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HennLab for population genetics. Human origins, Africa, genomics, TB, bioinformatics. Brenna Henn & co #UCDavis #PopulationGenetics
Websitehttps://hennlab.ucdavis.edu/
Websitehttps://nctb.ucdavis.edu/

The UC Davis Center for Population Biology postdoctoral fellowship is now being advertised. This is a great opportunity to come join our wonderful community of Evolution & Ecology here at Davis. Please RT.

https://cpb.sf.ucdavis.edu/cpb-postdoc-fellowship

CPB Postdoctoral Fellowship

POSTDOCTORAL FELLOW IN POPULATION BIOLOGY EFFECTIVE:  September 27, 2024 DEADLINE:  November 1, 2024 

Center for Population Biology

University of California, Davis invites applications for a tenure-track Assistant Professor position focused on evolutionary approaches to understanding the origins of human morphological and/or physiological diversity, by studying changes in the biological characteristics of humans, our living and/or fossil relatives and the causes of these changes.

https://recruit.ucdavis.edu/JPF05997

Nov. 20 deadline

Assistant Professor in Biological Anthropology

University of California, Davis is hiring. Apply now!

Our latest on the dramatic impact of colonial admixture and slave trade in South Africa. We identify strong male founder effects and displacement of Khoe-San peoples. 🇿🇦

https://www.biorxiv.org/content/10.1101/2023.09.06.556626v1

Check out our new paper on long-read single-cell WGS! Here we show that SNVs, SVs and TRs can be analyzed in individual human T-cells and present results of de novo assembly https://www.nature.com/articles/s41467-023-40898-3
Long-read whole-genome analysis of human single cells - Nature Communications

Here the authors introduce a new method to study DNA in single cells by long-read sequencing. Their method gives a more complete view of the genomic structure of individual cells and allows to study genetic differences at the single-cell level.

Nature

About us:

We care about making accessible, reliable, and well-documented tools to lower barriers to everyone to doing good, reliable, and cutting-edge science. To do this we work to establish a supportive, open, and collaborative environment, by lowering barriers to entry, freely sharing access and resources, and prioritizing justice- and equity-focused contributions. See https://tskit.dev/community/ and https://kr-colab.github.io/expectations for more.

tskit-dev - Community

The tskit-dev community.

I'm looking for good resources to help new students organize comp bio projects. Best practices in data organization, reproducible code, documentation, collaboration. Any favourites?

I got a lot of mileage from Noble 2009 for data organization. (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424), but looking for more recent alternatives (incl. version control).

A Quick Guide to Organizing Computational Biology Projects

I finally took a stab at creating an ancestral recombination graph visualizer in D3.js. It takes in a tskit tree sequence from Python and uses a force simulation to calculate the positions of the nodes. Nodes have a fixed position on the y-axis, as this correspond with time, and can be slid along the x-axis to reduce line crosses. I'm partial to the orthogonal branching visualization, but the current pathing method doesn't yet handle recombination events. A fun excuse to learn some D3.js.

Today's #CornFax will also be it's own 🧵on a new preprint from yours truly and colleagues!

🌽 Where does maize come from? 🌽

(if threads ain't your thing, the preprint is https://www.biorxiv.org/content/10.1101/2023.01.31.526540v1)

Maize doesn't look like other grasses, and this led to more than 100 years of confusion about its origins. Even accomplished 20th century botanists like Edgar Anderson were still unsure of what continent maize came from!

1/8

A recent preprint "Impact of cross-ancestry genetic architecture on GWAS in admixed populations"
https://www.biorxiv.org/content/10.1101/2023.01.20.524946v1.abstract
which considers what is the most appropriate model for GWAS in admixed populations? Effect size heterogeneity, MAF differences, local ancestry explored. Take a peek!

RT @[email protected]

Lots to see on polar-orbiting satellite🛰️ today.

Let's go on a tour.

First: Zoomed out to all of California. Mostly clear skies over the Golden State today reveals the Sierra snowpack, green valley/hills, and water.

Let's zoom-in... #CAwx

(1 of 3)

🐦🔗: https://twitter.com/NWSSacramento/status/1616980999434547202

NWS Sacramento on Twitter

“Lots to see on polar-orbiting satellite🛰️ today. Let's go on a tour. First: Zoomed out to all of California. Mostly clear skies over the Golden State today reveals the Sierra snowpack, green valley/hills, and water. Let's zoom-in... #CAwx (1 of 3)”

Twitter