John Novembre @jnovembre
Developing computational tools to understand genetic diversity. Professor @UChicago. Art: Eduardo Korba “Ellis Island” mural. jnpopgen.org Chicago, IL Joined July 2012-
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Two new chapters from my open-access textbook in human population genetics are now online: - Population structure: I. Ancestry estimation - Population structure: II. More about admixture web.stanford.edu/group/pritchar…
Two new chapters from my open-access textbook in human population genetics are now online: - Population structure: I. Ancestry estimation - Population structure: II. More about admixture web.stanford.edu/group/pritchar…
Looking forward to our symposium this Friday! An amazing lineup of speakers who are all alumni of our GGSB graduate program, plus a career-focused panel discussion, and a reception Friday, 9:30am, KCBD auditorium, UChicago All are welcome! Please RT & share!
New work from the lab! We present a novel method for inferring the geographic locations of shared genetic ancestors and use it to infer the geographic history of human genetic ancestry biorxiv.org/content/10.110…
Surfing trees!!! 🏄♀️🌊🌳 I really enjoyed writing this perspective with @dortega_delv @CharlestonCWKC @christiandhuber. We talk about the promises of using the ARG for evolutionary inferences. Abstract in Portuguese, Spanish and Chinese in the supplement doi.org/10.1093/gbe/ev…
The use of the phrase “ancestry-specific variant” is increasing, particularly to describe rare Single-nucleotide variants (SNVs). But these alleles are not ancestry-specific. They have not yet been found elsewhere, but they will be. 1/n
I've written about race, genetic ancestry, analyses of large biobanks, and human history gusevlab.org/projects/hsq/#… I'll summarize the key points here 🧵:
Reposting this criticism of All of Us and their use of ancestry labels x.com/graham_coop/st…
Reposting this criticism of All of Us and their use of ancestry labels x.com/graham_coop/st…
Beyond the UMAP issues, this paper also conflates ancestry, race, and ethnicity to do nonsensical analyses that can easily be misused for race science. You would hope AllofUs would have minimally read the National Academies population descriptors paper (nap.nationalacademies.org/read/26902/cha…)
Beyond the UMAP issues, this paper also conflates ancestry, race, and ethnicity to do nonsensical analyses that can easily be misused for race science. You would hope AllofUs would have minimally read the National Academies population descriptors paper (nap.nationalacademies.org/read/26902/cha…)
It's a pity that All of Us used UMAP to visualize ancestry variation in their new marker paper, out today in Nature. The UMAP algorithm, by design, exaggerates the distinctiveness of the most frequent ancestries, a message that can be misinterpreted by the public.
UMAP pulls unusual genotypes towards the majority clusters; in particular it fails to represent admixture in a sensible way (admixture is fundamentally additive, while UMAP is not). In this setting the messiness of Admixture or PCA plots yield a better reflection of the data
Glad to see our paper, with @xinhe2 @mstephens999 @wescrouse Sheng and Kevin, is out today at @NatureGenet! nature.com/articles/s4158…. We developed a new statistical method, causal-TWAS or cTWAS, to reliably identify causal genes in genome-wide association studies (GWAS). 1/n
I’m looking for a postdoc to work in theoretical population genetics. Come join our awesome community in lovely Chicago. More info here: voices.uchicago.edu/steinrueckenla…
Excited for the NHGRI workshop on Advances in Genetic Architecture of Complex Traits @NeuroMinded genome.gov/event-calendar… Bonus: you may see some of @SashaGusevPosts tweets in my slides x.com/sashagusevpost…
Excited for the NHGRI workshop on Advances in Genetic Architecture of Complex Traits @NeuroMinded genome.gov/event-calendar… Bonus: you may see some of @SashaGusevPosts tweets in my slides x.com/sashagusevpost…
Thrilled to contribute to this workshop on the population history of Central Anatolia organized by @UChicago! 🌎Our collaboration with @GenSCAPE_Lab is taking new heights. Here's a snapshot from the vibrant gathering in Chicago, with part of our Ankara team joining virtually.📷💗
❤️
Helpful description of the choices of population designators in gnomad: gnomad.broadinstitute.org/news/2023-11-g…
A few excellent recent papers on important and often misunderstood population parameters in genetics. A short 🧵:
Posting on twitter right now feels a little like putting up an informational flyer on the deck of the Titanic, but I'm recruiting PhD students to work on spatial population genetics in my lab at @UMichEEB!
Heritability within groups is uninformative about differences among groups: cases from behavioral, evolutionary, and statistical genetics biorxiv.org/cgi/content/sh… #biorxiv_genetic
Another way we looked at genetic patterns across the landscape was with an Estimated Effective Migration Surface (EEMS) in which we see that especially reduced gene flow (darkest brick-red tone) traces the path of the Amazon and Ucayali rivers for over 3000 km!
