Carlos Alfonso
@carlosalfonsog.bsky.social
RNA biologist. @embl.org
Reposted by Carlos Alfonso
🔔Join us next Wednesday for #FragileNucleosome! 2 fantastic talks on chromatin regulation:🔬 @mariamafau.bsky.social on ZIC2's dual role in neural induction 🔬 @jhenninger.bsky.social on how RNA-binding proteins drive transcription
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
November 26, 2025 at 10:16 AM
🔔Join us next Wednesday for #FragileNucleosome! 2 fantastic talks on chromatin regulation:🔬 @mariamafau.bsky.social on ZIC2's dual role in neural induction 🔬 @jhenninger.bsky.social on how RNA-binding proteins drive transcription
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
📋Register here for the entire series: us06web.zoom.us/webinar/regi...
Reposted by Carlos Alfonso
"In particular, we show that, if it is true that some degree of talent is necessary to be successful in life, almost never the most talented people reach the highest peaks of success, being overtaken by mediocre but sensibly luckier individuals"
arxiv.org/abs/1802.07068
arxiv.org/abs/1802.07068
Talent vs Luck: the role of randomness in success and failure
The largely dominant meritocratic paradigm of highly competitive Western cultures is rooted on the belief that success is due mainly, if not exclusively, to personal qualities such as talent, intellig...
arxiv.org
November 23, 2025 at 3:13 PM
"In particular, we show that, if it is true that some degree of talent is necessary to be successful in life, almost never the most talented people reach the highest peaks of success, being overtaken by mediocre but sensibly luckier individuals"
arxiv.org/abs/1802.07068
arxiv.org/abs/1802.07068
Reposted by Carlos Alfonso
The scientific world would be a better place if reviews routinely reflected this degree of critical thinking and graphical excellence.
Thanks for putting this together @plaschkalab.bsky.social @rupertfaraway.bsky.social and @thezenklusen.bsky.social
Thanks for putting this together @plaschkalab.bsky.social @rupertfaraway.bsky.social and @thezenklusen.bsky.social
How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take: www.annualreviews.org/content/jour... (1/3)
November 24, 2025 at 9:54 AM
The scientific world would be a better place if reviews routinely reflected this degree of critical thinking and graphical excellence.
Thanks for putting this together @plaschkalab.bsky.social @rupertfaraway.bsky.social and @thezenklusen.bsky.social
Thanks for putting this together @plaschkalab.bsky.social @rupertfaraway.bsky.social and @thezenklusen.bsky.social
Reposted by Carlos Alfonso
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
Engineered chromatin readers track damaged chromatin dynamics in live cells and animals
->Nature | More from Lil Dr Glen EcoChat at BigEarthData.ai
->Nature | More from Lil Dr Glen EcoChat at BigEarthData.ai
Engineered chromatin readers track damaged chromatin dynamics in live cells and animals
All singleton BRCT domains from Mus musculus (Fig. 1a) were manually retrieved from Uniprot. Tandem BRCT domains, comprising two or more closely located BRCT domains linked by a variable linker region, were manually retrieved, and their association in tandem was...
www.nature.com
November 22, 2025 at 11:46 AM
Reposted by Carlos Alfonso
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
November 20, 2025 at 2:02 PM
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
Reposted by Carlos Alfonso
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field
open.substack.com/pub/blekhman...
open.substack.com/pub/blekhman...
The Autism-Microbiome Hypothesis Is Falling Apart
Why this new review paper should be required reading for every microbiome researcher
open.substack.com
November 19, 2025 at 5:12 PM
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field
open.substack.com/pub/blekhman...
open.substack.com/pub/blekhman...
Reposted by Carlos Alfonso
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.
www.science.org
November 20, 2025 at 7:46 AM
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
www.nature.com
November 19, 2025 at 6:43 PM
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Carlos Alfonso
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes @natgenet.nature.com @qmul.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 18, 2025 at 6:02 PM
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes @natgenet.nature.com @qmul.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Nature research paper: Estimation and mapping of the missing heritability of human phenotypes
go.nature.com/3LZQsph
go.nature.com/3LZQsph
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 complex traits and diseases.
go.nature.com
November 18, 2025 at 6:07 PM
Nature research paper: Estimation and mapping of the missing heritability of human phenotypes
go.nature.com/3LZQsph
go.nature.com/3LZQsph
Reposted by Carlos Alfonso
Analysis of the three-dimensional genome of exhausted CD8+ T cells reveals a critical role of IRF8 in their differentiation and functions in cancer @natimmunol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Analysis of the three-dimensional genome of exhausted CD8+ T cells reveals a critical role of IRF8 in their differentiation and functions in cancer - Nature Immunology
Dong and colleagues examine the 3D chromatin structure changes that accompany CD8⁺ T cell exhaustion. They identify a role for IRF8, which is required for recruitment of the chromatin topology organiz...
www.nature.com
November 18, 2025 at 6:09 PM
Analysis of the three-dimensional genome of exhausted CD8+ T cells reveals a critical role of IRF8 in their differentiation and functions in cancer @natimmunol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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