Cedric Boeckx
@cedricboeckx.bsky.social
ICREA Research Professor. Evolution, Genetics, Neuroscience, Linguistic Cognition
Pinned
Cedric Boeckx
@cedricboeckx.bsky.social
· Nov 16
![cortical organoid [image credit: O. Leonardi, who is leading this collaborative project]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ljcyk7tem65k7epgu5pkwuuh/bafkreico75nbiyo5zg6kzzahk5kxmcpcajygslloxkndmry2tnzr5q72pu@jpeg)
First post on this platform 👋. Glad to reconnect with old friends, and also learn from new contacts. Will post about intersecting themes: human evolution, genetics (esp. aDNA), neuroscience & cognition. Currently focusing on brain organoids and early developmental changes that may have had an impact
Reposted by Cedric Boeckx
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:30 AM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
“Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits”
Very nice @medrxivpreprint.bsky.social study by @zeyunlu.bsky.social @sashagusevposts.bsky.social & colleagues 🧪🧬
www.medrxiv.org/content/10.6...
Very nice @medrxivpreprint.bsky.social study by @zeyunlu.bsky.social @sashagusevposts.bsky.social & colleagues 🧪🧬
www.medrxiv.org/content/10.6...
Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits
Most current GWAS-eQTL approaches prioritize genes whose mediating effects on complex traits act through cis-regulation, while trans-acting genes remain largely underexplored. Recent perturbational sc...
www.medrxiv.org
January 6, 2026 at 7:24 AM
“Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits”
Very nice @medrxivpreprint.bsky.social study by @zeyunlu.bsky.social @sashagusevposts.bsky.social & colleagues 🧪🧬
www.medrxiv.org/content/10.6...
Very nice @medrxivpreprint.bsky.social study by @zeyunlu.bsky.social @sashagusevposts.bsky.social & colleagues 🧪🧬
www.medrxiv.org/content/10.6...
Reposted by Cedric Boeckx
Gene regulatory networks encode the logic of cellular functions, but it has been hard to map these at genome-scale, especially in disease-relevant cell types.
Here we report the first genome-wide perturb-seq in primary human cells, and show what we can learn from it
Here we report the first genome-wide perturb-seq in primary human cells, and show what we can learn from it
January 5, 2026 at 6:42 PM
Gene regulatory networks encode the logic of cellular functions, but it has been hard to map these at genome-scale, especially in disease-relevant cell types.
Here we report the first genome-wide perturb-seq in primary human cells, and show what we can learn from it
Here we report the first genome-wide perturb-seq in primary human cells, and show what we can learn from it
Reposted by Cedric Boeckx
Ever wondered how white matter tracts actually map onto the cortical hierarchy and cognition—beyond the usual “projection vs association” labels?
Our new preprint tackles exactly that! 🧠✨ doi.org/10.64898/202...
Thread below 🧵
Our new preprint tackles exactly that! 🧠✨ doi.org/10.64898/202...
Thread below 🧵
Anatomical White Matter Tracts Span the Cortical Hierarchy to Support Cognitive Diversity
Long-range white matter (WM) tracts support cognition by enabling communication between distant cortical regions, which are organized along a hierarchy defined by the sensorimotor-to-association (S-A)...
doi.org
January 5, 2026 at 4:21 PM
Ever wondered how white matter tracts actually map onto the cortical hierarchy and cognition—beyond the usual “projection vs association” labels?
Our new preprint tackles exactly that! 🧠✨ doi.org/10.64898/202...
Thread below 🧵
Our new preprint tackles exactly that! 🧠✨ doi.org/10.64898/202...
Thread below 🧵
Reposted by Cedric Boeckx
First of my #BooksOf2026 and it’s a cracker. Or should I say a ‘Cricker’! @matthewcobb.bsky.social’s biography of Francis Crick is a propulsive and compelling portrait of a complex figure who towered over 20th century biology. Brims with insight. A superlative achievement.
