Sign in

Linh N Tran

@lntran.bsky.social
96 followers 313 following 0 posts

Clinical informatics @bcgsc.ca🍁 Postdoc @uwgenome 🐶 PhD Genetics @uarizona 🐱 BA Chemistry @brynmawrcollege 🦉 Population Genomics, Machine Learning, Cancer Evolution 🧬💻 📍Seattle, WA & Vancouver, BC www.linkedin.com/in/linhnhtran

PostsRepliesMedia
Reposted by Linh N Tran
Molecular Biology and Evolution @molbioevol.bsky.social · 24/10/2025
@lntran.bsky.social @castellanoed.bsky.social @ryangutenkunst.bsky.social introduce a systematic permutation approach for interpreting haplotype matrix-based methods in population genomics. 🔗 doi.org/10.1093/molbev/msaf250 #evobio #molbio
doi.org
Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations
Abstract. Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful
075
Reposted by Linh N Tran
David Castellano @castellanoed.bsky.social · 07/10/2025
🧵1/ Excited to share our new paper in Molecular Biology & Evolution! 👉 [doi.org/10.1093/molbev/msaf250] It started as a lab-meeting sanity check for another project — and ended up turning into a new way to interpret machine-learning models in population genomics.
286
Reposted by Linh N Tran
Ryan Gutenkunst @ryangutenkunst.bsky.social · 21/08/2025
Me promoting the Genomic History Inference Strategies Tournament at #eseb2025! ghi.st Population geneticists: join, compete, earn cash, become an author, learn, help the community! ghi.st
0227
Reposted by Linh N Tran
Alison Feder @alisonfeder.bsky.social · 20/05/2025
Really excited about this new work from Sam Hart (and joint with @kelleyharris.bsky.social) trying to disentangle mutational differences between groups of cancers. Check out Kelley's thread with the major results!
0216
Reposted by Linh N Tran
Kelley Harris @kelleyharris.bsky.social · 21/05/2025
. @pnas.org just published the final version of our manuscript on how generation time and effective population size interact to shape vertebrate germline mutation rates, led by Luke Zhu and Annabel Beichman: www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
18132
Reposted by Linh N Tran
Kelley Harris @kelleyharris.bsky.social · 20/05/2025
If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
biorxiv.org
A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects
Mutational signatures contain valuable information about the mutational processes shaping cancer genomes. However, despite dozens of tools to identify signatures in cancer samples, there is not an est...
13311
Reposted by Linh N Tran
David Castellano @castellanoed.bsky.social · 27/03/2025
🚨 New preprint alert! 🚨 We introduce ConfuseNN, a method to interpret convolutional neural network (CNN) inferences in population genomics using data shuffling. Curious about how CNNs make decisions in genomic analyses? Check it out! 🧵👇https://www.biorxiv.org/content/10.1101/2025.03.24.644668v1
155
Reposted by Linh N Tran
Murillo R. @mufernando.bsky.social · 24/03/2025
We are excited to share our new preprint describing the inclusion of selection models to stdpopsim, our community-maintained library with an extensive catalog of population genetic models. 1/n www.biorxiv.org/content/10.1...
biorxiv.org
22220
Reposted by Linh N Tran
Ryan Gutenkunst @ryangutenkunst.bsky.social · 17/03/2025
Amid the chaos, it was great to share results from the first Genomic History Inference Strategies Tournament at ProbGen25. Watch the talk to learn about the future of GHIST and @andrewhvaughn.bsky.social's nefarious metagaming of demographic inference. 😀 www.youtube.com/watch?v=3_dv...
youtube.com
Talk describing the results of GHIST1 at ProbGen 25.
YouTube video by Ryan Gutenkunst
11912
Reposted by Linh N Tran
Ryan Gutenkunst @ryangutenkunst.bsky.social · 13/02/2025
I'm looking forward to Evolution this summer! I'll be leading a *free* workshop on the Genomic History Inference Strategies Tournament (ghi.st) during the Monday lunch break. Sign up during registration and join this fun community event. In an hour, you'll analyze data to make your first submission!
ghi.st
Genomic History Inference Strategies Tournament (GHIST)
033
Reposted by Linh N Tran
Ryan Gutenkunst @ryangutenkunst.bsky.social · 24/01/2025
Our paper on fitting population genetic models to low-pass sequencing data is now out in Molecular Biology and Evolution! doi.org/10.1093/molb...
Comparison of allele frequency spectra for 3x coverage, with and without our bias model.
13122