Lino Ferreira
@linoafferreira.bsky.social
Researcher in statistical genetics looking for new professional opportunities
PhD from Oxford
lfe.pt
PhD from Oxford
lfe.pt
New paper on the problem of "missing regulation" (limited overlap between GWAS signals and eQTLs) from Shamil Sunyaev's lab. Led by Noah Connally.
Farm animal evolution demonstrates hidden molecular basis of human traits https://www.biorxiv.org/content/10.64898/2026.02.02.703413v1
February 9, 2026 at 10:39 AM
New paper on the problem of "missing regulation" (limited overlap between GWAS signals and eQTLs) from Shamil Sunyaev's lab. Led by Noah Connally.
Reposted by Lino Ferreira
Our work on the generalizability of polygenic scores (PGS) from the @arbelharpak.bsky.social Lab is now officially out!
We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.”
rdcu.be/e0LAr
(1/27)
We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.”
rdcu.be/e0LAr
(1/27)
Three open questions in polygenic score portability
Nature Communications - Genetic predictors of health outcomes often drop in accuracy when applied to people dissimilar to participants of large genetic studies. Here, the authors investigate the...
rdcu.be
January 26, 2026 at 11:20 PM
Our work on the generalizability of polygenic scores (PGS) from the @arbelharpak.bsky.social Lab is now officially out!
We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.”
rdcu.be/e0LAr
(1/27)
We examine the accuracy of PGS predictions at the individual level. We make 3 observations that expose gaps in our understanding of PGS “portability.”
rdcu.be/e0LAr
(1/27)
Insightful paper on the importance of phenotypic scale when testing for interactions involving genetic variants (specifically, GxE effects). From Iain Mathieson's and Andy Dahl's labs, and led by Manuela Costantino.
Choice of phenotype scale is critical in biobank-based GxE tests https://www.biorxiv.org/content/10.64898/2026.01.20.694695v1
January 26, 2026 at 3:44 PM
Insightful paper on the importance of phenotypic scale when testing for interactions involving genetic variants (specifically, GxE effects). From Iain Mathieson's and Andy Dahl's labs, and led by Manuela Costantino.
Reposted by Lino Ferreira
Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.
January 14, 2026 at 9:37 PM
Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.
Reposted by Lino Ferreira
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
www.biorxiv.org
December 22, 2025 at 3:09 PM
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
Reposted by Lino Ferreira
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 Lino Ferreira
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies
Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla
academic.oup.com
October 3, 2025 at 9:54 AM
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
Reposted by Lino Ferreira
SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction https://www.biorxiv.org/content/10.1101/2025.11.25.690514v1
November 28, 2025 at 10:46 AM
SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction https://www.biorxiv.org/content/10.1101/2025.11.25.690514v1
Reposted by Lino Ferreira
🚨 New preprint from the lab!
We’re excited to share “Improving population-scale disease prediction through multi-omics integration” by Ng et al. www.medrxiv.org/content/10.1...
We’re excited to share “Improving population-scale disease prediction through multi-omics integration” by Ng et al. www.medrxiv.org/content/10.1...
November 28, 2025 at 9:56 AM
🚨 New preprint from the lab!
We’re excited to share “Improving population-scale disease prediction through multi-omics integration” by Ng et al. www.medrxiv.org/content/10.1...
We’re excited to share “Improving population-scale disease prediction through multi-omics integration” by Ng et al. www.medrxiv.org/content/10.1...
...for interactions involving the HLA region in collaboration with @y-luo.bsky.social.
Thanks for reading!
Thanks for reading!
November 24, 2025 at 5:26 PM
...for interactions involving the HLA region in collaboration with @y-luo.bsky.social.
Thanks for reading!
Thanks for reading!
...might allow for detecting many more of these effects.
I'd like to thank Sile Hu for his help and Simon Myers for his supervision. 🙏
I'm also very grateful to @mollyprz.bsky.social for generous financial support in the final stages of the project.
In ongoing work, we are testing...
I'd like to thank Sile Hu for his help and Simon Myers for his supervision. 🙏
I'm also very grateful to @mollyprz.bsky.social for generous financial support in the final stages of the project.
In ongoing work, we are testing...
November 24, 2025 at 5:26 PM
...might allow for detecting many more of these effects.
I'd like to thank Sile Hu for his help and Simon Myers for his supervision. 🙏
I'm also very grateful to @mollyprz.bsky.social for generous financial support in the final stages of the project.
In ongoing work, we are testing...
I'd like to thank Sile Hu for his help and Simon Myers for his supervision. 🙏
I'm also very grateful to @mollyprz.bsky.social for generous financial support in the final stages of the project.