January 4, 2026 at 11:24 AM
First of my #BooksOf2026 and it’s a cracker. Or should I say a ‘Cricker’! @matthewcobb.bsky.social’s biography of Francis Crick is a propulsive and compelling portrait of a complex figure who towered over 20th century biology. Brims with insight. A superlative achievement.
Very interesting new work from P. Claes’ lab & collaborators, on genomic signatures of evolution, diversity & clinical conditions associated with craniofacial shape. Key role of sapiens-derived alleles in the origin of the chin + effects of Neandertal introgression on craniofacial diversity today 🧪💀
The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions
Human craniofacial morphology is a hallmark of our species' diversity and evolutionary history, shaped by adaptation, introgression, and global dispersal. Cranial globularization and chin emergence ar...
www.biorxiv.org
January 4, 2026 at 9:57 AM
Very interesting new work from P. Claes’ lab & collaborators, on genomic signatures of evolution, diversity & clinical conditions associated with craniofacial shape. Key role of sapiens-derived alleles in the origin of the chin + effects of Neandertal introgression on craniofacial diversity today 🧪💀
Great @natneuro.nature.com study by @sroig.bsky.social @djabaudon.bsky.social @jbmanent.bsky.social & colleagues,
showing “equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes” 🧪🧠🧬
showing “equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes” 🧪🧠🧬
Position-independent emergence of neocortical neuron molecular identity, connectivity and function - Nature Neuroscience
Even when neocortical neurons form in abnormal locations, they retain their identity and function, revealing that brain circuit formation can be guided by intrinsic developmental programs rather than ...
www.nature.com
January 1, 2026 at 6:18 PM
Great @natneuro.nature.com study by @sroig.bsky.social @djabaudon.bsky.social @jbmanent.bsky.social & colleagues,
showing “equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes” 🧪🧠🧬
showing “equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes” 🧪🧠🧬
Reposted by Cedric Boeckx
📢 We're hiring a postdoc (33 months) in human evolutionary genomics / paleogenomics / statistical genetics, Paris 🇫🇷
Project on selection on disease-associated variants, integrating ancient genomes, GWAS, and Ancestral Rec. Graphs.
Start May 2026 (flexible).
Apply here: emploi.cnrs.fr/Offres/CDD/U...
Project on selection on disease-associated variants, integrating ancient genomes, GWAS, and Ancestral Rec. Graphs.
Start May 2026 (flexible).
Apply here: emploi.cnrs.fr/Offres/CDD/U...
Portail Emploi CNRS - Offre d'emploi - Postdoc in human evolutionary genetics and bioinformatics (M/F)
Assurez-vous que votre profil candidat soit correctement renseigné avant de postuler
emploi.cnrs.fr
December 31, 2025 at 10:26 AM
📢 We're hiring a postdoc (33 months) in human evolutionary genomics / paleogenomics / statistical genetics, Paris 🇫🇷
Project on selection on disease-associated variants, integrating ancient genomes, GWAS, and Ancestral Rec. Graphs.
Start May 2026 (flexible).
Apply here: emploi.cnrs.fr/Offres/CDD/U...
Project on selection on disease-associated variants, integrating ancient genomes, GWAS, and Ancestral Rec. Graphs.
Start May 2026 (flexible).
Apply here: emploi.cnrs.fr/Offres/CDD/U...
Reposted by Cedric Boeckx
Very happy to see this great study by @skrohn.bsky.social @carstenfinke.bsky.social @engra.me @sofievalk.bsky.social on brain shape & human brain development, out in @natneuro.nature.com
🧪🧠
www.nature.com/articles/s41...
🧪🧠
www.nature.com/articles/s41...
Fractal analysis of brain shape formation predicts age and genetic similarity in human newborns - Nature Neuroscience
Fractal analysis of structural MRI captures the formation of brain shape in human newborns and outperforms other morphological measures in predicting infant age and genetic similarity, including the i...
www.nature.com
December 30, 2025 at 12:40 PM
Very happy to see this great study by @skrohn.bsky.social @carstenfinke.bsky.social @engra.me @sofievalk.bsky.social on brain shape & human brain development, out in @natneuro.nature.com
🧪🧠
www.nature.com/articles/s41...
