Ali Akbari

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.

Our paper on the theoretical properties of SNP heritability in admixed populations is out in Genetics:
academic.oup.com/genetics/adv...

with @jinguohuang.bsky.social, @nicole-kleman.bsky.social , Saonli Basu, and Mark Shriver

Excited to share our work on using pathway-specific polygenic scores to discover gene-environment interactions www.medrxiv.org/content/10.1...

When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1

For neutrophil count, J-PEP expands interpretation beyond immune cells, highlighting hepatic-inflammatory and neuroimmune axes.

For hypertension (HTN), it identifies stromal and adrenal-endocrine processes missed by prior methods.

For type 2 diabetes (T2D), J-PEP refines known pathways like β-cell dysfunction and uncovers underexplored immune and developmental signals.

Mapping disease loci to biological processes via joint pleiotropic and epigenomic partitioning Genome-wide association studies (GWAS) have identified thousands of disease-associated loci, yet their interpretation remains limited by the heterogeneity of underlying biological processes. We propos...

J-PEP is a new method that clusters disease-associated loci by combining pleiotropic SNP effects with tissue-specific epigenomic data. It improves biological resolution across complex traits.
doi.org/10.1101/2025...

Integrative multi-omics QTL colocalization maps regulatory architecture in aging human brain https://www.medrxiv.org/content/10.1101/2025.04.17.25326042v1

Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social

Robust detection of specific epistasis using rank statistics The phenotypic effect of a mutation may depend on the genetic background in which it occurs, a phenomenon referred to as epistasis. One source of epistasis in proteins is direct interactions between r...

What is epistasis?

New preprint Blue-torial!

(Work by the wonderful postdocs Maryn Carlson and Bryan Andrews)
www.biorxiv.org/content/10.1...

If we take regional averages, genes associated with education predict height better than genes associated with height. Why? On a regional level, education-associated genes pick up environmental differences between richer and poorer neighborhoods 🧬💰

From www.nature.com/articles/s41...

A line graph titled "Confirmed cases of influenza B Yamagata" shows weekly confirmed cases of B Yamagata influenza worldwide from various types of influenza surveillance. The vertical axis represents the number of cases, ranging from zero to 5,000, while the horizontal axis covers the years from 2013 to 2025. The graph indicates significant fluctuations in case numbers over the years, with a noticeable peak just below 5,000 cases around 2019, followed by a steep decline. A data source note mentions that only a fraction of potential influenza cases is tested by labs for confirmation and strain identification. The data comes from FluNet, World Health Organization, and is dated 2023. The graph is licensed under CC BY.

A flu lineage has likely gone extinct since 2020 🧵

Opinion | Should Human Life Be Optimized? Advances in genetic testing and artificial intelligence are changing what’s possible for those undergoing I.V.F. Are we ready for the future of fertility?

The New York Times recently had an article on IVF and embryo selection which I think buries a few important ledes about these products ...

Did you get a chance to read the thread on our new @naturehumbehav.bsky.social paper on SES yet?

If not, don't worry, I have something better for you!

Check out this comic by the amazing @lizahaart.bsky.social

Complete comic: communities.springernature.com/posts/are-we...

Or in this thread 👇🏾

In every civilization, people end up sorted into levels of socio-economic status (SES). We explore the history, present, and future of scientific research on the complicated relationship between SES and DNA in @naturehumbehav.bsky.social💰🧬🎓

Link: rdcu.be/efacK

Thread below 👇🏽

Evidence Aggregator: AI reasoning applied to rare disease diagnostics Retrieving, reviewing, and synthesizing technical information can be time-consuming and challenging, particularly when requiring specialized expertise, as is the case of variant assessment for rare di...

New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...

Experimental evolution of evolvability Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...

How selection can incorporate evolutionary history into the genetic architecture of a single cell, giving rise to a hypermutable locus that appears to anticipate environmental change, thereby accelerating adaptive evolution.

www.science.org/doi/10.1126/...

Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees

I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published.

I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria.

www.nature.com/articles/s41...

Insufficient evidence for natural selection associated with the Black Death - Nature Nature - Insufficient evidence for natural selection associated with the Black Death

Insufficient evidence for natural selection associated with the Black Death

These claims are unsupported for four reasons...

Finally, we find no evidence of significant change in frequency of the ERAP2 variant rs2549794...

www.nature.com/articles/s41...

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

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

Distinct explanations underlie gene-environment interactions in the UK Biobank The role of gene-environment (GxE) interaction in disease and complex trait architectures is widely hypothesized but currently unknown. Here, we apply three statistical approaches to quantify and dist...

Distinct explanations underlie gene-environment interactions in the UK Biobank.
www.cell.com/ajhg/abstrac...

Multiple-testing corrections in selection scans using identity-by-descent segments https://www.biorxiv.org/content/10.1101/2025.01.29.635528v1

Genomics of rare diseases in the Greater Middle East - Nature Genetics The Greater Middle East is home to a rich genetic diversity that remains largely untapped in genomic research. This Perspective explores its potential for rare disease research, obstacles limiting pro...

Our review on the genomics of rare disease in the Greater Middle East is out this week in @naturegenet.bsky.social

www.nature.com/articles/s41...

Our papers, out today in @nature.com, show how ancient DNA from the Eneolithic and Bronze Age steppe points to a North Pontic origin of the Indo-European language family and a Caucasus-Lower Volga (CLV) origin of Indo-Anatolian (inclusive of the now extinct Anatolian languages). 1/

The distribution of highly deleterious variants across human ancestry groups A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...

“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...

Think of a polygenic score you care about. Are direct genetic effects driving variation among people in this predictor? Or perhaps other, confounding factors? We at the @arbelharpak.bsky.social & @docedge.bsky.social Labs developed a method to tackle this question. [1/n]

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...

A homozygous SVA retrotransposon insertion is discovered to be likely the most common mutation in ASPA (encodes aspartoacylase) underlying Canavan disease. 1/

Gonzalez, Bell, et al. medRxiv
www.medrxiv.org/content/10.1...

Within-Family GWAS does not Ameliorate the Decline in Prediction Accuracy across Populations As polygenic prediction extends beyond the research domain to involve clinical applications, the urgency of solving the "portability problem" becomes amplified -- that is, the fact that polygenic indi...

www.biorxiv.org/content/10.1...

Smart study to test whether lower prediction accuracy in non-Europeans is due to between-population differences in population structure, genetic nurture, or assortative mating.

I've always wondered about the pigmentation GWAS signals like TYR, OCA2 etc. in the GWAS of OCT-derived phenotypes. A new preprint elegantly investigates the phenotypic and genetic correlation between retinal pigment epithelium (RPE) thickness (which is measured using OCT) 1/