Research Scientist @StanfordMed | Evolution, Population Genetics, Sex Chromosomes | views my own
Stanford, CA
Joined December 2013
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Danny Cotter retweeted
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 👇🏽
1/7 🧬 New Preprint Alert: Our study highlights the risks of using divergent reference genomes in population genomics. The choice of reference genome can skew key inferences about demography, diversity, and selection. Read on for insights! biorxiv.org/content/10.1101/…
Danny Cotter retweeted
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?
Danny Cotter retweeted
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.
Danny Cotter retweeted
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 [email protected], and please RT!
Danny Cotter retweeted
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
It was recently reported that Africans experienced a sharp, severe bottleneck around 900kya and that this signal is absent in non-Africans. Here, we present evidence to show why this is likely a statistical artifact:
@ras_nielsen @yun_s_song
biorxiv.org/content/10.1101/… 1/4
Danny Cotter retweeted
Step aside Monty Hall, Blackwell’s N=2 case for the secretary problem is way weirder.
Danny Cotter retweeted
Super excited this work with @_ellie_cat is finally out. Hopefully the first (publishing wise) of many collabs 😎
There are more captive tigers than wild tigers on Earth. A study of the genetic diversity of captive tigers finds that they are not more inbred than wild tigers but do not represent a reservoir of genetic diversity that has been lost in the wild. In PNAS: ow.ly/hFjM50TwgA3
ALT A captive tiger. Stock photo.
Danny Cotter retweeted
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.
Danny Cotter retweeted
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/10.1101/… (1/9)
Danny Cotter retweeted
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/fullt…
Danny Cotter retweeted
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-visua…
Danny Cotter retweeted
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%2Fsagmb-2023…
Danny Cotter retweeted
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
Danny Cotter retweeted
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.
Danny Cotter retweeted
I've written about race, genetic ancestry, analyses of large biobanks, and human history
gusevlab.org/projects/hsq/#h…
I'll summarize the key points here 🧵:
Danny Cotter retweeted
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
Danny Cotter retweeted
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
Danny Cotter retweeted
For those who want to know what the issues are, read these threads:
xitter.gq/graham_coop/status/162…
xitter.gq/jkpritch/status/175976…
This paper from @AllofUsResearch needs to be retracted by @nature immediately. Under pretext of inclusivity it features a scientifically invalid representation of genetic diversity and race that is going to feature in racist literature for decades. nature.com/articles/s41586-0…
Danny Cotter retweeted
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)
Danny Cotter retweeted
I'm delighted to release the first half of my new open-access online textbook in human population genetics:
web.stanford.edu/group/pritc…
