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Ana Ignatieva @anaignatieva.bsky.social · 5d

The software (DoLoReS) is available on github. Thanks to Simon Myers and our coauthors Jaro Sant, Martina Favero, Jere Koskela. (8/8)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

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Ana Ignatieva @anaignatieva.bsky.social · 5d

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

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Ana Ignatieva @anaignatieva.bsky.social · 23d

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...

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Reposted by Ana Ignatieva

Nicky Whiffin @nickywhiffin.bsky.social · Jul 31

📣 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

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'

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Reposted by Ana Ignatieva

Jonathan Pritchard @jkpritch.bsky.social · Jul 7

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

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Reposted by Ana Ignatieva

Anders Bergström @anders-bergstrom.bsky.social · Jun 13

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...

Senior Research Associate in Population Genomics (RA2327) in University of East Anglia | UEA

View details and apply for this Senior Research Associate in Population Genomics (RA2327) vacancy in University of East Anglia. Faculty of Science School of Biological Sciences Senior Research A...

vacancies.uea.ac.uk

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Reposted by Ana Ignatieva

Leo Speidel @leospeidel.bsky.social · Jun 25

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

Seeking a few Postdoctoral Researchers at Mathematical Genomics RIKEN ECL Research Unit (25-695)

www.riken.jp

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Reposted by Ana Ignatieva

Arun Durvasula @arundurvasula.bsky.social · Jun 11

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)

Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies

Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Ma...

arxiv.org

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Reposted by Ana Ignatieva

Simon Cauchemez @scauchemez.bsky.social · Jun 5

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...

Postdoctoral positions in epidemic mathematical/statistical modelling - Research

Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...

research.pasteur.fr

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Reposted by Ana Ignatieva

Jonathan Pritchard @jkpritch.bsky.social · Jun 1

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.

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Reposted by Ana Ignatieva

Ian Henderson @hendersi.bsky.social · May 30

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/

Research Assistant / Research Associate (Fixed Term) - Job Opportunities - University of Cambridge

Research Assistant / Research Associate (Fixed Term) in the Department of Plant Sciences at the University of Cambridge.

www.jobs.cam.ac.uk

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Reposted by Ana Ignatieva

Arun Durvasula @arundurvasula.bsky.social · Feb 17

Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition
academic.oup.com/mbe/advance-...

Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition

Abstract. A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during the Early to Middle Pleistoc

academic.oup.com

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Reposted by Ana Ignatieva

Arun Durvasula @arundurvasula.bsky.social · Feb 17

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

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Reposted by Ana Ignatieva

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Feb 2

Polarizing SNPs without outgroup https://www.biorxiv.org/content/10.1101/2025.01.31.635919v1

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Reposted by Ana Ignatieva

danielfalush.bsky.social @danielfalush.bsky.social · Jan 27

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...

A putative ecocline in Klebsiella pneumoniae

Are quantitative traits important for bacteriology? The quantitative trait models used in animal and plant genetics assume that the trait takes continuous values and is influenced by many variants cir...

www.biorxiv.org

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Reposted by Ana Ignatieva

Leo Speidel @leospeidel.bsky.social · Jan 23

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.

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Ana Ignatieva @anaignatieva.bsky.social · Dec 9

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...

Phantom epistasis through the lens of genealogies

Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant (with a purely additive effect on the phenotype) causes the spurious inference o...

www.biorxiv.org

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Reposted by Ana Ignatieva

Laurits Skov @lauritsskov.bsky.social · Dec 2

Very excited (and a bit nervous) to announce that I will be hiring two Postdocs for my new group(!) in Copenhagen to study the Neanderthal and Denisovan DNA which survives in present-day humans. Retweet will be much appreciated :)

Link for application:
candidate.hr-manager.net/ApplicationI...

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Reposted by Ana Ignatieva

Department of Statistics @oxfordstatistics.bsky.social · Nov 21

🎇A brand-new CDT: the Fundamentals of AI, has been launched!🚀

Applications are being accepted for 2025/26.
There are 20 places available, with full funding for home and overseas candidates.

⏳Deadline: 08.01.2025

For more info, visit: dtc.ox.ac.uk/foai-cdt

#eraofAI #AI #CDT #AIforhumanity

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