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Carlos Alfonso

@carlosalfonsog.bsky.social
1.1K followers 1.2K following 26 posts

RNA biologist. @embl.org

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Reposted by Carlos Alfonso
Science Magazine @science.org · 05/10/2026
A recent analysis in Science of more than 116,000 bird songs has revealed that the astonishing variety of passerine birdsong is built from just eight basic acoustic motifs, like trills, whistles, and harmonic notes. Learn more on #WorldAnimalDay: scim.ag/3SziyeL
A phylogenetic distribution and trait correlates of acoustic motifs in passerine birds. Hedline reads: The global biogeography of passerine songs
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Reposted by Carlos Alfonso
Javi Ibarrondo @jibarrondo.bsky.social · 01/10/2026
www.nature.com/articles/s41... 🧪
nature.com
Maternal influences on infant gut microbiome and health - Nature
The maternal gut microbiome is a predictor of infant eczema.
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Reposted by Carlos Alfonso
Javi Ibarrondo @jibarrondo.bsky.social · 01/10/2026
Live-cell transcriptomics with engineered virus-like particles: Cell www.cell.com/cell/fulltex... 🧪
cell.com
Live-cell transcriptomics with engineered virus-like particles
Najia, Le, Borrajo et al. establish “cellular self-reporting,” a technology to export molecular analytes from cells in virus-like particles. The authors demonstrate how mRNA export enables longitudina...
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Reposted by Carlos Alfonso
Philip Ball @philipcball.bsky.social · 01/10/2026
I'm not going to make this a long WTF biology thread, but just a few comments on this paper. It's about a protein implicated in the stress-adaptive plasticity of intenstinal wound healing and metastasis of colorectal cancer cells. /1 www.nature.com/articles/s41...
nature.com
ZFP36L2 orchestrates stress-adaptive plasticity in regeneration and cancer - Nature
The RNA-binding protein ZFP36L2 mediates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis.
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Reposted by Carlos Alfonso
Nature Biotechnology @natbiotech.nature.com · 01/10/2026
Deep learning perturbation models can outperform baselines on calibrated metrics www.nature.com/articles/s41...
nature.com
Deep learning perturbation models can outperform baselines on calibrated metrics - Nature Biotechnology
Calibration-aware evaluation of perturbation models shows that deep learning models can outperform baselines.
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Reposted by Carlos Alfonso
Science Magazine @science.org · 01/10/2026
A new special issue of Science highlights the research that is seeking to close the critical gaps in women’s health. Learn more: scim.ag/4z7H8mG
Women make up more than half the population, but most of what we know about women’s biology comes from extrapolation of studies in men. This has been changing in recent years, and this special issue highlights some of the progress in understanding the biological basis of sex differences in health and disease and medical issues relevant to women’s health across different stages of life.

Illustration: Chiara Vercesi
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Reposted by Carlos Alfonso
PLOS Biology @plosbiology.org · 01/10/2026
#TrendingNow | Sequencing of lab-cultured Drosophilidae species can result in a bias in taxon sampling. This study presents assembled #genomes from 183 single wild-collected drosophilids and inbred lines, aiming to redress the bias towards laboratory organisms 🧪 #ICYMI #Drosophila plos.io/3zS3Fe4
plos.io
Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
Sequencing of species that can be cultured in the laboratory results in a bias in taxon sampling. This study uses cost-effective, amplification-free, low-input sequencing methods to assemble genomes…
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Reposted by Carlos Alfonso
Science Magazine @science.org · 29/09/2026
Heart attacks and strokes triggered by electrical misfiring in the heart are among the biggest killers on the planet. In 2022, researchers created a “liquid wire” that, when injected into pig hearts, can guide the organs to a normal rhythm. Learn more on #WorldHeartDay: scim.ag/4iUYkai
Injectable electrodes could prevent deadly heart arrhythmias
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Reposted by Carlos Alfonso
Molecular Cell @cp-molcell.bsky.social · 29/09/2026
Online Now: Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics Online now:
dlvr.it
Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics
Cadar et al. show that the transcription factor Dorsal forms clusters at genes carrying many binding sites in living fly embryos. Losing these clusters is lethal, yet they do not switch genes on; they merely boost output from already-active genes, challenging prevailing views of how condensates control transcription.
