In a new GBE Review, @david-peede.bsky.social et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods.
🔗 doi.org/10.1093/gbe/...
#genome #evolution #compbio
Graphic advertising the Florence Nightingale Bicentenary Fellow in Statistics at the University of Oxford, with application deadline 12 January 2026, and a portrait of Florence Nightingale.
📢 Come and work with us!
We have two postdoctoral Florence Nightingale Bicentenary Fellowships available in the Department of Statistics, starting in September 2026.
Applications close at 12 noon on Monday 12 January 2026.
➡️ Find out more at: tinyurl.com/yc5jxdrm
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...
The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.
Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...
The software (DoLoReS) is available on github. Thanks to Simon Myers and our coauthors Jaro Sant, Martina Favero, Jere Koskela. (8/8)
Our results also show that, perhaps unsurprisingly, since ARG reconstruction methods are not optimised to recover the right distribution of edge and clade spans, they do relatively poorly at this across the board. We hope our theoretical results can be used to help correct this. (7/n)
The other significant regions we find include other known and novel SVs, as well as regions that span genes that are expressed in meiosis (suggestive of allele-dependent suppression of recombination within these genes). (6/n)
We also find a ~760kb inversion on chr10, common in S. Asian populations (21%), and seemingly not previously detected by reads-based methods. This spans a number of genes associated with lung function and immunity, and is correlated with a number of GWAS hits. (5/n)
Localised suppression of recombination can arise for multiple reasons, including chromosomal inversions - since recombination is suppressed in heterozygous individuals. Using the 1000 Genomes Project Relate ARGs, we find many significant hits along the genome, including the chr17 inversion. (4/n)
Using the sequentially Markovian coalescent (SMC), we derive the theoretical distribution of this span. This lets us take an observed (simulated or reconstructed) ARG, and test each clade for deviation from this neutral model - to detect clades that have longer genomic spans than expected. (3/n)
Each edge or clade in an ancestral recombination graph (ARG, genealogy of a sample of sequences) has a genomic span: from where the edge/clade first appears along the genome, to when it's broken up by recombination. (2/n)
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)
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...
Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'
📣 We are recruiting! Please share!!
Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺
We have two roles available 👇
🧵 1/4
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
A 4-year postdoc position in population genomics is available in my group at the University of East Anglia, to work on a project sequencing a thousand fox genomes across rural and urban environments in the UK.
vacancies.uea.ac.uk/vacancies/15...
Postdoc position in my group in Tokyo!
Please get in touch if you are interested.
And happy to discuss projects - these would range from developing new methods to analysis of new genomes that we are now sequencing in the lab.
Job Ad: www.riken.jp/en/careers/r...
Lab page: speidellab.github.io
Our review of recent Sequentially Markovian Coalescent methods is up on arXiv: arxiv.org/abs/2506.00692 (based on last year's @official-smbe.bsky.social symposium)
New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
A three year postdoctoral position is available in my group, investigating plant centromere structure, function and evolution @camplantsci.bsky.social
www.jobs.cam.ac.uk/job/51488/
Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition
academic.oup.com/mbe/advance-...
Excited to share a couple of new items (links below):
1. Our work on gene-environment interactions in the UKBiobank is up at the American Journal of Human Genetics
2. Our work on modeling ancient human population size history is up at Molecular Biology and Evolution
Polarizing SNPs without outgroup https://www.biorxiv.org/content/10.1101/2025.01.31.635919v1
Excited to share our preprint "A putative ecocline in Klebsiella pneumoniae" and super-interested to get your feedback. Really want to use the hive mind to get to the bottom of this phenomenon ASAP. www.biorxiv.org/content/10.1...
My bluesky debut!
One week to the submission deadline for SMBE 2025, Beijing 20-24 July smbe2025.scimeeting.cn
@anaignatieva.bsky.social and I are organising a symposium on popgen through time: using ARGs, aDNA, or otherwise to understand the evolutionary processes that shape genomes through time.
New 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...
