Gillian

Computer Science x Biology. I like to think about algorithms, graphs and statistical models. Free time spent running, volunteering, and learning about security.

[Gokul Swamy @g_k_swamy]

This story makes me smile every time I get to tell it. Back when I was an undergrad, a bunch of my friends who were much smarter than me were getting into this thing called "research." So, I also cold-emailed a few professors and one got back to me, asking me to read some paper:

[Gillian @gillianychu]

The culmination of several PhD years — today LAML is published! LAML infers max likelihood time-resolved cell lineage trees from dynamic lineage tracing data accurately and efficiently. Thanks to @benjraphael for his guidance! https://t.co/Juk74XuXcd

[Gillian @gillianychu]

Congratulations Ashwinee!!

[Ashwinee Panda @ICML2026 @PandaAshwinee]

thrilled to receive the outstanding paper award for our work on shallow alignment!
i’ll be giving the talk at 10:42am tomorrow (Thursday) in oral session 1D. the poster will be Friday 3PM.

[Jelani Nelson @minilek]

Sad news all … Satish Rao has informed me he discovered a bug in the O~(m sqrt(n)) preprint he had for negative weight SSSP and that he withdraws the claim. 😞

[CSHL Meetings @cshlmeetings]

#cshldata24

[Gillian @gillianychu]

@jim_elevator @RECOMBconf congrats Jim!!

[Gillian @gillianychu]

chatgpt hallucinates so many functions that should exist. i wonder if they’re giving that data to the open source package maintainers… @ThePSF

[Uthsav Chitra @uthsavc]

What I’ve been working on for the past year! A new mathematical framework + deep learning algorithm, GASTON, for modeling spatial gradients in ‘omics data

(I’m also open to input for the next climbing-themed algorithm name 🧗 😀)

[Gillian @gillianychu]

@minilek Congratulations!!

[Gillian @gillianychu]

New paper on phylogenetic placement pipelines to place into yet larger trees. Surprisingly, we find it’s important to use FastTree for numeric parameter estimation over RAxML https://t.co/wCvazGFxYv

[Jia-Bin Huang @jbhuang0604]

Graduate school application

[Jesse Zhang @thejessezhang]

Had a ton of fun this weekend building a demo project: PapersGPT. It enables you to feed any scientific papers into GPT to give it deep customized knowledge. Moreover, it’s a proof-of-concept UX of the end goal of connecting arbitrary data. Demo: https://t.co/aMm7Tn5oCo [1/4]

[Google DeepMind @GoogleDeepMind]

Today in @NatureComms, we explore how AI agents can better communicate and cooperate in Diplomacy - a 7-player board game of coordination and alliance formation. 🤝

Find out more: https://t.co/OOUlxZU1zK

[PLOS Genetics @PLOSGenetics]

Tournebize et al present ASCEND:
a method to infer timing & strength of founder events
▪️ suitable for sparse datasets
▪️ reliable across a wide range of demographic scenarios

@ArcimBoldique @gillianychu @moorjani_priya @berkeleyMCB @CCBBerkeley

🔎: https://t.co/gge4lsACUf

[Claire McWhite @clairemcwhite]

New preprint with @ProfMonaSingh. We present vcMSA, a totally new algorithm for multiple sequence alignment that's based on clustering protein language representations of amino acids. No gaps penalties, substitution matrices, or guide trees required. https://t.co/TR1Tz3zPCj

[Simone Zaccaria @ZaccaSimo]

@gillianychu has prepared a comprehensive collection of screencasts and video demos to guide you in every step at: https://t.co/NzELKkEk34

For example, please check out this great CNAViz video demo from @gillianychu :
https://t.co/jH0jUzCPXj

[Simone Zaccaria @ZaccaSimo]

@melkebir and I are glad to present CNAViz by Zubair @gillianychu et al., an easy-to-use webtool for aiding in copy-number analysis and manually correcting copy-number segmentations. Try now one-click demos directly in your browser at:

👉 https://t.co/wFY3XvkWPw

👇GIF examples

[PLOS Comp Biol @PLOSCompBiol]

Want to improve segmentation & copy-number calling given a tumor's DNA sequencing data? Check out CNAViz, an intuitive, interactive web-based visual analytics tool.
@melkebir @zaccasimo @gillianychu
https://t.co/ZgprhNqY93

[Gillian @gillianychu]

Some famous voices on the keys to success as a computational biologist! @melkebir https://t.co/56nhueLrYE

[Gillian @gillianychu]

#PLOSCompBio: CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data https://t.co/RAONtoDRLC