Carlos Alfonso
@carlosalfonsog.bsky.social
RNA biologist. @embl.org
Reposted by Carlos Alfonso
A prize for the best translation of the title.
My own try: “When bound to transport receptors RNA-binding proteins cannot interact with target cellular compartments”
My own try: “When bound to transport receptors RNA-binding proteins cannot interact with target cellular compartments”
www.biorxiv.org/content/10.1... @rohitpappu68.bsky.social and Jim Shorter latest banger just dropped
Nuclear-import receptors remodel the dilute phase to suppress phase transitions of RNA-binding proteins with prion-like domains.
RNA-binding proteins (RBPs) with prion-like domains, including FUS, hnRNPA1, and hnRNPA2, assemble into functional, metastable condensates that organize ribostasis, but can also transition into self-t...
www.biorxiv.org
November 16, 2025 at 1:42 PM
A prize for the best translation of the title.
My own try: “When bound to transport receptors RNA-binding proteins cannot interact with target cellular compartments”
My own try: “When bound to transport receptors RNA-binding proteins cannot interact with target cellular compartments”
Reposted by Carlos Alfonso
Wow
'MHRA-led study reveals major inconsistencies in global microbiome research'
www.gov.uk/government/n...
'Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample'
'MHRA-led study reveals major inconsistencies in global microbiome research'
www.gov.uk/government/n...
'Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample'
MHRA-led study reveals major inconsistencies in global microbiome research
International collaboration establishes new quality standards to improve reliability of gut health studies – improving accuracy to provide better diagnosis and treatment.
www.gov.uk
November 16, 2025 at 12:51 PM
Wow
'MHRA-led study reveals major inconsistencies in global microbiome research'
www.gov.uk/government/n...
'Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample'
'MHRA-led study reveals major inconsistencies in global microbiome research'
www.gov.uk/government/n...
'Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample'
Reposted by Carlos Alfonso
New research reveals how genetic changes in the barley MKK3 gene fine-tune seed dormancy, determining whether grains stay dormant or sprout too soon.
The findings offer breeders new genetic tools to balance seed dormancy and crop resilience under changing climate conditions. https://scim.ag/47KfEHG
The findings offer breeders new genetic tools to balance seed dormancy and crop resilience under changing climate conditions. https://scim.ag/47KfEHG
Postdomestication selection of MKK3 shaped seed dormancy and end-use traits in barley
Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crops. In cereals, shortening dormancy provides rapid and even post-harvest germination, but incre...
scim.ag
November 16, 2025 at 6:20 PM
New research reveals how genetic changes in the barley MKK3 gene fine-tune seed dormancy, determining whether grains stay dormant or sprout too soon.
The findings offer breeders new genetic tools to balance seed dormancy and crop resilience under changing climate conditions. https://scim.ag/47KfEHG
The findings offer breeders new genetic tools to balance seed dormancy and crop resilience under changing climate conditions. https://scim.ag/47KfEHG
Reposted by Carlos Alfonso
I'm getting old. 👴
Sometimes I have to reread old papers that I've already read but have little or no memory of.
Like this one, for example
www.cell.com/molecular-ce...
Sometimes I have to reread old papers that I've already read but have little or no memory of.
Like this one, for example
www.cell.com/molecular-ce...
Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals
Transcription of eukaryotic genes requires an efficient termination to avoid pervasive
transcript synthesis. Here, Shah and Maqbool et al. show that tyrosine residues of
RNA polymerase II CTD are esse...
www.cell.com
November 14, 2025 at 8:57 AM
I'm getting old. 👴
Sometimes I have to reread old papers that I've already read but have little or no memory of.
Like this one, for example
www.cell.com/molecular-ce...
Sometimes I have to reread old papers that I've already read but have little or no memory of.
Like this one, for example
www.cell.com/molecular-ce...
Reposted by Carlos Alfonso
How to tackle emerging questions in cellular organisation, adaptation, and robustness? Join #EESPhaseSeparation! 🧬🦠
Bringing together scientists from diverse fields to foster new discoveries in condensate biology.
Submit your abstract by 10 Feb: s.embl.org/ees26-08-bl
📅 19 – 22 May 2026
Bringing together scientists from diverse fields to foster new discoveries in condensate biology.
Submit your abstract by 10 Feb: s.embl.org/ees26-08-bl
📅 19 – 22 May 2026
November 13, 2025 at 10:05 AM
How to tackle emerging questions in cellular organisation, adaptation, and robustness? Join #EESPhaseSeparation! 🧬🦠
Bringing together scientists from diverse fields to foster new discoveries in condensate biology.
Submit your abstract by 10 Feb: s.embl.org/ees26-08-bl
📅 19 – 22 May 2026
Bringing together scientists from diverse fields to foster new discoveries in condensate biology.
Submit your abstract by 10 Feb: s.embl.org/ees26-08-bl
📅 19 – 22 May 2026
Reposted by Carlos Alfonso
Beyond the niche - unlocking the full potential of synthetic riboswitches
doi.org/10.1038/s414...
doi.org/10.1038/s414...
November 13, 2025 at 5:44 AM
Beyond the niche - unlocking the full potential of synthetic riboswitches
doi.org/10.1038/s414...
doi.org/10.1038/s414...
