PhD Student at UCR 🐻 Genetics, Genomics, & Bioinformatic Wessler/Stajich Lab TEs and SVs 💚 🧬
Joined February 2022
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Nathan Mathieu retweeted
In retrospect, I think Astra may have been the most disappointing release of the year
Having a great first experience at #PEQG26 ! So many cool projects and friendly people. Come visit me at my poster tomorrow to talk about TEs and SVs!
Nathan Mathieu retweeted
Happy to share that our collaboration with Ben Blencowe's lab on studying Alu repeats and exon skipping in primates is now out in Genome Biology. Congrats to the team!
link.springer.com/article/10…
Nathan Mathieu retweeted
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs.
New preprint on longcallD: a unified framework for joint calling and phasing of small, structural and mosaic variants from long reads. Improved SV calling and competitive small variant calling. Supervised by @lh3lh3 , co-work with @QianAlvinQin1, @wwliao88 and @irahall9.
Nathan Mathieu retweeted
PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences academic.oup.com/bioinformat… 🧬🖥️🧪
Nathan Mathieu retweeted
Here's the short story of how I got into flower bioengineering! 🌹🧬✨
This was my application for the @osvllc fellowship (they're taking applications now!)
Nathan Mathieu retweeted
Now published in gigascience: academic.oup.com/gigascience…. Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/on-…. Work with @QianAlvinQin1
Nathan Mathieu retweeted
Another great collaboration with @sedlazeck lab published at last. We amplify and long read sequence human brain single cell genomes, and provide insights into transposon-related structural changes. Caveats of course apply including small sample size. nature.com/articles/s42003-0…
Nathan Mathieu retweeted
Interested in how we can leverage all this fancy new omics data to improve plants for productivity under climate change? @jnbserres and I share our ideas in this new review: nature.com/articles/s41588-0…
Nathan Mathieu retweeted
This week in Nature: One year. Ten stories - 10 people who helped shape science in 2023
Browse the full issue: nature.com/nature/volumes/62…
Nathan Mathieu retweeted
Local registration for the 2024 round of my Statistical Rethinking course has begun. I'll open up registration on Sunday 3 December. Registration link will appear on the course github page: github.com/rmcelreath/stat_r…
Nathan Mathieu retweeted
How Git works under the HOOD?
We've made a video about this topic (Find link at the end).
To begin with, it's essential to identify where our code is stored. The common assumption is that there are only two locations - one on a remote server like Github and the other on our local machine. However, this isn't entirely accurate. Git maintains three local storages on our machine, which means that our code can be found in four places:
- Working directory: where we edit files
- Staging area: a temporary location where files are kept for the next commit
- Local repository: contains the code that has been committed
- Remote repository: the remote server that stores the code
Most Git commands primarily move files between these four locations.
Over to you: Do you know which storage location the "git tag" command operates on? This command can add annotations to a commit.
Watch the video here: youtu.be/e9lnsKot_SQ
Nathan Mathieu retweeted
congrats to @abramocruz @JonsAguirre3 et al. !!!
news: news.uci.edu/2023/06/15/stud…
paper: nature.com/articles/s42003-0…
Nathan Mathieu retweeted
Happy Transposon Day 2023! Today is the 121st birthday of Barbara McClintock, founder of the #transposon field and Nobel laureate. Please celebrate with us by using the hashtag #TransposonDay2023. How has Barbara McClintock or her work influenced you? mobilednajournal.biomedcentr…
Nathan Mathieu retweeted
Corn plants producing betalain, the red pigment found in beets.
ALT Figure 1. Wang, D., Zhong, Y., Feng, B., Qi, X., Yan, T., Liu, J., ... & Chen, S. (2023). The RUBY reporter enables efficient haploid identification in maize and tomato. Plant Biotechnology Journal. doi: 10.1111/pbi.14071
Nathan Mathieu retweeted
UV reflectance in crop remote sensing: Assessing the current state of knowledge and extending research with strawberry cultivars. biorxiv.org/cgi/content/shor… #biorxiv_plants
Nathan Mathieu retweeted
African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the ... biorxiv.org/cgi/content/shor… #biorxiv_plants