Danny Cotter

For folks still here, the first big project from my group is pre-printed. Super talented postdoc @mariaakop explored how reference bias can skew estimates of diversity, demography, divergence and recombination rate with help from @_ellie_cat and @GMenchev. Thread 👇🏽

For many traits there is a correlation between the number of duplications or loss-of-function (LoF) mutations someone carries, and their phenotype. Curiously, for most traits, these effects are aligned in the SAME direction. Why?

I want to try something new at #ASHG24 this year: I'm going to block some time on Friday afternoon to meet with any trainees who would be interested to chat on any topic.

Hi all, my lab at UC Riverside is recruiting PhD students for Fall 2025! These positions will be fully funded and include NIH-funded projects on recombination rate evolution and chromosomal inversions. Get in touch with me at ksamuk@ucr.edu, and please RT!

In this short article, we construct an explicit example to demonstrate that a recent claim about an extreme ancient bottleneck in the ancestry of African populations is likely a statistical artifact. Great work by our joint student @yun_deng

Step aside Monty Hall, Blackwell’s N=2 case for the secretary problem is way weirder.

Super excited this work with @_ellie_cat is finally out. Hopefully the first (publishing wise) of many collabs 😎

The Goldberg lab is moving to @UCLA Human Genetics summer 2025! Excited for new opportunities and collaborations. We will be recruiting at all levels to work on the evolutionary and population genetics of humans, our primate relatives, and the malaria parasites we share.

Excited to share the last paper from my PhD, advised by @spence_jeffrey_ and @jkpritch! We explore a new way to study selection on complex traits that circumvents some of the most troublesome limitations of GWAS biorxiv.org/content/10.110… (1/9)

thrilled to share @raungar's and my paper on our genetics + ethics course! still shocked, awed, and incredibly grateful that our little idea grew into a full-fledged course and accompanying paper cell.com/cell-genomics/…

Just finished teaching another semester of genomic #datavisualization 🥳 Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data Check out the course notes + #Rstats code to explore for yourself: jef.works/genomic-data-v…

Second time at #TAGC24/PEQG! Presenting a poster tonight (785T) on my PhD work with @NoahARosenberg on mathematical properties of allele-sharing dissimilarities (and how they explain phenomena observed in human population-genetic data)! Part 1 paper at doi.org/10.1515%2Fsagm…

the All of Us discourse has been making me think about this tweet and how it is so hard to nudge science in the right direction, but it is especially hard to do so with empathy

PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.

I've written about race, genetic ancestry, analyses of large biobanks, and human history #h.v8wagygagcry" target="_blank" rel="nofollow noopener">gusevlab.org/projects/hsq/#… I'll summarize the key points here 🧵:

we need to guarantee that anyone publishing on human genetics (especially if the work involves classifying individuals into populations of any sort) understands the history of the field, the risks and harms associated with classification, and the importance of getting it right

The All of Us paper is rightly being criticized for its UMAP figure, which suggests an overly discrete view of human variation—a problem that is compounded by colouring the plot with self-identified race and then omitting the “self-identified” from the title & legend. 1/n

For those who want to know what the issues are, read these threads: x.com/graham_coop/st… x.com/jkpritch/statu…

UMAP aside, I think there is tremendous ambiguity in the use and definition of race, ancestry, and ethnicity throughout the AllOfUs paper (not to mention conflation of genetic ancestry and genetic similarity)

I'm delighted to release the first half of my new open-access online textbook in human population genetics: web.stanford.edu/group/pritchar…