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Reposted by Carlos Alfonso
Alan Gerber @alangerber.bsky.social · 28/09/2026
Preprint alert 🚨: We built a CRISPRi screen for a part of the genome that is unusually awkward to perturb: the RNA Pol III transcriptome. Hundreds of tRNA genes, lots of sequence similarity, plenty of redundancy... Turns out the biology had a few surprises for us 👇 www.biorxiv.org/content/10.6...
biorxiv.org
Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome
Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains uncl...
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Reposted by Carlos Alfonso
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 26/09/2026
🧬 Highly related @natgenet.nature.com paper from @binzmit.bsky.social group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface www.nature.com/articles/s41... Congratulations! 🎉
nature.com
Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics
Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...
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Reposted by Carlos Alfonso
Harmit Singh Malik @harmitmalik.bsky.social · 25/09/2026
Tenure process in the age of Trump and Vought
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Reposted by Carlos Alfonso
Arnaud Krebs @arnaudkr.bsky.social · 25/09/2026
When a scientific revolution happens on your doorstep. Simply spectacular.
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Reposted by Carlos Alfonso
Maya Voichek @mayavoichek.bsky.social · 24/09/2026
Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)
AI-generated illustration of the soma-to-germline transmission of retrotransposons described in our work
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Reposted by Carlos Alfonso
Cedric Feschotte @cedricfeschotte.bsky.social · 24/09/2026
Thrilled to see this published today! Truly special because we made the initial discovery >15 yrs ago! We found two copies of a human gene called BC200 embedded in a human poxvirus. BC200 blurs the line between gene & transposon—both functional & mutagenic! www.science.org/doi/10.1126/... 🧵1/n
science.org
Escape of the BC200 gene to a human poxvirus reveals its persistent transposition in primates
Transposable elements mobilize within and occasionally between genomes, including from host to virus. We identified two insertions of the human BC200 noncoding RNA gene in the poxvirus molluscum conta...
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Reposted by Carlos Alfonso
Nature @nature.com · 24/09/2026
A fruit-fly protein thought only to store amino acids in fact responds to nutritional deficiency in both development and adulthood, resulting in lifespan extension go.nature.com/4d6rRdo
go.nature.com
Surprising protein links dietary restriction to increased lifespan in flies
A fruit-fly protein thought only to store amino acids in fact responds to nutritional deficiency in both development and adulthood, resulting in lifespan extension.
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Reposted by Carlos Alfonso
Nature @nature.com · 23/09/2026
Nature research paper: The gene-regulatory evolution of the human skeleton go.nature.com/46GUxG8
go.nature.com
The gene-regulatory evolution of the human skeleton - Nature
Massively parallel reporter assays and human–ape hybrid skeletal cells are used to study the evolution of human cis-regulatory elements (CREs), revealing how differences in CREs have shaped the composition of human skeletal tissue.
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Reposted by Carlos Alfonso
Teif lab @teiflab.bsky.social · 23/09/2026
Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"
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Carlos Alfonso @carlosalfonsog.bsky.social · 23/09/2026
🤯
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Reposted by Carlos Alfonso
Trends in Chemistry @cp-trendschem.bsky.social · 23/09/2026
Online now: How smart can molecules become?
dlvr.it
How smart can molecules become?
The development of novel adaptable functional materials is essential for addressing the increasingly complex challenges of modern society. A recent advance by Hoshino and Ohgo showed that [12]cycloparaphenylene, composed entirely of sp2-hybridized carbon atoms, can dynamically reorganize its molecular structure in response to incoming guest molecules.
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Reposted by Carlos Alfonso
Cell Reports @cp-cellreports.bsky.social · 22/09/2026
The R-loop-SPT6-SETD2 axis safeguards H3K36me3 to prevent broad H3K4me3 invasion in mouse oocytes
dlvr.it
The R-loop-SPT6-SETD2 axis safeguards H3K36me3 to prevent broad H3K4me3 invasion in mouse oocytes
Sheng et al. show R-loops safeguard the chromatin and transcriptional landscape of mouse SN oocytes by stabilizing SPT6 at specific genomic loci, thereby promoting SETD2-dependent H3K36me3 deposition. RNASEH1-mediated R-loop loss disrupts the balance between gene-body H3K36me3 and broad H3K4me3, causing widespread transcriptional dysregulation, defective meiotic progression, and compromised oocyte maturation.