🧪🧠
www.nature.com/articles/s41...
Reposted by Cedric Boeckx
⚠️ New paper alert and what a way to end 2025! 🎉
Happy to share our story “Sleep-dependent infraslow rhythms are evolutionarily conserved across reptiles and mammals.” published today in Nature Neuroscience.
Sleeping dragons 🦎 and functional ultrasound!
Read the full paper here: rdcu.be/eWJHb 1/8
Happy to share our story “Sleep-dependent infraslow rhythms are evolutionarily conserved across reptiles and mammals.” published today in Nature Neuroscience.
Sleeping dragons 🦎 and functional ultrasound!
Read the full paper here: rdcu.be/eWJHb 1/8
Sleep-dependent infraslow rhythms are evolutionarily conserved across reptiles and mammals
Nature Neuroscience - Bergel et al. show that an infraslow rhythm connecting the brain and body during sleep is shared by lizards, mammals and birds, revealing an ancestral process and reshaping...
rdcu.be
December 29, 2025 at 4:17 PM
⚠️ New paper alert and what a way to end 2025! 🎉
Happy to share our story “Sleep-dependent infraslow rhythms are evolutionarily conserved across reptiles and mammals.” published today in Nature Neuroscience.
Sleeping dragons 🦎 and functional ultrasound!
Read the full paper here: rdcu.be/eWJHb 1/8
Happy to share our story “Sleep-dependent infraslow rhythms are evolutionarily conserved across reptiles and mammals.” published today in Nature Neuroscience.
Sleeping dragons 🦎 and functional ultrasound!
Read the full paper here: rdcu.be/eWJHb 1/8
Very happy to see this great study by @skrohn.bsky.social @carstenfinke.bsky.social @engra.me @sofievalk.bsky.social on brain shape & human brain development, out in @natneuro.nature.com
🧪🧠
www.nature.com/articles/s41...
🧪🧠
www.nature.com/articles/s41...
Fractal analysis of brain shape formation predicts age and genetic similarity in human newborns - Nature Neuroscience
Fractal analysis of structural MRI captures the formation of brain shape in human newborns and outperforms other morphological measures in predicting infant age and genetic similarity, including the i...
www.nature.com
December 30, 2025 at 12:40 PM
Very happy to see this great study by @skrohn.bsky.social @carstenfinke.bsky.social @engra.me @sofievalk.bsky.social on brain shape & human brain development, out in @natneuro.nature.com
🧪🧠
www.nature.com/articles/s41...
🧪🧠
www.nature.com/articles/s41...
Reposted by Cedric Boeckx
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
December 24, 2025 at 3:51 PM
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
Reposted by Cedric Boeckx
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...
www.biorxiv.org
December 24, 2025 at 3:06 PM
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Reposted by Cedric Boeckx
New Perspective from myself, Sarah Heilbronner and @myoo.bsky.social . “Rethinking the centrality of brain areas in understanding functional organization” in Nature Neuroscience. 🧵
rdcu.be/eVZ1A
rdcu.be/eVZ1A
Rethinking the centrality of brain areas in understanding functional organization
Nature Neuroscience - Parcellation of the cortex into functionally modular brain areas is foundational to neuroscience. Here, Hayden, Heilbronner and Yoo question the central status of brain areas...
rdcu.be
December 23, 2025 at 1:02 PM
New Perspective from myself, Sarah Heilbronner and @myoo.bsky.social . “Rethinking the centrality of brain areas in understanding functional organization” in Nature Neuroscience. 🧵
rdcu.be/eVZ1A
rdcu.be/eVZ1A
Reposted by Cedric Boeckx
Saving face: SALL4 is required for early specification of craniofacial precursors
This Research Highlight showcases work by Martina Demurtas, Marco Trizzino (@marcotrizzino.bsky.social) and colleagues:
journals.biologists.com/dev/article/...
