tau tangles, amyloid plaques, neurodegeneration, and neuroinflammation—the pathologica...

I have to comment here. The idea is interesting, the results compelling, but choose your models wisely. An APOE4 on a P301S background is just an unfeasible bomb.

If you want to show that APOE4 carries pathology independently, you put it on regular hTau knock in.

www.biorxiv.org/content/10.1...

This week's selection of articles and #preprints on #proteostasis thanks to @biomednews.bsky.social --https://biomed.news/bims-proteo/2025-11-30
Highlight: Defining the role of β-cell IRE1α/XBP1 and its gene regulatory network components in non-obese diabetic mice www.nature.com/articles/s41...

Hex Color Palette With Live Color Blocks

Mapping spatial gradients in spatial transcriptomics data with score matching https://www.biorxiv.org/content/10.1101/2025.11.24.690257v1

Functions of RNA m6A methylation at the molecular, genomic and organismal level: go.nature.com/484M6pB
Free to read here: rdcu.be/eR4zx

Proteome-wide model for human disease genetics Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.

popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K

Cell Trajectory Inference based on Optimal Transport and a mechanistic stochastic gene expression model https://www.biorxiv.org/content/10.1101/2025.11.21.689689v1