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Reposted by Carlos Alfonso
Richard Lenski @relenski.bsky.social · 22/09/2026
"Philosophy of Biology: The power of theory in the life sciences" elifesciences.org/articles/112... @zdblount.bsky.social shared this thought-provoking paper with the lab group.
elifesciences.org
Philosophy of Biology: The power of theory in the life sciences
Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.
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Reposted by Carlos Alfonso
Nature @nature.com · 22/09/2026
Nature research paper: Molecular-level observation of the self-assembly of a virus-like particle go.nature.com/4yDE29I
go.nature.com
Molecular-level observation of the self-assembly of a virus-like particle - Nature
Using mass photometry combined with a single-molecule trapping method allows real-time monitoring of the assembly of individual virus-like particles with molecular resolution, enabling observation and quantification of their self-assembly pathways and dynamics.
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Reposted by Carlos Alfonso
Molecular Cell @cp-molcell.bsky.social · 21/09/2026
An IRAK1-snRNA axis activates ATM to promote accurate repair within transcriptionally active chromatin
dlvr.it
An IRAK1-snRNA axis activates ATM to promote accurate repair within transcriptionally active chromatin
Nie et al. demonstrate that the IRAK1-snRNA axis promotes MRN complex condensate formation to enhance ATM activation and maintain genomic stability at transcriptionally active regions.
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Reposted by Carlos Alfonso
Nature @nature.com · 21/09/2026
Nature research paper: Cohesin reshapes replication fork contacts to aid fork slowing and reversal go.nature.com/4xY4vyP
go.nature.com
Cohesin reshapes replication fork contacts to aid fork slowing and reversal - Nature
Cohesin-mediated loop extrusion limits sister-fork coupling and tethers nearby replication forks under replication stress, promoting fork reversal and slowing fork progression to safeguard genome stability.
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Reposted by Carlos Alfonso
Molecular Cell @cp-molcell.bsky.social · 20/09/2026
Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state
dlvr.it
Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state
Kainth et al. show that WDR5, a subunit of the MLL1 histone methyltransferase complex, binds RNA broadly rather than through specific sequences or motifs as proposed. This promiscuous binding competes with MLL1 complex formation to inhibit histone methylation, suggesting that local RNA abundance can feed back to tune chromatin modification activity.
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Reposted by Carlos Alfonso
bioRxivpreprint @biorxivpreprint.bsky.social · 14/09/2026
Engineering chromatin to encode transcriptional immune memory in Arabidopsis www.biorxiv.org/content/10.64898/20…
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Reposted by Carlos Alfonso
Doudna Lab @doudna-lab.bsky.social · 19/09/2026
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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Reposted by Carlos Alfonso
Stella Hurtley @smhsci.bsky.social · 18/09/2026
Out now in @science.org Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
science.org
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues
Cell-state diversity drives tissue adaptability, repair, and disease resilience, but capturing this complexity is a challenge. Current approaches rely on transcriptional profiling and overlook organel...
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Reposted by Carlos Alfonso
Philip Ball @philipcball.bsky.social · 11/09/2026
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1 www.science.org/doi/10.1126/...
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the ...
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Reposted by Carlos Alfonso
Nature Cell Biology @natcellbio.nature.com · 16/09/2026
☕ @gabrijelad.bsky.social & co report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the nuclear speckle periphery and undergo synchronous splicing at mitosis, thus contributing to their temporal regulation. bit.ly/4xpanzZ
bit.ly
The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis - Nature Cell Biology
Biayna, Baranovskii and colleagues report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the periphery of nuclear speckles and undergo synchronou...
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Reposted by Carlos Alfonso
Molecular Cell @cp-molcell.bsky.social · 16/09/2026
Online Now: Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2 Online now:
dlvr.it
Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2
Contreras-Pérez et al. address the puzzling role of cohesin on transcription by focusing on the mitotic exit, when cohesin firstly contact chromatin. Combining in vivo labeling, cell-cycle synchronization, and acute protein depletion, authors demonstrate the preservation of cohesin across mitosis and its fundamental role on transcription reactivation of tissue-related genes.