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ICCB @ICCB2025
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Molecular Biology and.. @MolBioEvol
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Jan Pieter Waagmeest @Jietermanis
134 Followers 350 Following Sailing, woodworking, maps, software development, work @zosteraTwo new chapters from my open-access textbook in human population genetics are now online: - Population structure: I. Ancestry estimation - Population structure: II. More about admixture web.stanford.edu/group/pritchar…
I'm delighted to release the first half of my new open-access online textbook in human population genetics: web.stanford.edu/group/pritchar…
ancIBD update available! ⬇️ @YileiHuang317 implemented two new modes: 1) Calling IBD on the X 2) Calling double IBD (e.g. in full siblings) We hope that helps to resolves some aDNA pedigree riddles 🦴🧬🕵♀️
Time for an update for our IBD caller for ancient DNA! Today we released ancIBD v0.6 ancibd.readthedocs.io/en/latest/inde… We added two new functions: 1) IBD2 calling and 2) IBD calling on X chromosomes
Looking forward to our symposium this Friday! An amazing lineup of speakers who are all alumni of our GGSB graduate program, plus a career-focused panel discussion, and a reception Friday, 9:30am, KCBD auditorium, UChicago All are welcome! Please RT & share!
Time for an update for our IBD caller for ancient DNA! Today we released ancIBD v0.6 ancibd.readthedocs.io/en/latest/inde… We added two new functions: 1) IBD2 calling and 2) IBD calling on X chromosomes
.@carl_veller & @Graham_Coop present a theoretical analysis of the influence of #confounders in population- & family-based #GWAS, showing that family-based studies, though more rigorous, still carry subtle issues that arise from confounding. #PLOSBiology plos.io/3Qmu2hF
It's been great to see the positive response of @satijalab & @fabian_theis to our preprint biorxiv.org/content/10.110… on Seurat & Scanpy, and their commitment to work to improve transparency of their tools. One immediate benefit will be better practice of PCA in genomics. 1/🧵
Congratulations to @carl_veller on the publication of his article on confounding in population and family GWAS @PLOSBiology journals.plos.org/plosbiology/ar…
Wow! Full room at 9am!! Welcome and thanks for coming to The Microbiome Center symposium 2024!
momi3 is here! This is an impressive extension that achieves a 1000x speedup over momi2. Very pleased to see my former PhD student, Jonathan Terhorst, thriving in his career as a PI. doi.org/10.1101/2024.0…
We’re super excited to host @jnovembre in person at the @broadinstitute #MPG seminar tomorrow morning. Looking forward to hearing his #PopGen perspectives @CGM_MGH @ksamocha
New work from the lab! We present a novel method for inferring the geographic locations of shared genetic ancestors and use it to infer the geographic history of human genetic ancestry biorxiv.org/content/10.110…
In a previous thread I mentioned a neat result from Biddanda et al. [elifesciences.org/articles/60107] showing a pair of Yoruba individuals with more genetic differences than a Yoruba/French pair, consistent with a nested subsets model of human dispersion. Dr. (?) Khan raises a caveat:
africa is a big place. to a great extent non-africans can be nested within africans who themselves have deep structure. a succinct and still accurate way to say this is it's khoisan vs. non-khoisan
At last, my work with @pastramimachine on a quantitative genetics model of background selection in humans is live at PLoS Genetics! journals.plos.org/plosgenetics/a…
Extremely thankful to #AABA2024 #AAAG for this wonderful award and recognition! 🙏🙏 This wouldn’t have been possible without the endless support from my PI @MaanasaRaghavan, our collaborators and everyone else who have given feedback at different stages of this project! 🙏😊
Happy international women’s day to all my fabulous female colleagues, students, mentors and mentees! 💕💅An honor and pleasure to work with each of you. Let’s continue to be the change we believe in 💪🏾💪🏾💪🏾 #8M
poster is up! if you’re at #TAGC24 come say hi on Saturday and hear about selective sweeps across space
Very excited to go to my first (?!) #TAGC2024/PEQG meeting and catching up with colleagues! I'll be presenting some recent results on LD with both spatial and time-stratified sampling :) Reach out if you're interested!
Several of my lab members are headed to #TAGC24 this week. I hope it's a great meeting. Please check out their posters! @tlrdln22 @aabiddanda @saracarioscia
Why are VCFs more commonly distributed than BCFs? And why isn’t more variant data compressed with PBWT?
Excited to share our review paper in Cell! With @SashaGusevPosts @s_ramach @yang_i_li we discuss the genetic and molecular architecture of human traits, future opportunities and challenges and ways forward. authors.elsevier.com/a/1igrbL7PXqPfU
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