Alex Palazzo
@ribonucleicacids.bsky.social
Professor of Biochemistry at the University of Toronto. Studies mRNA processing, mRNA nuclear export, mRNA translation, genomic evolution, junk DNA, junk RNA.
https://www.palazzolab.com/
https://www.palazzolab.com/
Pinned
If any current PhD student is interested in a Postdoc position applying computational methods (including machine learning) to study the evolution of nucleotide content in human genes, please contact me.
For some context this is the average nucleotide content of human genes with five exons:
For some context this is the average nucleotide content of human genes with five exons:
"This suggests that these noncoding elements adhere to the CNE model (22, 70), which predicts that novel functionalities evolve without any direct impact on the fitness of the individual." www.science.org/doi/10.1126/...
Remodeling of XIST regulatory landscape during primate evolution
How gene regulation strategies rapidly evolve across short evolutionary timescales is explored.
www.science.org
January 20, 2026 at 1:34 PM
"This suggests that these noncoding elements adhere to the CNE model (22, 70), which predicts that novel functionalities evolve without any direct impact on the fitness of the individual." www.science.org/doi/10.1126/...
Reposted by Alex Palazzo
Putin, failing in his east European war, summons his American clients to organize a diversion in western Europe.
January 16, 2026 at 2:03 AM
Putin, failing in his east European war, summons his American clients to organize a diversion in western Europe.
Reposted by Alex Palazzo
Terribly uncanny how relevant this is to today.
January 16, 2026 at 5:35 PM
Terribly uncanny how relevant this is to today.
Reposted by Alex Palazzo
So cool - someone finally hacked 'the vault'.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
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...
www.science.org
January 16, 2026 at 1:10 PM
So cool - someone finally hacked 'the vault'.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Alex Palazzo
GERMAN PRESIDENT STEINMEIER:
“.. the United States has broken with the values that it helped to establish ..
“.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”
“.. the United States has broken with the values that it helped to establish ..
“.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”
January 9, 2026 at 9:15 AM
GERMAN PRESIDENT STEINMEIER:
“.. the United States has broken with the values that it helped to establish ..
“.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”
“.. the United States has broken with the values that it helped to establish ..
“.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”
Reposted by Alex Palazzo
Here's my latest contribution to the @nytimes "Lost Science" series. Brenna Henn's sweeping study of African genetics has been frozen. Gift link: nyti.ms/3Ypmm1A
January 5, 2026 at 5:32 PM
Here's my latest contribution to the @nytimes "Lost Science" series. Brenna Henn's sweeping study of African genetics has been frozen. Gift link: nyti.ms/3Ypmm1A
Reposted by Alex Palazzo
👇👇👇👇👇
In 2012 the ENCODE project claimed that most of our genome 🧬 wasn't junk after all on the basis that most of it was active in some way 🧪
In response, @cryptogenomicon.bsky.social proposed the random genome project - even random DNA would be mostly active, he suggested 1/2
doi.org/10.1016/j.cu...
In response, @cryptogenomicon.bsky.social proposed the random genome project - even random DNA would be mostly active, he suggested 1/2
doi.org/10.1016/j.cu...
Redirecting
doi.org
December 31, 2025 at 1:35 PM
👇👇👇👇👇
Reposted by Alex Palazzo
Now a team at @aucklanduni.bsky.social have come the closest so far to realising the random genome project using plant-human 🌿👫 hybrid cells - and guess what they found... 2/2
www.newscientist.com/article/2508...
www.newscientist.com/article/2508...
Human-plant hybrid cells reveal truth about dark DNA in our genome
It has been claimed that because most of our DNA is active, it must be important, but now human-plant hybrid cells have been used to show this activity is mostly random noise
www.newscientist.com
December 31, 2025 at 12:50 PM
Now a team at @aucklanduni.bsky.social have come the closest so far to realising the random genome project using plant-human 🌿👫 hybrid cells - and guess what they found... 2/2
www.newscientist.com/article/2508...
www.newscientist.com/article/2508...
