Nathan Mathieu

PhD Student at UCR 🐻
Genetics, Genomics, & Bioinformatic
Wessler/Stajich Lab
TEs and SVs
💚 🧬

[Nathan Mathieu @N_F_Mathieu]

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!

[Yue Wan @ywan_wan]

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!
https://t.co/1NArrBYtZG

[Heng Li @lh3lh3]

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.

[Stephen Turner 🦋 @stephenturner.us @strnr]

PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences https://t.co/8W5LftlRRE 🧬🖥️🧪

[Nathan Mathieu @N_F_Mathieu]

@typecraft_dev @opencode Thought that was a Tecate in the back for a second 😂

[Nick Desnoyer @NickDesnoyer]

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!)

[Heng Li @lh3lh3]

Now published in gigascience: https://t.co/2ZB1eRNSfA. 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.

[Christos Proukakis @proukakis]

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. https://t.co/YIx50AfxVz

[Nathan Mathieu @N_F_Mathieu]

@sedlazeck @JHUCompSci @bcmhouston @traingene @RiceCompSci @BCMFromtheLabs @BCM_HGSC @bcmgenetics @TXMedCenter Will there be an online option or recording? 🙏🏻

[Alex Borowsky @atborowsky]

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: https://t.co/ezXV7TvHct

[nature @Nature]

This week in Nature: One year. Ten stories - 10 people who helped shape science in 2023

Browse the full issue: https://t.co/nW7V9kQNZV

[𝕐 @nomad421]

Text editor recommendation for beginners:
neovim + lunarvim

text editor recommendations for experts:
neovim + lunarvim

😁

[Richard McElreath 🐈‍⬛ @rlmcelreath]

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: https://t.co/w014wsghxd

[Alex Xu @alexxubyte]

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: https://t.co/VciGTUXPto

[Chris Fiscus @fiscuscj]

congrats to @abramocruz @JonsAguirre3 et al. !!!

news: https://t.co/0WwRu7AXlg

paper: https://t.co/jjUgVLyklk

[Nathan Mathieu @N_F_Mathieu]

@MobDNAjournal I'm just starting my PhD, but thanks to her I'm working with an awesome team to look at genomic evolution in rice!!

[Mobile DNA @MobDNAjournal]

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? https://t.co/rRm70T0MUf

[James Schnable @szintri]

Corn plants producing betalain, the red pigment found in beets.

[Nathan Mathieu @N_F_Mathieu]

@hyphaltip @GreatSmokyNPS Looks like fun! 🍄🧬

[bioRxiv Plant Bio @biorxiv_plants]

UV reflectance in crop remote sensing: Assessing the current state of knowledge and extending research with strawberry cultivars. https://t.co/qpFaHVmVoz #biorxiv_plants