In ongoing work, we are testing...
...are partly mediated through modulating the effects of other SNPs.
Another takeaway is that we find more interactions for molecular phenotypes than for more complex and polygenic phenotypes (probably due to greater statistical power to detect them), and so novel proteomics datasets...
Another takeaway is that we find more interactions for molecular phenotypes than for more complex and polygenic phenotypes (probably due to greater statistical power to detect them), and so novel proteomics datasets...
November 24, 2025 at 5:13 PM
...are partly mediated through modulating the effects of other SNPs.
Another takeaway is that we find more interactions for molecular phenotypes than for more complex and polygenic phenotypes (probably due to greater statistical power to detect them), and so novel proteomics datasets...
Another takeaway is that we find more interactions for molecular phenotypes than for more complex and polygenic phenotypes (probably due to greater statistical power to detect them), and so novel proteomics datasets...
...functional relationships between genes.
Moreover, many phenotypes (more than half of those we analysed) show interactions, and in fact some well-known hits from standard GWASs (at FTO for obesity or TCF7L2 for diabetes, for example) have effects on disease-relevant phenotypes that...
Moreover, many phenotypes (more than half of those we analysed) show interactions, and in fact some well-known hits from standard GWASs (at FTO for obesity or TCF7L2 for diabetes, for example) have effects on disease-relevant phenotypes that...
November 24, 2025 at 5:13 PM
...functional relationships between genes.
Moreover, many phenotypes (more than half of those we analysed) show interactions, and in fact some well-known hits from standard GWASs (at FTO for obesity or TCF7L2 for diabetes, for example) have effects on disease-relevant phenotypes that...
Moreover, many phenotypes (more than half of those we analysed) show interactions, and in fact some well-known hits from standard GWASs (at FTO for obesity or TCF7L2 for diabetes, for example) have effects on disease-relevant phenotypes that...
...the Wnt signalling pathway (itself important in diabetes aetiology) which points to the potential relevance of this interaction in the architecture of this disease.
Our results show that, even though interactions explain very little phenotypic variance, they can be useful by pointing to...
Our results show that, even though interactions explain very little phenotypic variance, they can be useful by pointing to...
November 24, 2025 at 5:13 PM
...the Wnt signalling pathway (itself important in diabetes aetiology) which points to the potential relevance of this interaction in the architecture of this disease.
Our results show that, even though interactions explain very little phenotypic variance, they can be useful by pointing to...
Our results show that, even though interactions explain very little phenotypic variance, they can be useful by pointing to...
...to partition PGSs and test the same 144 hits for interactions with partitioned scores. We identify 12 interactions, including one between the strongest T2D-associated SNP found to date (at TCF7L2) and the KDM2A TF for HbA1c levels. KDM2A has been found to interact physically with TCF7L2 within...
November 24, 2025 at 5:13 PM
...to partition PGSs and test the same 144 hits for interactions with partitioned scores. We identify 12 interactions, including one between the strongest T2D-associated SNP found to date (at TCF7L2) and the KDM2A TF for HbA1c levels. KDM2A has been found to interact physically with TCF7L2 within...
...and IL33 for eosinophil levels, which could reflect a functional interaction between these genes recently implicated in eosinophilic asthma.
We then look for interactions that are more precise than SNP-by-PGS but broader than SNP-by-SNP: we use data on transcription factor binding motifs...
We then look for interactions that are more precise than SNP-by-PGS but broader than SNP-by-SNP: we use data on transcription factor binding motifs...
November 24, 2025 at 5:13 PM
...and IL33 for eosinophil levels, which could reflect a functional interaction between these genes recently implicated in eosinophilic asthma.
We then look for interactions that are more precise than SNP-by-PGS but broader than SNP-by-SNP: we use data on transcription factor binding motifs...
We then look for interactions that are more precise than SNP-by-PGS but broader than SNP-by-SNP: we use data on transcription factor binding motifs...
...for SNP-by-SNP interactions but within a much smaller search space, and allows us to find 38 pairs (of which 32 are novel to our knowledge).
Our results recover and extend a known network involving ABO, FUT2 and TREH for alkaline phosphatase. Another highlight is an interaction between ALOX15...
Our results recover and extend a known network involving ABO, FUT2 and TREH for alkaline phosphatase. Another highlight is an interaction between ALOX15...
November 24, 2025 at 5:13 PM
...for SNP-by-SNP interactions but within a much smaller search space, and allows us to find 38 pairs (of which 32 are novel to our knowledge).
Our results recover and extend a known network involving ABO, FUT2 and TREH for alkaline phosphatase. Another highlight is an interaction between ALOX15...
