Lino Ferreira
@linoafferreira.bsky.social
Researcher in statistical genetics PhD from Oxford lfe.pt
I am delighted to share new work with Simon Myers (www.biorxiv.org/content/10.6...), on how genetic variants that influence binding patterns of PRDM9 and slow down the repair of meiotic double-strand breaks impact mammalian spermatogenesis and fertility. 1/n
biorxiv.org
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
biorxiv.org
New preprint led by Hrushikesh Loya, me, and Simon Myers where we introduce GhostBuster! www.biorxiv.org/content/10.6... The idea is to find all the different ways a target individual relates to reference groups in genealogies, to "bust the ghosts" in our ancestry.
biorxiv.org
Some Open Problems in Probability that are Relevant to Applied Statistics (my talk this Wed noon at the Columbia statistics department student seminar) statmodeling.stat.columbia.edu/2026/02/10/m...
Some Open Problems in Probability that are Relevant to Applied Statistics (my talk this Wed noon at the Columbia statistics department student seminar) | Statistical Modeling, Causal Inference, and S...
statmodeling.stat.columbia.edu
New paper on the problem of "missing regulation" (limited overlap between GWAS signals and eQTLs) from Shamil Sunyaev's lab. Led by Noah Connally.
bioRxiv Genetics@biorxiv-genetic.bsky.social · 6mo agoFarm animal evolution demonstrates hidden molecular basis of human traits https://www.biorxiv.org/content/10.64898/2026.02.02.703413v1
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)
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
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.
bioRxiv Genetics@biorxiv-genetic.bsky.social · 7mo agoChoice of phenotype scale is critical in biobank-based GxE tests https://www.biorxiv.org/content/10.64898/2026.01.20.694695v1
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*.
Home - NY Population Genetics meeting
events.simonsfoundation.org
Molly Przeworski@mollyprz.bsky.social · 9mo agoSAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.
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
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...
biorxiv.org
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🧵:
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.
nature.com
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
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
🚨 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...
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...
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...
medrxiv.org
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
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...
Phantom epistasis through the lens of genealogies
Abstract. Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant with a purely additive ef
academic.oup.com
Lino Ferreira@linoafferreira.bsky.social · 11mo agoDelighted to see this paper with @anaignatieva.bsky.social now published in Genetics! academic.oup.com/genetics/adv... We tackle a thorny issue arising in statistical tests for genetic interactions (epistasis) using ancestral recombination graphs (ARGs)... 🧵
Delighted to see this paper with @anaignatieva.bsky.social now published in Genetics! academic.oup.com/genetics/adv... We tackle a thorny issue arising in statistical tests for genetic interactions (epistasis) using ancestral recombination graphs (ARGs)... 🧵
Phantom epistasis through the lens of genealogies
Abstract. Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant with a purely additive ef
academic.oup.com
Excited to have this out there! Comments are very welcome.
Ana Ignatieva@anaignatieva.bsky.social · 2y agoNew preprint (with @linoafferreira.bsky.social) where we explore the idea of using genealogies (in the form of ancestral recombination graphs, ARGs) to tell apart real GxG interaction signals between nearby variants from false positives www.biorxiv.org/content/10.1...
📣 Two ERC-funded positions are available in the lab! If you are interested in exploring the mechanisms underlying mutation, we’d love to hear from you. PhD: shorturl.at/Oc04N Postdoc: shorturl.at/1ShHB RPs and shares would be greatly appreciated! 🧪🧬🖥️ #ScienceJobs #PostdocJobs
Congratulations to Carl Veller on the publication of his article on confounding in population and family GWAS journals.plos.org/plosbiology/...
Interpreting population- and family-based genome-wide association studies in the presence of confounding
GWASs aim to estimate direct effects of genotype on an individual’s phenotype, but this can be subject to genetic and environmental confounds and
journals.plos.org
My PhD programme, the 'DPhil in Genomic Medicine and Statistics' at the Wellcome Centre for Human Genetics in Oxford, is accepting applications for next year! I'm coming to the end of my studies after four years and feel so fortunate to have been part of it. Students get...
First post on this celestial platform to mark a happy occasion: I've submitted my PhD thesis! I've celebrated and rested well and am now back to working on research after all the writing... Excited for what's to come!
