Carlos Alfonso

Revisiting the human sociobiology debate What have we learned 50 years on?

🚨 New, short article by myself, Clark Barrett and @kevinlala.bsky.social on the legacy of Wilson's 'Sociobiology: The New Synthesis', which was published 50 years ago.

@science.org #ehbea #histbiol #evobio #psyscisky

Revisiting the human sociobiology debate |Science www.science.org/doi/10.1126/...

The most interesting report of the week (IMHO) 🧵

library(tidyplots) gene_expression |> head(n = 180) |> tidyplot(x = group, y = expression, color = group) |> add_mean_bar(alpha = 0.3) |> add_sem_errorbar() |> add_data_points_beeswarm(white_border = TRUE) |> adjust_size(width = 25, height = 25) |> split_plot(by = external_gene_name, ncol = 3, nrow = 3)

This is how you can split a plot into multiple subplots using #tidyplots 🚀

#rstats #dataviz #phd

library(tidyplots) study |> tidyplot(x = treatment, y = score, color = treatment) |> add_mean_dash() |> save_plot("stage_1.pdf") |> add_sem_errorbar() |> save_plot("stage_2.pdf") |> add_data_points_beeswarm() |> save_plot("final.pdf")

This is how you can save intermediate stages of #tidyplots by using `save_plot()` in the middle of a pipeline 💡

#rstats #dataviz #phd

Monoclonal antibodies revolutionized biomedical science and health care The story of the discovery of these molecules 50 years ago shows how the free exchange of ideas can lead to life-changing treatments.

The story of the discovery of monoclonal antibodies 50 years ago shows how the free exchange of ideas can lead to life-changing treatments

go.nature.com/45GeSM0

Excited to share that my first-author publication from my PhD on the interplay of p53 with cofactors on chromatin is now online in Molecular Cell @cp-molcell.bsky.social : www.cell.com/molecular-ce...
Nucleosomes filter cofactor access to p53 - USP7 can bind whereas E6AP-E6 fails to form a complex.

Read the latest issue here: www.cell.com/molecular-ce...

Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks - Nature Cell Biology Saur, Lesage et al. report that RNA:DNA hybrids arise at double-strand breaks in transcribed genes, independently of de novo recruitment of RNA polymerase II/III, as a result of DSB-induced transcript...

Transcriptional repression facilitates RNA:DNA hybrid accumulation at DNA double-strand breaks. #rnasky A function for R-loops on DNA damage repair? www.nature.com/articles/s41...

A rapid, simple, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies Nature Communications - Here, the authors present a method to rapidly isolate actively translating ribosomes in a time- and cost-effective manner using poly-lysine. The method is compatible with a...

Our RAPPL purification of ribosomes and associated material is out. I am really proud of this study in collaboration primary with Pavlovic-Djuranovic lab, as well as Jovanovic and Hashem Labs. This method aims to replace 60 years old purification of ribosomes by sucrose cushions

rdcu.be/ezlhg

Panel of figure 2 of Choquet et al. 2023 "Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts" (Nat. Struct. Mol. Biol.) that uses zig-zagging lines of different thicknesses and (gray) colors to show frequencies of permutations of splicing order of four introns in a representative transcript.

fascinated by this plot for listing permutations (namely, the orders in which four introns can be spliced from a given RNA transcript) and denoting their frequencies with line thickness and shade. It avoids needing to enumerate all 4! permutations. from Choquet et al. 2023 (Nat. Struct. Mol. Biol.)

The 9th Rhineland RNA Club on 1AUG #RNADay with great local speakers and @lenasteckelberg.bsky.social as invited speaker from Columbia was a super fun and well attended event with lots of #RNA discussions and networking. Organized and hosted by @katleppek.bsky.social at @dzne.science. #RNAsky

This is figure 1, which shows a resilience model and factors.

Unique biological, exposomal, economic and sociocultural factors shape resilience and brain health across the globe. A Review in Nature Medicine discusses underlying mechanisms of resilience. go.nature.com/4l76HNh #medsky 🧪

Low-dose metformin requires brain Rap1 for its antidiabetic action Metformin lowers blood glucose by inhibiting Rap1 in ventromedial hypothalamic neurons that regulate glucose balance.