Reposted by Carlos Alfonso
Reposted by Carlos Alfonso
This year marks the bicentennial of the birth of Thomas Henry Huxley, born 4 May 1825. The only notice I've seen for this is John van Wyhe's short piece for the @linneansociety.bsky.social: bit.ly/4oVPZmq
#HPS #histsci
#HPS #histsci
November 11, 2025 at 12:24 AM
This year marks the bicentennial of the birth of Thomas Henry Huxley, born 4 May 1825. The only notice I've seen for this is John van Wyhe's short piece for the @linneansociety.bsky.social: bit.ly/4oVPZmq
#HPS #histsci
#HPS #histsci
Reposted by Carlos Alfonso
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
November 10, 2025 at 9:01 PM
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Reposted by Carlos Alfonso
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
November 9, 2025 at 2:45 PM
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
Reposted by Carlos Alfonso
💫NEW: @sarawickstrom.bsky.social @katemiro.bsky.social & co show that mechano-osmotic changes in the #nucleus induce general #transcriptional repression and prime #chromatin for cell fate transitions by relieving repression of specific differentiation genes. #pluripotency
bit.ly/3VMcyNZ
bit.ly/3VMcyNZ
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology
McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.
bit.ly
October 4, 2025 at 2:40 PM
💫NEW: @sarawickstrom.bsky.social @katemiro.bsky.social & co show that mechano-osmotic changes in the #nucleus induce general #transcriptional repression and prime #chromatin for cell fate transitions by relieving repression of specific differentiation genes. #pluripotency
bit.ly/3VMcyNZ
bit.ly/3VMcyNZ
Reposted by Carlos Alfonso
🧪 Absolutely wonderful - Rosalind Franklin, by her sister. Learned a lot @zetkin.bsky.social
„The pile of family letters talk far more about her holidays, her friends, or living conditions in postwar Paris, than about her work. She had a love of grand scenery, and became a formidable climber.“
„The pile of family letters talk far more about her holidays, her friends, or living conditions in postwar Paris, than about her work. She had a love of grand scenery, and became a formidable climber.“
Sharing this, quite relevant this week. www.thelancet.com/journals/lan...
Remembering my sister Rosalind Franklin
Rosalind Franklin died of ovarian cancer in 1958 aged 37 years. Sympathy and feminism
have combined to give us her familiar image as a downtrodden woman scientist, brilliant
but neglected, a heroine t...
www.thelancet.com
November 9, 2025 at 8:39 AM
🧪 Absolutely wonderful - Rosalind Franklin, by her sister. Learned a lot @zetkin.bsky.social
„The pile of family letters talk far more about her holidays, her friends, or living conditions in postwar Paris, than about her work. She had a love of grand scenery, and became a formidable climber.“
„The pile of family letters talk far more about her holidays, her friends, or living conditions in postwar Paris, than about her work. She had a love of grand scenery, and became a formidable climber.“
Reposted by Carlos Alfonso
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
November 8, 2025 at 1:58 PM
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
Reposted by Carlos Alfonso
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
James Watson in his own words
“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…
liorpachter.wordpress.com
November 8, 2025 at 4:29 AM
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
Reposted by Carlos Alfonso
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications
KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...
www.nature.com
November 6, 2025 at 9:40 AM
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Check out the latest work from our lab, led by Daniel Lin and Lara Elcavage: www.biorxiv.org/content/10.1... (1/3)
mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers the degradation of a microRNA. This target-directed microRNA degradatio...
www.biorxiv.org
November 7, 2025 at 6:33 PM
Check out the latest work from our lab, led by Daniel Lin and Lara Elcavage: www.biorxiv.org/content/10.1... (1/3)
Reposted by Carlos Alfonso
wait, wait, what 😱
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
November 7, 2025 at 8:32 AM
wait, wait, what 😱
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
RNA stability enhancers for durable base-modified mRNA therapeutics go.nature.com/4opTAsV
RNA stability enhancers for durable base-modified mRNA therapeutics - Nature Biotechnology
A systematic screen identifies RNA elements that enhance the stability and translation of base-modified mRNA.
go.nature.com
November 7, 2025 at 5:06 PM
RNA stability enhancers for durable base-modified mRNA therapeutics go.nature.com/4opTAsV
Reposted by Carlos Alfonso
This week, we published in @science.org an article outlining the current ethical and societal implications of research involving human neural #organoids and #assembloids, their transplantation, and highlighted potential next steps.
November 7, 2025 at 12:12 PM
This week, we published in @science.org an article outlining the current ethical and societal implications of research involving human neural #organoids and #assembloids, their transplantation, and highlighted potential next steps.
Reposted by Carlos Alfonso
Reposted by Carlos Alfonso
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
Reposted by Carlos Alfonso
As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41...
#HumanGenomics #Pangenomes #ReferenceGenomes
#HumanGenomics #Pangenomes #ReferenceGenomes
Choose your human genome reference wisely - Nature Methods
Scientists can choose between multiple human genome references, and a pangenome reference is coming. Deciding what to use when is not quite straightforward.
www.nature.com
November 4, 2025 at 12:28 PM
As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41...
#HumanGenomics #Pangenomes #ReferenceGenomes
#HumanGenomics #Pangenomes #ReferenceGenomes
Reposted by Carlos Alfonso
🥁This Wednesday , in #FragileNucleosome seminar, we are excited to host @hannahlong.bsky.social and @jeffvierstra.bsky.social to tell us about amazing work they are doing!
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
November 3, 2025 at 12:03 PM
🥁This Wednesday , in #FragileNucleosome seminar, we are excited to host @hannahlong.bsky.social and @jeffvierstra.bsky.social to tell us about amazing work they are doing!
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
Reposted by Carlos Alfonso
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:33 AM
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com