Reposted by Alex Palazzo
Activator-promoter compatibility in mammals - Hcfc1 is a key and intrinsically CGI-promoter-specific co-activator that cannot activate non-CGI promoters. Lead by @nemcko.bsky.social & Kevin Sabath in collab. with @plaschkalab.bsky.social @impvienna.bsky.social www.biorxiv.org/content/10.6... (1/2)
Activator-promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID
Transcription from CpG island (CGI) promoters controls the expression of two-thirds of mammalian genes, yet despite their prevalence, it remains unknown whether CGI-specific co-activators with intrins...
www.biorxiv.org
December 30, 2025 at 8:02 AM
Activator-promoter compatibility in mammals - Hcfc1 is a key and intrinsically CGI-promoter-specific co-activator that cannot activate non-CGI promoters. Lead by @nemcko.bsky.social & Kevin Sabath in collab. with @plaschkalab.bsky.social @impvienna.bsky.social www.biorxiv.org/content/10.6... (1/2)
Reposted by Alex Palazzo
5′ UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins
5′ UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins
Han et al. demonstrate that binding of eIF3 to distinct sites in mRNA 5′ UTRs mediates chaperone recruitment to translating 80S ribosomes. This recruitment is essential for the correct folding of nascent ER membrane proteins, indicating that instructions for ER membrane protein folding are hardwired in the genome.
dlvr.it
December 28, 2025 at 3:39 PM
5′ UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins
Reposted by Alex Palazzo
GCN2 monitors mRNA translation termination
GCN2 monitors mRNA translation termination
Worner et al. show that GCN2 monitors mRNA translation termination. When translation termination is compromised, GCN2 is activated to prevent ribosome collisions and translation readthrough.
dlvr.it
December 19, 2025 at 8:14 PM
GCN2 monitors mRNA translation termination
Reposted by Alex Palazzo
Dear God, Jay Bhattacharya is just hopeless. He can't simply say getting polio is bad and is far worse than any side effects from the vaccine. He's is so far gone. It's tragic really. Too bad for all of us that he runs the National Institutes of Health.
We gave Jay Bhattacharya an opportunity to clarify his vaccine stance: does he REALLY believe that the vaccine is worse than the disease? Instead, he launched into a defense of MAHA as the future of scientific inquiry, and never really gave us a straight answer...
@repauchincloss.bsky.social
@repauchincloss.bsky.social
December 17, 2025 at 1:20 AM
Dear God, Jay Bhattacharya is just hopeless. He can't simply say getting polio is bad and is far worse than any side effects from the vaccine. He's is so far gone. It's tragic really. Too bad for all of us that he runs the National Institutes of Health.
Reposted by Alex Palazzo
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...
I heard this story from Scott Kennedy a few years back. This is very cool. The war between TEs and host genomes continues!
December 12, 2025 at 2:32 PM
I heard this story from Scott Kennedy a few years back. This is very cool. The war between TEs and host genomes continues!
Reposted by Alex Palazzo
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 Alex Palazzo
NSF
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
December 11, 2025 at 11:16 AM
NSF
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
Reposted by Alex Palazzo
Happy to share our fun team-up with @centriolelab.bsky.social & @stearnslab.bsky.social to reveal the architecture of the mammalian centriole’s Distal Ring 🛟. Very cool multiscale integration of #UExM 📏🔬with #CryoET ❄️🔬. Congrats to @ebertiaux.bsky.social & @computingcaitie.bsky.social #TeamTomo 🧪
How does C2CD3 contribute to distal appendage formation in centrioles? @centriolelab.bsky.social show that C2CD3 acts as a central architectural organizer of the distal #centriole, bridging the luminal distal ring complex & peripheral appendage sites @plosbiology.org 🧪 plos.io/496XZuH
December 10, 2025 at 11:02 AM
Happy to share our fun team-up with @centriolelab.bsky.social & @stearnslab.bsky.social to reveal the architecture of the mammalian centriole’s Distal Ring 🛟. Very cool multiscale integration of #UExM 📏🔬with #CryoET ❄️🔬. Congrats to @ebertiaux.bsky.social & @computingcaitie.bsky.social #TeamTomo 🧪
Reposted by Alex Palazzo
My collaborator (out of the blue) received an email from an LLM that made some scientific suggestions on the paper we just submitted to bioRxiv.
