Mauricio Oliveira
@oliveiramauri.bsky.social
Neurobiologist @NYU’s Klann lab studying the molecular dynamics of diverse neuron types during cognitive tasks, and how it converges to behavior modification. Protein synthesis, mRNAs, RBPs and memory.
Pinned
Hey all! Just another scientist trying to steer clear from the hell the other website became! Hopefully a bit more science here and less fanaticism. If you like neurobiology, protein synthesis and memory follow this account. Also may have occasional dog pictures from Santi, my guitarist Daschund
Reposted by Mauricio Oliveira
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
#Review by @carolinamonzo.bsky.social, Tianyuan Liu & @anaconesa.bsky.social @conesalab.bsky.social @csic.es
Free to read here: rdcu.be/efBjP
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...
rdcu.be
December 17, 2025 at 12:31 PM
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
#Review by @carolinamonzo.bsky.social, Tianyuan Liu & @anaconesa.bsky.social @conesalab.bsky.social @csic.es
Free to read here: rdcu.be/efBjP
Reposted by Mauricio Oliveira
@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...
#neuroskyence
www.thetransmitter.org/artificial-i...
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.
www.thetransmitter.org
December 16, 2025 at 3:00 PM
@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...
#neuroskyence
www.thetransmitter.org/artificial-i...
Reposted by Mauricio Oliveira
☕@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
bit.ly/4j2rIcG
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.
bit.ly
December 16, 2025 at 10:16 PM
☕@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
bit.ly/4j2rIcG
Reposted by Mauricio Oliveira
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...
#CellBiology #WTFology
www.biorxiv.org/content/10.6...
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 ...
www.biorxiv.org
December 16, 2025 at 6:35 AM
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...
#CellBiology #WTFology
www.biorxiv.org/content/10.6...
Reposted by Mauricio Oliveira
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
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.
www.nature.com
December 11, 2025 at 5:54 PM
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Mauricio Oliveira
Reposted by Mauricio Oliveira
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
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
December 7, 2025 at 2:45 PM
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
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html
Reposted by Mauricio Oliveira
Hot off the press from the RTI: Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1
buff.ly/UCQRlnd #RNA #RNATherapeutics
buff.ly/UCQRlnd #RNA #RNATherapeutics
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....
buff.ly
December 6, 2025 at 6:00 PM
Hot off the press from the RTI: Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1
buff.ly/UCQRlnd #RNA #RNATherapeutics
buff.ly/UCQRlnd #RNA #RNATherapeutics
Reposted by Mauricio Oliveira
How distributed is the brain-wide network that is recruited for cognition?
www.nature.com/articles/s41...
#neuroscience
www.nature.com/articles/s41...
#neuroscience
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 ...
www.nature.com
December 5, 2025 at 7:06 PM
How distributed is the brain-wide network that is recruited for cognition?
www.nature.com/articles/s41...
#neuroscience
www.nature.com/articles/s41...
#neuroscience
Reposted by Mauricio Oliveira
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
Learn more in #ScienceAdvances: https://scim.ag/4av1cpR
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.
scim.ag
December 5, 2025 at 7:18 PM
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
Learn more in #ScienceAdvances: https://scim.ag/4av1cpR
Reposted by Mauricio Oliveira
👇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...
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...
authors.elsevier.com
December 5, 2025 at 8:24 AM
👇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...
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...
Reposted by Mauricio Oliveira
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...
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
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...
www.biologists.com
December 3, 2025 at 6:56 AM
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...
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
Reposted by Mauricio Oliveira
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
December 1, 2025 at 10:15 PM
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
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...
If you want to show that APOE4 carries pathology independently, you put it on regular hTau knock in.
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
December 1, 2025 at 3:41 PM
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...
If you want to show that APOE4 carries pathology independently, you put it on regular hTau knock in.
www.biorxiv.org/content/10.1...
Reposted by Mauricio Oliveira
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...
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...
bims-proteo 2025-11-30 papers
biomed.news
November 30, 2025 at 9:10 AM
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...
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...
Reposted by Mauricio Oliveira
Hex Color Palette With Live Color Blocks
November 28, 2025 at 7:39 AM
Hex Color Palette With Live Color Blocks
Reposted by Mauricio Oliveira
Mapping spatial gradients in spatial transcriptomics data with score matching https://www.biorxiv.org/content/10.1101/2025.11.24.690257v1
November 27, 2025 at 4:46 PM
Mapping spatial gradients in spatial transcriptomics data with score matching https://www.biorxiv.org/content/10.1101/2025.11.24.690257v1
Reposted by Mauricio Oliveira
Functions of RNA m6A methylation at the molecular, genomic and organismal level: go.nature.com/484M6pB
Free to read here: rdcu.be/eR4zx
Free to read here: rdcu.be/eR4zx
November 27, 2025 at 12:51 PM
Functions of RNA m6A methylation at the molecular, genomic and organismal level: go.nature.com/484M6pB
Free to read here: rdcu.be/eR4zx
Free to read here: rdcu.be/eR4zx
Reposted by Mauricio Oliveira
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
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
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.
rdcu.be
November 24, 2025 at 1:35 PM
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
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
Reposted by Mauricio Oliveira
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
November 22, 2025 at 1:04 PM
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
Reposted by Mauricio Oliveira
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome https://www.biorxiv.org/content/10.1101/2025.11.18.689017v1
November 18, 2025 at 11:03 PM
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome https://www.biorxiv.org/content/10.1101/2025.11.18.689017v1
Reposted by Mauricio Oliveira
Recurrent neural network dynamics may not purely reflect cognitive strategies: A commentary on Ji-An et al. (Nature, 2025) https://www.biorxiv.org/content/10.1101/2025.10.30.685524v1
November 17, 2025 at 10:45 PM
Recurrent neural network dynamics may not purely reflect cognitive strategies: A commentary on Ji-An et al. (Nature, 2025) https://www.biorxiv.org/content/10.1101/2025.10.30.685524v1
Reposted by Mauricio Oliveira
ProtAttn-QuadNet: An attention-based deep learning framework for protein-protein interaction prediction using ProtBERT embeddings https://www.biorxiv.org/content/10.1101/2025.11.17.688786v1
November 17, 2025 at 11:46 PM
ProtAttn-QuadNet: An attention-based deep learning framework for protein-protein interaction prediction using ProtBERT embeddings https://www.biorxiv.org/content/10.1101/2025.11.17.688786v1
Reposted by Mauricio Oliveira
Journals should request a notepad file containing sessionInfo for every paper that uses clustering algorithms… reproducing a single cell clustering is almost impossible 😂😂
November 13, 2025 at 1:52 PM
Journals should request a notepad file containing sessionInfo for every paper that uses clustering algorithms… reproducing a single cell clustering is almost impossible 😂😂