Ellen Leffler

My department at University of Utah is recruiting new faculty, with "Human" and "Genetics" broadly defined. It is a fantastic place to start a lab, with collaboration, creativity and conviviality encouraged. Applications due Oct 16. Please share and apply! utah.peopleadmin.com/postings/208...

academic.oup.comEvolutionary Rate Covariation Across Malaria Parasite Species Enables Inference of Protein InteractionsAbstract. Despite publication of the Plasmodium falciparum reference genome over 20 years ago, one-third of its genes remain functionally unannotated, and

Led by @helenahopson.bsky.social, with ERC doyen @nclark.bsky.social and labwork in collab with @sigalalab.bsky.social, we are happy to release an Evolutionary Rate Covariation (ERC) resource for Plasmodium, published in @genomebiolevol.bsky.social. academic.oup.com/gbe/article/...

We uncover and functionally validate a new connection between a relatively uncharacterized protein (PF3D7_0811600, aka MAP1) and the RhopH complex. We hope others will look up their Plasmodium proteins of interest and it can help prioritize and discover new interactions!

You can download the dataset (datadryad.org/dataset/doi:...), search it on our Rshiny app (lefflerlab.chpc.utah.edu/erc_plasmodi...), and *hopefully soon* find it on plasmoDB. Please also feel free to reach out with any questions including on interpretation!

Functionally related proteins tend to show similar shifts in evolutionary constraint over a phylogeny, captured as a correlation in relative evolutionary rates. In Plasmodium, we calculated ERC between every pair of proteins and show that known pathways and complexes tend to have high ERC.

There are lots of Plasmodium genes with no annotation, no known function, and/or no close ortholog in other model species. Evolutionary rate covariation gives another clue to help infer functional connections between proteins and integrate with candidates from molecular screens.

10 July

Job opening: I'm looking for a lab tech primarily supporting ongoing projects and running computational analyses for the lab. Apply here and reach out with questions! utah.peopleadmin.com/postings/205...

@aaronquinlan.bsky.social

10 July

This would be a good fit for someone coming out of undergrad with a biology background and basic bioinformatics skills they want to build on by applying to some interesting host-parasite genomic/transcriptomic data.

Ellen Leffler reposted

Aaron Quinlan (he/him)

3 May

A deserved highlight from World Malaria Day on the fantastic host parasite conflict research from @ellenleffler.bsky.social's lab!

University of Utah Health Research@uuhsresearch.bsky.social

Malaria is a life-threatening disease that continues to impact millions worldwide. Researchers at @uofuhealth.bsky.social are working from multiple angles to better understand, prevent, and treat it. Learn more about their work. https://bit.ly/4txuBGE

Ellen Leffler reposted

James Gagnon

@james-gagnon.bsky.social

29 Apr

Applications due tomorrow!

Aaron Quinlan (he/him)@aaronquinlan.bsky.social

We are holding our annual Rising Stars in Genetics and Genomics Postdoc Symposium on September 24-25, 2026! Please nominate postdocs who are conducting cutting edge, creative work, and are likely to be a leader in their field. Please nominate by April 30, 2026: forms.gle/85NZaxFezUk8... (1/2)

forms.gleforms.gle

24 Apr

University of Utah Health Research@uuhsresearch.bsky.social

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

Nonetheless, it is protective against this infection and so could have contributed to a historically lower P. vivax prevalence in the southern Arabian peninsula than nearby countries with lower Duffy null allele frequency. 11/n

onlinelibrary.wiley.comCharacterization of blood group variants in an Omani population by comparison of whole genome sequencing and serologyBackground Although blood group variation was first described over a century ago, our understanding of the genetic variation affecting antigenic expression on the red blood cell surface in many popu...