This Research Highlight showcases work by Martina Demurtas, Marco Trizzino (@marcotrizzino.bsky.social) and colleagues:
journals.biologists.com/dev/article/...
December 23, 2025 at 9:29 AM
Saving face: SALL4 is required for early specification of craniofacial precursors
This Research Highlight showcases work by Martina Demurtas, Marco Trizzino (@marcotrizzino.bsky.social) and colleagues:
journals.biologists.com/dev/article/...
This Research Highlight showcases work by Martina Demurtas, Marco Trizzino (@marcotrizzino.bsky.social) and colleagues:
journals.biologists.com/dev/article/...
Excellent preprint by @joelleba.bsky.social @ted-satterthwaite.bsky.social and collaborators, shedding light on how white matter tracts are positioned within the cortical hierarchy to support cognition 🧪🧠
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Anatomical White Matter Tracts Span the Cortical Hierarchy to Support Cognitive Diversity
Long-range white matter (WM) tracts support cognition by enabling communication between distant cortical regions, which are organized along a hierarchy defined by the sensorimotor-to-association (S-A)...
www.biorxiv.org
December 23, 2025 at 8:00 AM
Excellent preprint by @joelleba.bsky.social @ted-satterthwaite.bsky.social and collaborators, shedding light on how white matter tracts are positioned within the cortical hierarchy to support cognition 🧪🧠
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Cedric Boeckx
Cool basal ganglia preprints today!
2 on DA/ACh
1. @paulkramer.bsky.social
www.biorxiv.org/content/10.6...
2. @arifahamid.bsky.social
www.biorxiv.org/content/10.6...
Motor learning @juangallego.bsky.social and @clopathlab.bsky.social
www.biorxiv.org/content/10.6...
2 on DA/ACh
1. @paulkramer.bsky.social
www.biorxiv.org/content/10.6...
2. @arifahamid.bsky.social
www.biorxiv.org/content/10.6...
Motor learning @juangallego.bsky.social and @clopathlab.bsky.social
www.biorxiv.org/content/10.6...
Excitatory nicotinic signaling drives action potential bursting in dopaminergic axons
Axons of dopamine (DA) neurons express nicotinic receptors (nAChRs) that have been shown to both facilitate and suppress striatal DA release, but the mechanisms underlying these opposing actions are u...
www.biorxiv.org
December 21, 2025 at 12:05 PM
Cool basal ganglia preprints today!
2 on DA/ACh
1. @paulkramer.bsky.social
www.biorxiv.org/content/10.6...
2. @arifahamid.bsky.social
www.biorxiv.org/content/10.6...
Motor learning @juangallego.bsky.social and @clopathlab.bsky.social
www.biorxiv.org/content/10.6...
2 on DA/ACh
1. @paulkramer.bsky.social
www.biorxiv.org/content/10.6...
2. @arifahamid.bsky.social
www.biorxiv.org/content/10.6...
Motor learning @juangallego.bsky.social and @clopathlab.bsky.social
www.biorxiv.org/content/10.6...
Reposted by Cedric Boeckx
It's been quite a year for hypothalamic development. With this heroic analysis of developmental cell lineage, coupled with earlier multimode-based gene regulatory network analysis, the prosomere model looks like it has passed into history.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Resolving forebrain developmental organisation by analysis of differential growth patterns - Nature Communications
Experiments on the embryonic chick brain reveal distinct directional growth patterns and a tripartite hypothalamus, challenging the classic segmented prosomere model and offering an updated view of ho...
www.nature.com
December 22, 2025 at 5:08 PM
It's been quite a year for hypothalamic development. With this heroic analysis of developmental cell lineage, coupled with earlier multimode-based gene regulatory network analysis, the prosomere model looks like it has passed into history.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Cedric Boeckx
This is a good time to talk about the TRUE genetics revolution brought in by sequencing the human genome:
The genetic underpinning of traits is not simple, will never be simple. Complex gene-gene interactions are the rule, not the exception 🧵
www.nature.com/articles/d41...