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Reposted by Carlos Alfonso
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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Reposted by Carlos Alfonso
Science Magazine @science.org · 15/09/2026
Although your hair is much softer than steel, razors typically only last for a handful of shaves. Previously, researchers attributed this to the sharp edge gradually wearing down after each use. But a 2020 study reveals a different process. Learn more: scim.ag/3TvggxK #ScienceMagArchives
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Reposted by Carlos Alfonso
Nature @nature.com · 14/09/2026
Nature research paper: Predicting genome-wide functional constraints with GPN-Star go.nature.com/4r3oObw
go.nature.com
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species.
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Reposted by Carlos Alfonso
Arnaud Krebs @arnaudkr.bsky.social · 14/09/2026
your starter pack for Single Molecule Genomics! Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
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Reposted by Carlos Alfonso
Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 11/09/2026
New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices
dlvr.it
PRC2–RNA interactions through the lens of bioinformatics pipeline choices
Nature Reviews Molecular Cell Biology, Published online: 11 September 2026; doi:10.1038/s41580-026-01028-1Four recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field.
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Carlos Alfonso @carlosalfonsog.bsky.social · 11/09/2026
Fantastic work!
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Reposted by Carlos Alfonso
Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Reposted by Carlos Alfonso
Arnaud Krebs @arnaudkr.bsky.social · 10/09/2026
EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields. The abstract deadline is the end of this week, so don’t miss out! www.embl.org/about/info/c...
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Reposted by Carlos Alfonso
Wendy Bickmore @wbickmor.bsky.social · 08/09/2026
It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...
nature.com
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
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Reposted by Carlos Alfonso
Arnaud Krebs @arnaudkr.bsky.social · 07/09/2026
Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...
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Reposted by Carlos Alfonso
Nature @nature.com · 07/09/2026
Nature review: Designing physics experiments with artificial intelligence go.nature.com/4zKXiDA
go.nature.com
Designing physics experiments with artificial intelligence - Nature
Artificial intelligence in physics experimental design is explored on the basis of searching for optima over a vast space of hardware configurations and proposing entirely new experimental layouts, rather than tuning a handful of parameters.
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Reposted by Carlos Alfonso
The EMBO Journal @embojournal.org · 07/09/2026
Dynamic control of cell state transitions during tissue morphogenesis Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis link.springer.com/article/10.1...
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Reposted by Carlos Alfonso
Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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Reposted by Carlos Alfonso
Nature Cell Biology @natcellbio.nature.com · 04/09/2026
☕Have you read this? This Perspective highlights the use of current #proteomics technologies to understand reproductive #aging, improve #oocyte quality, and refine the outcomes of assisted reproductive technology (ART). 👉Read here: rdcu.be/BgbMZ6KYkesa www.nature.com/articles/s41...
nature.com
Proteomics-based insights into mammalian oocyte and early embryo development - Nature Cell Biology
This Perspective highlights the use of current proteomics technologies in defining stage-specific reprogramming events to understand reproductive ageing, improve oocyte quality, and refine the outcome...
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Reposted by Carlos Alfonso
Nature Methods @natmethods.nature.com · 03/09/2026
Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples. www.nature.com/articles/s41...
nature.com
Spatial chromatin architecture and accessibility co-profiling of mammalian tissues - Nature Methods
Spatial-ATAC-Hi-C enables the profiling of both chromatin accessibility and organization in a spatially resolved manner, as demonstrated on mouse brain and human glioblastoma and astrocytoma samples.
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Reposted by Carlos Alfonso
Nature @nature.com · 01/09/2026
Nature research paper: Automated prototyping of genetic codes go.nature.com/4iwiqqU
go.nature.com
Automated prototyping of genetic codes - Nature
A robotic, cell–free platform rapidly prototypes redesigned genetic codes, enabling the translation of proteins with reassigned codons and non-standard amino acids without altering living genomes.
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Reposted by Carlos Alfonso
Nature @nature.com · 30/08/2026
The world’s most popular antidepressant drugs are under fire go.nature.com/4y4KYMG
go.nature.com
The baffling science of SSRIs: how do they really work?
Nature - The world’s most popular antidepressant drugs are under fire. But are they really harder to quit than heroin?
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