Metformin, the first line drug for Type 2 diabetes, has been used for 60 years without a clearcut mechanism of action. It turns out it's not just reducing glucose output from the liver. Metformin also works via the brain www.science.org/doi/10.1126/...

PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility - Nature Communications Gene regulation in oocytes relies heavily on poly(A) tail-length changes. Here, the authors develop PAL-AI, a neural network model that predicts tail-length changes, identifies regulatory motifs, and ...

Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬

Review @cp-trendspharma.bsky.social
Structure–function-guided drug development efforts to target lncRNAs
www.cell.com/trends/pharm...

Mary K. Gaillard, 86, Physicist Who Probed the Subatomic Universe, Dies

Mary K Gaillard, a theorist who had a knack for telling experimental physicists where to look, died in her home on May 23 at 86.

Dr. Gaillard was an unpaid scientist at CERN for more than a decade, & the first woman physicist hired & tenured at Berkeley:

www.nytimes.com/2025/07/31/s...

New from our lab in @narjournal.bsky.social:
We dissect the folding dynamics of a fundamental element of RNA secondary structure—a stem-loop—at single-molecule and microsecond resolution.
doi.org/10.1093/nar/... 1/5

DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution - Nature Communications Transcription factors shape cell identity, but mapping their genomic targets remains challenging. Here the authors present DynaTag, a modified CUT&Tag method for profiling TF occupancy in bulk and...

DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution @natcomms.nature.com @epistrucstab.bsky.social
www.nature.com/articles/s41...

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox - Nature Communications The majority of human genes can produce multiple isoforms, but studying their functional relevance requires tools to target specific isoforms. Here, the authors develop a CRISPR-based exon-exon juncti...

Excited for this to be out officially! It was a great team effort and has a lot of useful tidbits for studying isoform function. www.nature.com/articles/s41...

Thanks to @riyavsinha.bsky.social in my lab, the IGV browser will natively support dynseq (dynamic sequence tracks) in an upcoming release. These tracks are very useful to directly visualize base-resolution scores (e.g. contribution scores from ML models, conservation etc). 1/

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

This 👇

Predicting the direction of phenotypic difference Nature Communications - Here authors reveal a method to predict key information on phenotypes - their direction. This is achievable even for phenotypes with incomplete genotype-to-phenotype...

Given two genomes, can you tell who’s taller or more prone to a disease? How confident can you be? A fresh take on phenotypic inference, now out:
rdcu.be/exW4f
See thread🧵👇:

RNA can control cell migration by acting at focal adhesions - Scientific editing and writing experts - Life Science Editors Scientific editing and writing experts for manuscripts and grants

RNA can control cell migration by acting at focal adhesions www.lifescienceeditors.com/2025/06/24/r...

Translation efficiency covariation identifies conserved coordination patterns across cell types - Nature Biotechnology Matched ribosome profiling and RNA sequencing data quantify translation efficiency patterns across 140 human and mouse cell lines.

Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZy

Predicting the translation efficiency of messenger RNA in mammalian cells - Nature Biotechnology A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.

Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C

R-loops and Genetic Instability: a Chicken and Egg Problem Investigating the relationships between R-loops and genetic instability led to the discovery that some DNA:RNA hybrids actually arise as a consequence of DNA lesions.

🐣 What comes first — R-loops or genome instability?

There’s now a Behind the Paper to go with our recent study on the interplay between R-loops and DNA damage — with some context, backstory, and the chicken-and-egg question at its core.

Check it out 👉 go.nature.com/4ldXbJm

Opinion | Science Suffers With Trump’s Funding Freeze America’s scientific enterprise demands reliable stewardship, not destabilizing political intervention.

My father-in-law, Jack Strominger, and I wrote a letter to the @wsj.com editor about the current threats to science due to Trump's funding freeze. Please repost! www.wsj.com/opinion/scie...

1/16 New pre-print from the Sternberg Lab!
We uncover how temperate phages can use RNA-guided transcription factors to remodel the flagellar composition of their bacterial host and enhance their fitness.
Find the preprint and full story here: tinyurl.com/mshwjd77