(The suggestions were not very good.)
(The suggestions were not very good.)
December 9, 2025 at 2:52 PM
My collaborator (out of the blue) received an email from an LLM that made some scientific suggestions on the paper we just submitted to bioRxiv.
(The suggestions were not very good.)
(The suggestions were not very good.)
Reposted by Alex Palazzo
Reposted by Alex Palazzo
this is raw Lysenkoism — using one’s status as a government official to create a false equivalence between scientific facts and nonscientific feelings pushed by grifters
Wow. Tracy Beth Høeg, the FDA's new acting director of the Center for Drug Evaluation and Research (CDER) just put this slide up during her presentation to ACIP.
We have left reality.
We have left reality.
December 5, 2025 at 7:44 PM
this is raw Lysenkoism — using one’s status as a government official to create a false equivalence between scientific facts and nonscientific feelings pushed by grifters
ANOTHER PAPER from Yi Liu's lab. This one is a bit crazy - codon effects on mRNA translation happens at the initiation step and requires looping - viruses don't circularize their mRNAs and thus evade the requirement for common codons to have efficient mRNA translation.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Viral RNA blocks circularization to evade host codon usage control - Nature
Rather than adapting to the codon usage of their host, viruses use viral 5′ untranslated regions to initiate translation, which allows them to produce viral proteins in host cells efficiently despite ...
www.nature.com
December 4, 2025 at 9:10 PM
ANOTHER PAPER from Yi Liu's lab. This one is a bit crazy - codon effects on mRNA translation happens at the initiation step and requires looping - viruses don't circularize their mRNAs and thus evade the requirement for common codons to have efficient mRNA translation.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Very nice paper from Yi Liu's lab on how the CCR4-NOT and PAXT complexes repress expression of mRNAs with low codon usage values by promoting their nuclear decay. Many codon effects likely boil down to GC-content.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nuclear effects play an important role in determining codon usage-dependent human gene expression - Nature Communications
Codon usage influences gene expression by affecting how efficiently genes are read and processed. Here, the authors identify nuclear factors, including CNOT4, the RNA exosome, and the PAXT complex, th...
www.nature.com
December 4, 2025 at 8:13 PM
Very nice paper from Yi Liu's lab on how the CCR4-NOT and PAXT complexes repress expression of mRNAs with low codon usage values by promoting their nuclear decay. Many codon effects likely boil down to GC-content.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alex Palazzo
I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...
Twins Are So Much More Interesting Than Heritability Estimates
On starting places, "missing environmentality," and the Waddington landscape of life
kathrynpaigeharden.substack.com
December 4, 2025 at 7:08 PM
I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...
Reposted by Alex Palazzo
Today, our animation synthesizing decades of research on actin-mediated endocytosis in budding yeast was published:
journals.biologists.com/jcs/article/...
The result of a fantastic Iwasa-Drubin lab collaboration.
@margotriggi.bsky.social @jiwasa.bsky.social
movie.biologists.com/video/10.124...
journals.biologists.com/jcs/article/...
The result of a fantastic Iwasa-Drubin lab collaboration.
@margotriggi.bsky.social @jiwasa.bsky.social
movie.biologists.com/video/10.124...
December 2, 2025 at 9:02 PM
Today, our animation synthesizing decades of research on actin-mediated endocytosis in budding yeast was published:
journals.biologists.com/jcs/article/...
The result of a fantastic Iwasa-Drubin lab collaboration.
@margotriggi.bsky.social @jiwasa.bsky.social
movie.biologists.com/video/10.124...
journals.biologists.com/jcs/article/...
The result of a fantastic Iwasa-Drubin lab collaboration.
@margotriggi.bsky.social @jiwasa.bsky.social
movie.biologists.com/video/10.124...