Alex Palazzo

More like the Sh-it-dex, but W-index may help cover up the smell.

Paul Maddox for Congress, NC-11 Paul Maddox, professor, entrepreneur, and world-renowned cancer researcher, is running for Congress because working families in Western North Carolina deserve a representative who cares for all our co...

Support Paul Maddox for congress!!! He's running in NC-11. Paul is an Associate Professor in the Biology Department at UNC. I've known Paul since grad school days - he's a generous, smart and hard working guy. Having scientists in politics is critical our collective future.
www.maddoxforcongress.com

mRNA initiation and termination are spatially coordinated Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage o...

Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! www.science.org/doi/10.1126/...

Millionaire Tax That Inspired Mamdani Fuels $5.7 Billion Haul in Massachusetts A millionaire levy in Massachusetts that New York City mayoral frontrunner Zohran Mamdani holds up as a model for taxing the rich has generated $3 billion more in revenue than expected without forcing...

"In the two years since the state started charging a 4% surtax on incomes over $1 million, the effort has created a $5.7 billion windfall, with the surplus being used to fund bridge repairs, bolster literacy programs and address the transportation system’s budget deficit."

Taxing the rich works!

All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods Structural RNAs exhibit a vast array of recurrent short three-dimensional (3D) elements found in loop regions involving non-Watson–Crick interactions that help arrange canonical double helices into tertiary structures. Here we present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation. Here we further introduce the R3D grammars, which also exploit helix covariation that constrains the positioning of the mostly noncovarying RNA 3D motifs. Our method runs predictions over an almost-exhaustive list of over 50 known RNA motifs (‘everything’). Motifs can appear in any nonhelical loop region (including three-way, four-way and higher junctions) (‘everywhere’). All structural motifs as well as the canonical helices are arranged into one single structure predicted by one single joint probabilistic grammar (‘all-at-once’). Our results demonstrate that CaCoFold-R3D is a valid alternative for predicting the all-residue interactions present in a RNA 3D structure. CaCoFold-R3D is fast and easily customizable for novel motif discovery and shows promising value both as a strong input for deep learning approaches to all-atom structure prediction as well as toward guiding RNA design as drug targets for therapeutic small molecules.

Integrated prediction of RNA secondary structure jointly with 3D motifs and pseudoknots guided by evolutionary information.
@aakaran31.bsky.social and @rivaselenarivas.bsky.social

link.springer.com/article/10.1...

Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.

Nobel laureate Jennifer Doudna tells Jeffrey Goldberg that vaccinations have been so successful that "there's been a collective forgetting that measles, and mumps, and rubella—these used to be diseases that would kill people in fairly large numbers." #TAF25 bit.ly/46a5DUE

Opinion: To counter Trump’s tariffs, Canada must invest in life sciences We can take advantage of the increasingly hostile climate in the United States toward the sector

www.theglobeandmail.com/business/com...

This year's Lasker Awards went to scientists who studied the wiring diagram of life, a new state of biological matter, and a potent treatment for cystic fibrosis. Here's my story with Gina Kolata. Gift link: nyti.ms/4mZlH1F

History of Molecular Biology Collection This unparalleled collection includes Rosalind Franklin's historic 'Photo 51,' which revealed the double-helix structure of DNA.

News in the history of molecular biology. The Science History Institute in Philadelphia has acquired a huge archive of correspondence and other scientific material from the pioneers of molecular biology (Franklin, Klug, Perutz, Delbrück etc, with items from Crick and Watson, too). 1/n

I’ve spent a good chunk of my career relying on American science and engineering to keep me alive. Yesterday, RFK Jr. testified at the U.S. Senate Finance Committee. It was sad to see him try to destroy the life’s work of so many American scientists. He shouldn’t be in this job.

#RNAsky

Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...

In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n
www.biorxiv.org/cgi/content/...

Here’s how the first proteins might have assembled, sparking life RNA could have helped amino acids join up without preexisting protein machinery, lab study suggests

New research offers a glimpse of how RNA might have helped form the first simple proteins—an event that could have set the stage for evolution. https://scim.ag/4mVxEok

Spatiotemporal NAIL-MS analysis shows that ALKBH5 does not affect global m6A turnover in human mRNA across subcellular compartments under standard growth conditions bit.ly/4lvVtC6

Want to know how lipidation of some nascent chains takes place by NMT2-- Check our latest work on how NAC couples Protein Synthesis with Nascent Polypeptide Myristoylation on the Ribosome out today @embojournal.org‬: www.embopress.org/doi/full/10....

The impact of insertion bias into piRNA clusters on the invasion of transposable elements - BMC Biology Background In our current understanding of transposable element (TE) invasions, TEs move freely until they accidentally insert into a piRNA cluster, where they are silenced by the production of piRNA ...

@shashankpritam.bsky.social first research paper on the effect of insertion bias on transposon fitness!! With @almoroscarpa.bsky.social and @rokofler.bsky.social link.springer.com/article/10.1...

Canada plans a 15% budget cut. Scientists are alarmed Cuts could erase promised boost, researchers fear

And defending this:

www.science.org/content/arti...

Protein language models reveal evolutionary constraints on synonymous codon choice Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Scatterplot showing fitness effect of ~7000 synonymous mutations in yeast: read count at start vs log2 fold change. Most data points are not significant but 204 points are significant outliers, either advantageous or deleterious.

At the same time, we made thousands of synonymous mutations in endogenous yeast genes and measured their growth. We used careful statistics and controls. Only 3%, 204 of 6874, had a fitness effect! This goes against a controversial recent result that most synonymous mutations had fitness effects.

Excited to share our latest work with @simonbullock11.bsky.social! We looked at how diverse mRNAs get selected for subcellular localization and it turns out that a single protein can recognize different RNA elements using shared features that weren’t apparent before.
www.biorxiv.org/content/10.1...

YouTube video by Ruby - Topic The Whole Is Equal to the Sum of Its Parts

I was just listening to Ruby's Salt Peter album for the first time in a long time. WOW, what a kick a$$ album!!!

youtu.be/m6Q6gtbd7Wo?...

we asked a simple question:
What does it take to learn the rules of RNA base pairing?

using standard deep-learning technics, got a simple answer:
don't need structures, nor alignments or many parameters
only a few RNA sequences and 21 parameters;
doi.org/10.1101/2025...

Spotify boycott: Artists leave 'garbage hole' platform after CEO invests in AI weapons Daniel Ek's investments in AI dronemaker Helsing have unnerved artists. One called Spotify a "violent armageddon portal."

Get off Spotify. www.latimes.com/entertainmen...

Happy RNA Day to those who celebrate! 🧪 It’s AUG 1: the day we Met 🤓

I hate when people use "research" to say that they looked up random "facts" on the internet. I hereby christen a new name for this sad activity: cheapsearch. Here is how you would use it in a phrase:

"I do my own cheapsearch on the internet"

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

And I'm not saying that there isn't bloat, but the idea that AI is going to make this efficient is laughable. AI will just be a convenient excuse to make random cuts without any accountability or justification (I can hear them now "the AI said so").

"but Academic institutions will fight this tooth and nail" I wish I could agree with you, but unfortunately much of the administration at our institutions is too feckless to oppose this. We as the faculty have to be vigilant.

As I just said on radio Ford banning political discussion from classrooms is ridiculous. With civic literacy at an all time low and terrible voter turnout rates we should be engaging students in discussions that effect their future, the economy, our democracy and society #Onpoli