Our results recover and extend a known network involving ABO, FUT2 and TREH for alkaline phosphatase. Another highlight is an interaction between ALOX15...
...the effect of the PGS on the trait; or the effect of a SNP varies depending on polygenic background. Our signals include well-know disease risk variants at APOE, FTO and TCF7L2.
We then take these 144 associations and look for pairwise interactions genome-wide. This is a classic search...
We then take these 144 associations and look for pairwise interactions genome-wide. This is a classic search...
November 24, 2025 at 5:13 PM
...the effect of the PGS on the trait; or the effect of a SNP varies depending on polygenic background. Our signals include well-know disease risk variants at APOE, FTO and TCF7L2.
We then take these 144 associations and look for pairwise interactions genome-wide. This is a classic search...
We then take these 144 associations and look for pairwise interactions genome-wide. This is a classic search...
We develop a method to test for interactions between SNPs and polygenic scores (PGSs) and apply it to 97 quantitative phenotypes in the @ukbiobank.bsky.social, identifying 144 associations for 52 different traits.
These can be interpreted in two equivalent ways: the genotype at a locus alters...
These can be interpreted in two equivalent ways: the genotype at a locus alters...
November 24, 2025 at 5:13 PM
We develop a method to test for interactions between SNPs and polygenic scores (PGSs) and apply it to 97 quantitative phenotypes in the @ukbiobank.bsky.social, identifying 144 associations for 52 different traits.
These can be interpreted in two equivalent ways: the genotype at a locus alters...
These can be interpreted in two equivalent ways: the genotype at a locus alters...
...a linear model of genotype > phenotype.
Interactions can help with understanding biological mechanisms by identifying different parts of the genome whose statistical effects on a phenotype are interdependent – and which are therefore likely to also interact functionally within a pathway.
Interactions can help with understanding biological mechanisms by identifying different parts of the genome whose statistical effects on a phenotype are interdependent – and which are therefore likely to also interact functionally within a pathway.
November 24, 2025 at 5:13 PM
...a linear model of genotype > phenotype.
Interactions can help with understanding biological mechanisms by identifying different parts of the genome whose statistical effects on a phenotype are interdependent – and which are therefore likely to also interact functionally within a pathway.
Interactions can help with understanding biological mechanisms by identifying different parts of the genome whose statistical effects on a phenotype are interdependent – and which are therefore likely to also interact functionally within a pathway.
GWASs have been hugely successful in finding genetic associations but understanding the function of associated loci remains a great challenge.
We address this question from the angle of genetic interactions (epistasis): statistical interaction terms between genetic variants in...
We address this question from the angle of genetic interactions (epistasis): statistical interaction terms between genetic variants in...
November 24, 2025 at 5:13 PM
GWASs have been hugely successful in finding genetic associations but understanding the function of associated loci remains a great challenge.
We address this question from the angle of genetic interactions (epistasis): statistical interaction terms between genetic variants in...
We address this question from the angle of genetic interactions (epistasis): statistical interaction terms between genetic variants in...
Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank!
A thread... 🧵
www.medrxiv.org/content/10.1...
A thread... 🧵
www.medrxiv.org/content/10.1...
Interactions with polygenic background impact quantitative traits in the UK Biobank
Association studies have linked many genetic variants to a variety of phenotypes but under-standing the biological mechanisms underlying these signals remains a major challenge. Since genes operate wi...
www.medrxiv.org
November 24, 2025 at 5:13 PM
Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank!
A thread... 🧵
www.medrxiv.org/content/10.1...
A thread... 🧵
www.medrxiv.org/content/10.1...
Reposted by Lino Ferreira
New study in #GENETICS from @anaignatieva.bsky.social and @linoafferreira.bsky.social shows how ancestral recombination graphs can help detect "phantom" genetic interaction signals that arise due to genealogy and not because of epistasis. buff.ly/TQARoDp
October 16, 2025 at 1:04 PM
New study in #GENETICS from @anaignatieva.bsky.social and @linoafferreira.bsky.social shows how ancestral recombination graphs can help detect "phantom" genetic interaction signals that arise due to genealogy and not because of epistasis. buff.ly/TQARoDp
Reposted by Lino Ferreira
Our paper about how ancestral recombination graphs can be used to detect "phantom" genetic interaction signals (that arise due to the genealogy, rather than "real" epistasis) is out in Genetics! Nice thread here by @linoafferreira.bsky.social
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
September 15, 2025 at 10:33 AM
Our paper about how ancestral recombination graphs can be used to detect "phantom" genetic interaction signals (that arise due to the genealogy, rather than "real" epistasis) is out in Genetics! Nice thread here by @linoafferreira.bsky.social
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...