Finally we also published a paper in Transfusion last year with more detailed comparison of whole genome sequencing and blood group serology for 24 antigens: onlinelibrary.wiley.com/doi/10.1111/... 12/12

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

Finally, we reflected on the multiple, consistent findings of strong selection for this allele in different African-admixed populations that others have reported (e.g., Cape Verde, Madagascar, Pakistan, Sudan). 9/n

Duffy negativity is associated with neutropenia and potentially other phenotypes and so we question whether P. vivax malaria is truly the driving selective pressure across such different environmental contexts... 10/n

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

Oman has a long history of interaction with East Africa, and we inferred a two-pulse model of admixture, 5 and 59 generations ago. The haplotypes surrounding the Duffy negative allele are short – much more consistent with an older introduction. 7/n

We think this makes sense – as soon as the Duffy negative allele was introduced, it appears to have spread. We did not see any signal of enrichment for African ancestry surrounding loci that have been associated with protection from P. falciparum malaria. 8/n

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

With funding from the Omani Research Council (and later NIH to my group), we performed paired blood group serology and whole genome sequencing. Indeed, we confirmed that absence of Duffy antigen was very common, with 87/100 lacking this important receptor for P. vivax on their RBCs. 5/n

Mostly this was due to the same RBC-specific enhancer mutation that is common across Africa, and the locus had a strong increase in local African ancestry to 78% (vs. 11% genome-wide). We also found a null frameshift allele that contributes to Duffy negativity specifically in the Middle East. 6/n

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

Arwa noted that in her studies of blood group antigens in Oman, some had more similar frequencies to African populations and some to European populations. 3/n

We wondered how admixture and selective pressure from malaria played a role. Some blood group alleles are associated with protection from P. vivax malaria, others with P. falciparum malaria, both of which have been present in Oman (though it is now malaria-free). 4/n

So pleased to share that our paper (led by Paige Haffener and in collaboration with @drriyamia.bsky.social) on genomic variation in Oman is now published in AJHG! www.cell.com/ajhg/fulltex... 1/n

We report analyses of whole genome sequence data from 100 Omani blood donors. This project stemmed from a conversation with Dr. Arwa Al-Riyami, a hematologist at Sultan Qaboos University in Muscat, at the International Society for Blood Transfusion meeting in Toronto in 2018. 2/n

employment.utah.eduJobs | University of UtahFounded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...

We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Every gift will be matched, up to $1,000, by Nels Elde. Click to see a message from Aaron Quinlan and to donate! www.givecampus.com/s/w46xg1

Ellen Leffler reposted

Mitchell R. Vollger

@mrvollger.bsky.social

12 Jan

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...

Ellen Leffler reposted

AmLarracuente

@amlarracuente.bsky.social

29 Oct 2025

Come be our colleague! The University of Rochester is hiring a TT Assistant Professor in evolutionary genetics and genomics: apply.interfolio.com/173431.

apply.interfolio.com Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

shorturl.atPhylogenetics and genomic variation of Hepatocystis isolated from shotgun sequencing of wild primate hostsAuthor summary Non-human primates are hosts to many species of Plasmodium, the parasites that cause malaria, and a closely related group of parasites called Hepatocystis. However, due to restrictions ...

Congrats to the lab! We were parasites of parasite data, and recovered DNA sequences from Hepatocystis (a close relative of human malaria parasites) from 37 wild non-human primates originally sequenced to look at the host genome, whose blood happened to be sampled while infected. shorturl.at/KluV8

We also identify genes with high SNP density, including genes in the Hep1 and Hep2 gene families, which are unique to Hepatocystis. This might suggest they are under selection for immune evasion, despite Hepatocystis lacking blood stage replication.

Thanks to a constructive peer review, the published paper in PLoS Pathogens is stronger than the preprint, so thanks to the editor and reviewers!

This gave us low-coverage whole-genome sequencing data for Hepatocystis from baboons and five species of Chlorocebus monkeys-- and so a first look at genetic variation and population structure genome-wide. There is support for substructure by host species, which was not as clear from mtDNA only.

grc.org2025 Quantitative Genetics and Genomics Conference GRCThe 2025 Gordon Research Conference on Quantitative Genetics and Genomics will be held in Lucca (Barga), Lucca Italy. Apply today to reserve your spot.

28 Apr 2025

Postdocs: Human Genetics at Utah will be hosting our annual Rising Stars in Genetics and Genomics Symposium in Sept. Apply here: shorturl.at/wBMg2 There will be sessions on developmental, evolutionary and disease genetics. A chance be invited to SLC to network here and with peers! Please share.

Ellen Leffler reposted

Na Cai

@caina89.bsky.social

5 Dec 2024

Quantgen GRC (16-21 Feb 2025) updates: we are now 75% subscribed! Deadline: 19 Jan 2025 BUT: We will pick talks from submitted abstracts 16 Dec and aim to send decisions before Xmas. So submit your abstracts now (even if not perfect - editable after submission)! www.grc.org/quantitative...