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David Gokhman @david-gokhman.bsky.social · Aug 28

Another truly amazing work by the Capellini lab

tdcapellini.bsky.social @tdcapellini.bsky.social · Aug 27

1) I am delighted to present this terrific tour de force research conducted by my post-doc Dr. Gayani Senevirathne @gayani.bsky.social and published today in Nature -
www.nature.com/articles/s41...

The evolution of hominin bipedalism in two steps - Nature

The human pelvis exhibits distinct spatiotemporal ossification patterns and an ilium cartilage growth plate that is shifted perpendicularly compared with those of other mammals and non-human primates—...

www.nature.com

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David Gokhman @david-gokhman.bsky.social · Aug 27

It was a true pleasure to work on this with @nadavmishol.bsky.social, @lirancarmel.bsky.social
, Gadi Herzlinger, Uzy Smilansky, and Yoel Rak

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David Gokhman @david-gokhman.bsky.social · Aug 27

Our approach was based on gene regulatory phenotyping, which predicts the direction, rather than magnitude, of phenotypic difference - a much more attainable goal. If you're interested in why and how this approach works, see: www.nature.com/articles/s41...

Predicting the direction of phenotypic difference - Nature Communications

Here authors reveal a method to predict key information on phenotypes - their direction. This is achievable even for phenotypes with incomplete genotype-to-phenotype mapping, and applicable for indivi...

www.nature.com

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David Gokhman @david-gokhman.bsky.social · Aug 27

This approach opens a new way to connect genetics & fossils, helping classify debated human remains and refine our evolutionary tree.

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David Gokhman @david-gokhman.bsky.social · Aug 27

Denisovans or their close relatives identified in the fossil record using a gene regulatory phenotyping method. Now out:
www.pnas.org/doi/10.1073/...

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Reposted by David Gokhman

Gili Greenbaum @gilig.bsky.social · Aug 1

🧵 Excited to share a new preprint from our lab looking into signals of disease-burden in aDNA (doi.org/10.1101/2025...)! It has long been speculated that transition to sedentary, agricultural and urbanized lifestyle increases disease burden, but can we see this in aDNA?

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David Gokhman @david-gokhman.bsky.social · Jul 26

Overall, we suggest that substantially more phenotypic information can be inferred from genetic data than previously appreciated. Had a great time working on this with @gilig.bsky.social @shaicarmi.bsky.social and Keith Harris

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David Gokhman @david-gokhman.bsky.social · Jul 26

Importantly, unlike quantitative phenotypic predictions (e.g., based on polygenic scores), we show that our qualitative approach circumvents one of the biggest problems in population genetics – the limited transferability of genotype-phenotype association data across populations

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David Gokhman @david-gokhman.bsky.social · Jul 26

This estimator can be applied to comparisons of individuals from the same family, same population, different populations, or even different species

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David Gokhman @david-gokhman.bsky.social · Jul 26

Our method works even when genotype-to-phenotype information is limited. For example, we show that even in phenotypes where known SNPs explain only 3% of phenotypic variation, you can often predict with >90% accuracy who has the higher phenotypic value

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David Gokhman @david-gokhman.bsky.social · Jul 26

Given two genomes, can you tell who’s taller or more prone to a disease? How confident can you be? A fresh take on phenotypic inference, now out:
rdcu.be/exW4f
See thread🧵👇:

Predicting the direction of phenotypic difference

Nature Communications - Here authors reveal a method to predict key information on phenotypes - their direction. This is achievable even for phenotypes with incomplete genotype-to-phenotype...

rdcu.be

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David Gokhman @david-gokhman.bsky.social · Jun 20

For additional specimens we think likely belong to Denisovans, see Nadav Mishol's beautiful preprint, in collaboration with
@lirancarmel.bsky.social www.biorxiv.org/content/10.1...

David Gokhman @david-gokhman.bsky.social · Jun 20

Although a Denisovan pinky bone has been discovered, testing our pinky-related prediction also requires the proximal and intermediate phalanges. Once those are found, we’ll also be able to test whether Denisovan phalanges exhibit the predicted tapering from proximal to distal

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David Gokhman @david-gokhman.bsky.social · Jun 20

Our approach was based on gene regulatory phenotyping, which predicts the direction, rather than magnitude, of phenotypic difference - a much more attainable goal. If you're interested in why and how this approach works, see: www.biorxiv.org/content/10.1...

www.biorxiv.org

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David Gokhman @david-gokhman.bsky.social · Jun 20

Interestingly, our Denisovan trait prediction accuracy now stands at 89% - matching the accuracy we estimated using Neanderthal and chimpanzee data. Always nice when the model does what it says on the tin.

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David Gokhman @david-gokhman.bsky.social · Jun 20

Overall 25/28 of our predictions have been confirmed. Not too shabby for profiling an extinct species from DNA methylation maps!

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David Gokhman @david-gokhman.bsky.social · Jun 20

6 years ago, we predicted what Denisovans probably looked like. Since then, every new Denisovan specimen💀 - Harbin, Penghu, Xiahe - matched it beautifully.
☑️ Xiahe: 4/4 features match the profile
☑️ Penghu: 5/6
☑️ and now: Harbin with 16/18!
See 🧵
pubmed.ncbi.nlm.nih.gov/31539495/

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David Gokhman @david-gokhman.bsky.social · Jun 18

Correct links here:
www.science.org/doi/10.1126/...
and
www.cell.com/cell/fulltex...

The proteome of the late Middle Pleistocene Harbin individual

Denisovans are a hominin group primarily known through genomes or proteins, but the precise morphological features of Denisovans remain elusive due to the fragmentary nature of discovered fossils. Her...

www.science.org

David Gokhman @david-gokhman.bsky.social · Jun 18

And the first genetic evidence supporting this was posted last year: www.biorxiv.org/content/10.1...

www.biorxiv.org

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David Gokhman @david-gokhman.bsky.social · Jun 18

First genetic evidence that Harbin was likely a Denisovan was here: www.biorxiv.org/content/10.1...

www.biorxiv.org

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David Gokhman @david-gokhman.bsky.social · Jun 18

We showed it first: www.biorxiv.org/content/10.1...

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David Gokhman @david-gokhman.bsky.social · Jun 18

Last year, we posted a preprint providing the first genetic evidence that the Harbin skull likely belonged to a Denisovan: www.biorxiv.org/content/10.1... Today, DNA evidence provided the final proof: www-sciencedirect-com.ezproxy.weizmann.ac.il/science/arti...

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David Gokhman @david-gokhman.bsky.social · May 7

It is! And yes, we’re going to have brain-related data soon and I’m super curious to see if the variants we report played a role in human brain evo too!

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David Gokhman @david-gokhman.bsky.social · Apr 18

Find out about other potential Denisovan specimens here, in a beautiful work led by Nadav Mishol: www.biorxiv.org/content/10.1... @lirancarmel.bsky.social

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David Gokhman @david-gokhman.bsky.social · Apr 18

A common mistake when evaluating the profile is normalizing features (e.g., by breadth). But since the profile includes independent predictions affecting length, height, and breadth, normalization cancels out key signals. Absolute values are the way to go here, and they align with our predictions.

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