Esha Bandyopadhyay, Ph.D.

Bioinformatician - Uppsala University Bioinformatician, Department of Organismal Biology, Uppsala University

The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment:

www.uu.se/en/about-uu/...

Accounting for Gene Flow from Unsampled Ghost Populations While Estimating Evolutionary History Abstract. Gene flow from unsampled or extinct ghost populations leave signatures on the genomes of individuals from extant, sampled populations, often intr

Oops - link appears to be broken. Try this: academic.oup.com/g3journal/ad...

MULTICLUST - Fast multinomial clustering of multiallelic genotypes to infer genetic population structure Identifying population structure from multilocus genotype data is key to downstream population genetic analyses in a variety of fields, including conservation, evolutionary genetics, Genome-Wide Assoc...

Excited for this to finally see the light of day - new preprint from my lab, where we present a fast, accurate maximum likelihood tool to estimate population structure, called MULTICLUST. We extend the model of Alexander et al 2009 (ADMIXTURE) to multiallelic data. www.biorxiv.org/content/10.1...

The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens…

#MetagenomicsMonday Analysis of aDNA from 1313 ancient human remains spanning 37k years revealed that the rise of infectious diseases coincided with animal domestication around 65k years ago, with disease spread intensifying during pastoralist migrations.
www.nature.com/articles/s41...

Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias Abstract. Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-rea

Results of our (extremely long-term) side project with @amygoldberg.bsky.social and @jgschraiber.bsky.social out now in G3: doi.org/10.1093/g3jo...

We benchmarked methods for estimating ancestry proportions under mapping bias and present an adjusted GenotypeLikelihood to mitigate its impact (1/2)

New in #GENETICS: Huang et al. describe biases in SNP & local ancestry heritability as functions of admixture history and the genetic architecture of the trait, clarifying their interpretation and implication for #GWAS & polygenic prediction in population admixture.

Read more: buff.ly/1xB3Mpu

Re-upping this! @cegamorim.bsky.social and I are stoked to be offering this workshop. Do join us!

The mini yet mighty stapes: a comparison of ancient DNA yields among ossicles and the petrous bone The petrous bone is considered the most efficient source of endogenous DNA across skeletal tissues in ancient DNA research as well as in forensic work. Recently, ancient DNA (aDNA) in auditory ossicle...

New preprint alert 🚨
The tiniest bone in the human body appears to have the best DNA preservation: "The mini yet mighty staples"
www.biorxiv.org/content/10.1...

last day tomorrow to register for a talk/poster at Midwest popgen. Please RT(? is that what they say here?)!

Whole-genome ancestry of an Old Kingdom Egyptian - Nature Whole-genome sequencing of an ancient male Egyptian revealed a mixture of North African Neolithic and eastern Fertile Crescent ancestry, suggesting human migration between Egypt and Mesopotamia by the...

Forty years after Svante Pääbo kicked off this extraordinary field of science, today sees report of the first whole-genome sequence of an ancient Egyptian (from 2855–2570BCE). Exciting work from @pontus-skoglund.bsky.social, @flinklinus.bsky.social, & co at @ljmuofficial.bsky.social, @crick.ac.uk.🧬🧪

MWPG2025 Join us for the 10th Midwest Population Genetics conference, held at the University of Minnesota Twin Cities from August 21 - August 22, 2025.

Please register if you haven't already done so.
MidWest PopGen is happening in August at the University of Minnesota (Twin Cities)—abstract deadline for talk: July 11th, and poster: August 1st.

sites.google.com/umn.edu/mwpg...

Thrilled to see the latest work from the lab (@genscapelab.bsky.social) out in Current Biology! Congratulations @jaurban2204.bsky.social ! 🎉

Grateful to have had the chance to contribute to this effort.

Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes Sri Lanka is home to diverse ethnic groups with different genetic histories. Urban Aragon et al. find that despite close genetic affinities, Indigenous Adivasi have more hunter-gatherer ancestry and l...

Delighted to share that one of my major PhD projects has been published today in Current Biology.

In this paper, we look into the genetic population structure and demographic histories of two populations in Sri Lanka: the Sinhalese and Adivasi [1/n]. www.cell.com/current-biol...

Very special thanks to the Adivasi and Sinhalese individuals involved in this study!!! They are a pivotal part of this study, and we'll engage with them again in outreach activities soon! [6/n]
Special note: Some of the supplementary links are still being fixed by the journal!

This was a true-collaborative effort involving teams from Sri Lanka, India, and the United States. Many thanks to my PI Maanasa Raghavan, co-authors @eshabandyopadhyay.bsky.social , PhD, Anjana Welikala and other co-authors!! [5/n]

6 years, 1 dissertation, 1 amazing supervisor, endless caffeine, many smiles, a few tears — and one unforgettable hooding ceremony. #PhDone👩‍🎓📜 @UniversityofChicago @genscapelab.bsky.social

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

“Genes and geography: understanding human genetic variation” by @jnovembre.bsky.social, second talk in this cycle of talks on Human genomics and Paleogenomics for a general audience.
Tuesday 29th November 12pm Mexico City time/1pm central time/2pm est.

colnal.mx/agenda/genes...

Posting on behalf of Shamil Sunyaev: Eimear(Vice Chair) and I (Chair) are organizing the 2025 Gordon Research Conference (GRC) on Human Genetics and Genomics, which will be held on July 6-11, 2025 in beautiful University of Southern Maine, Portland, Maine.

AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles Motivation DNA damage patterns, such as increased frequencies of C>T and G>A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In ...

aDNA/aeDNA folks: tired of eyeballing hundreds of damage plots? I am excited to introduce AdDeam—a tool to rapidly generate damage profiles, cluster them, and spot outliers. Great for large sample sets or flagging modern contigs in ancient metagenomics assemblies. www.biorxiv.org/content/10.1...

UCL – University College London UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).

Interested in a starting PI position at University College London to work on Genetics, Evolution or the Environment? My department has opened the call for expressions of interest for sponsorship of independent fellowship applications.

www.ucl.ac.uk/work-at-ucl/...