The genetic underpinning of traits is not simple, will never be simple. Complex gene-gene interactions are the rule, not the exception 🧵
www.nature.com/articles/d41...
Biobanks reveal genetic complexity in human evolution
Tiny genetic variations between humans, Neanderthals and Denisovans might not be all they were cracked up to be.
www.nature.com
December 19, 2025 at 5:29 PM
This is a good time to talk about the TRUE genetics revolution brought in by sequencing the human genome:
The genetic underpinning of traits is not simple, will never be simple. Complex gene-gene interactions are the rule, not the exception 🧵
www.nature.com/articles/d41...
The genetic underpinning of traits is not simple, will never be simple. Complex gene-gene interactions are the rule, not the exception 🧵
www.nature.com/articles/d41...
Reposted by Cedric Boeckx
Integrating brain structure and function for the neurobiology and genetics of language www.biorxiv.org/content/10.6... New study in which @jsamelink.bsky.social examined brain data from >32,000 people from @ukbiobank.bsky.social ... 1/4 ⬇️
December 19, 2025 at 11:41 AM
Integrating brain structure and function for the neurobiology and genetics of language www.biorxiv.org/content/10.6... New study in which @jsamelink.bsky.social examined brain data from >32,000 people from @ukbiobank.bsky.social ... 1/4 ⬇️
Reposted by Cedric Boeckx
Our findings resonate with important prior work by @kuhlwilm.bsky.social & @cedricboeckx.bsky.social which argued that evolution of human-specific traits involved cumulative changes across gene networks, encompassing not only fixed sites but also variants at high frequency in present-day humans.14/n
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins - Scientific Reports
Scientific Reports - A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
www.nature.com
December 19, 2025 at 11:42 AM
Our findings resonate with important prior work by @kuhlwilm.bsky.social & @cedricboeckx.bsky.social which argued that evolution of human-specific traits involved cumulative changes across gene networks, encompassing not only fixed sites but also variants at high frequency in present-day humans.14/n
Reposted by Cedric Boeckx
Incredible resource of ~1M single-cell transcriptomes, NeuRoDev, that captures temporal and cellular variation across human brain development. Congrats to Asia Zonca and Erik Bot from the Davila-Velderrain group at @humantechnopole.bsky.social for leading this work!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
December 19, 2025 at 7:25 AM
Incredible resource of ~1M single-cell transcriptomes, NeuRoDev, that captures temporal and cellular variation across human brain development. Congrats to Asia Zonca and Erik Bot from the Davila-Velderrain group at @humantechnopole.bsky.social for leading this work!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Great 🧵 by @profsimonfisher.bsky.social highlighting key points of their Science Advances study (led by Barabara Molz). Very happy to see how some of their conclusions align with what @kuhlwilm.bsky.social & I wrote in our 2019 paper
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 19, 2025 at 7:22 AM
Great 🧵 by @profsimonfisher.bsky.social highlighting key points of their Science Advances study (led by Barabara Molz). Very happy to see how some of their conclusions align with what @kuhlwilm.bsky.social & I wrote in our 2019 paper
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Cedric Boeckx
"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD. (...) These results suggest that TAD boundary architecture and gene activity are largely uncoupled"
TAD boundary architecture and gene activity are uncoupled
Topologically associating domains (TADs) are prominent features of genome organization. A proposed function of TADs is to contribute to gene regulation by promoting chromatin interactions within a TAD...
www.biorxiv.org
December 18, 2025 at 11:43 AM
"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD. (...) These results suggest that TAD boundary architecture and gene activity are largely uncoupled"
Reposted by Cedric Boeckx
netneurotools: a trainee-oriented approach to network neuroscience | doi.org/10.1101/2025...
Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging ⤵️
Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging ⤵️
December 18, 2025 at 3:00 PM
netneurotools: a trainee-oriented approach to network neuroscience | doi.org/10.1101/2025...
Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging ⤵️
Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging ⤵️