Please check out Albert’s new preprint on continuous optimization of DAG structure with both observational and interventional data! It’s a fun experience working with Sriram Sankararaman and Harold Pimentel. Details in Albert’s thread.

Excited that Harold Pimentel and I's new preprint on isoform-aware eQTL mapping is now available on bioRxiv! biorxiv.org/content/10.110… We show that taking into account isoform expression levels increases power to identify eGenes. But what is the best way to do so? A short 🧵...

Super excited this work is out! Congrats to Nathan LaPierre! A fun backstory: x.com/nlapier2/statu…

Hi #ESA2023 ! Come learn about the dynamics of colonization and community recovery in the human gut microbiome at my talk tomorrow, COS 87-2, at 10:15am in room E142. We see long lags in colonization even after major antibiotic perturbations. I'd love to discuss why!

Please check our newly accepted #naturecommunications paper: doi.org/10.1038/s41467… We developed FastKAST, a highly-scalable algorithm to identify non-linear genetic effects on complex traits in large datasets. Applying FastKAST on #UKBB, we discovered new epistatic evidence

Excited to share our preprint! 🎉 We find that the delta frequency is important in modulating the corticothalamic network, & that spatiotemporal dynamics vary based on seizure onset. This may eventually help with personalized neuromodulation for seizure detection & prevention

Excited that our new manuscript is out at Genome Research! We develop a family-based Mendelian Randomization (MR) test that is immune to confounding from population stratification, assortative mating, dynastic effects, & weak instrument bias! A short 🧵 dx.doi.org/10.1101/gr.277…

Recently, we presented FastKAST, which explores epistasis from a set-based perspective. But wait, there's more! In doi.org/10.1101/2023.0…, we tackle another fundamental question: identifying the epistatic effects at the genetic variants level on large-scale data.

Meet Rosace, a robust deep mutational scanning analysis tool that incorporates positional information and mean-variance shrinkage. Check it out if you are running DMS experiments or handling DMS data! (1/n) biorxiv.org/content/10.110…

a bit belated, but excited to see our paper out in Cell! cell.com/cell/fulltext/… (1/3)

RNA modifications play key roles in host immunity (some of which can be leveraged in cool ways for things like the design of cancer therapeutics) ... you can learn more about computational methods to study these events in my review paper, now out in Genome Research 🧬

sandy kim (she/her) and I will be at #cshldata24 ! Sandy’s giving a talk tomorrow on hierarchical modeling of CRISPR screens I’ll be presenting a poster on integrating polygenic risk to improve LDL-C measurement Come check us out :) Harold Pimentel CSHL Meetings

Thrilled to share that I'm starting my own lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! My lab will study how microbes interact and evolve in complex communities like the human gut microbiome. kxuelab.com 1/2

GASTON, our method to learn “topographic maps” of gene expression, is out now Nature Methods! IMO the coolest part is a new model of *spatial gradients in sparse data*. As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇

The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments biorxiv.org/content/10.110… #biorxiv_bioinfo

Does ambient RNA/DNA confound the genotype-based demultiplex of 10x Multi-ome data? Terence Li Terence Li, a bioinfo grad student in Noah Zaitlen lab and my lab investigated precisely this question and provided practical recommendations.

Want to write to your community about the importance of science funding? Join me on zoom this Friday at 12pm ET / 9am PT to learn to write an op-ed as part of the #McClintockLetters initiative! Sign up here: blogs.cornell.edu/asap/events-in…