Associate Professor, Dept. of Evolution, Ecology, & Behavior, University of Illinois at Urbana-Champaign. Computational biologist+population genomics practitioner.
I am pleased to release Stacks version 2.65: https://catchenlab.life.illinois.edu/stacks/
We have removed the need for specifying IDs in the component Stacks programs, improved the VCF filtering/export for variable/fixed sites, added HaeII restriction enzyme, and allowed for a second popmap so a user can have different sets of samples in the catalog compared to the whole pipeline run.
We will demonstrate the basics of UNIX, and how the main Stacks algorithms work with a focus on PCR duplicates. We'll then work through several common analysis paths: population structure, genome scans using Fst, and private allele analysis.
If you are planning or working with RAD data, please join us! The course will take place in the Chicago time zone, but also recorded. No prior computational experience required.
I am teaching an online course through PRStatistics:
The Practice of RADseq: Population Genomics Analysis with Stacks, October 2-6, 2023
The course will focus on de novo, (with parameter optimization), reference, and integrated analyses of RAD data.
What is the key element in a successful #RADseq experiment and analysis? How can you avoid the dreaded "missing data"?
tldr; it's the quality of input DNA, and controlling the resulting levels of PCR duplicates that matters.
Our latest work, led by Nicolas Rochette and Angel Rivera-Colón, (and in collaboration with Shane Campbell-Staton and Floragenex) shows this in great detail via modeling and experimental analysis. Now published in Molecular Ecology Resources:
A cold-specialized icefish species underwent major genetic changes as it migrated to temperate waters https://phys.org/news/2023-04-cold-specialized-icefish-species-underwent-major.html #xp #fish #biology #science
Our most recent work has just been published early access in MBE.
Very excited to see this in print -- it represents more than five years of work from my lab and includes all of my students!
In, "Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish" we describe a new chromosome-level genome assembly for Champsocephalus esox, the *only* #icefish outside Antarctic waters.
The study was led by my student (and now postdoc) Angel Rivera-Colón.
Nicely places the technology behind ChatGPT into a broader context of the research and pre-existing systems it is built on.
https://www.zdnet.com/article/chatgpt-is-not-particularly-innovative-and-nothing-revolutionary-says-metas-chief-ai-scientist/
When you use an unsigned integer to store the value of the outside temperature (currently -8F) in your thermostat app... 😆
