Kaiyu Qiu 邱锴宇

Graduate student at Max Planck Institute working on protein evolution

[Kaiyu Qiu 邱锴宇 @21qiu]

@lproc2006 @ChingteLai @DalaiLama 到你这没绷住

[James Horton @Jameshearsawho]

Our latest paper is now out in @MolBioEvol! In this work we show that T:A→G:C mutational hotspots in bacteria are created by short nucleotide sequences (≥8bp), which we call GnT motifs. [https://t.co/o2mrL9DodZ]. A short 🧵 below:

[Yo Akiyama @yoakiyama]

Excited to share work with @ZhidianZ, Milot Mirdita, Martin Steinegger, and @sokrypton
https://t.co/pkWeguhQ4l
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling
🧵

[Kaiyu Qiu 邱锴宇 @21qiu]

@Haoran_Cai @OfficialSMBE 北京见！

[Ralser Lab @RalserLab]

When #AlphaFold2 came out, we wondered: Could it help us understand how enzymes evolve? So we tried it—and it worked! https://t.co/rtGbSpeAvk

[Tokuriki lab @tokuriki_lab]

Our new perspective paper, led by Sevan Gholipour and Dongkyu Lee, is out @BiochemistryACS. We discussed molecular evolution and origins of antibiotic resistance genes" It is interesting to think how ARG evolved against natural vs synthetic antibiotics.

https://t.co/kdQZMBIAMp

[Harry Kane @HKane]

🏆

[Zaixiang Zheng @zaixiang_zheng]

Excited to be at #ICLR2025 in Singapore! Come check out the latest from ByteDance Research's Generative AI for Science team:

🧬CryoFM: A Flow-based Foundation Model for Cryo-EM Densities (Apr 24, 15:00-17:30, Poster #5) https://t.co/Vvv9Cv1G8z
🧬ProteinBench: A Holistic Evaluation of Protein Foundation Models (Apr 26, 10:00-12:30, Poster #556) https://t.co/uDIeefganw
🧬DPLM-2: A Multimodal Diffusion Protein Language Model (Apr 26, 10:00-12:30, Poster #4) https://t.co/Mcuo7WxPx5

Plus, I will be presenting a Lightning Talk at ByteDance Booth about our team's research roadmap and agenda on "Towards Large-scale Multimodal Generative Foundation Models for Protein Modeling and Design" (Apr 25, 15:00-15:30 at Booth L07).
Will also share some of our thoughts & recent advancements on multimodal PLMs, all-atom generative model for protein complex design and autoregressive modeling for conformation dynamics.

We'd love for you to stop by and exchange insights with our team members! @dugu9sword @eugenejyuan @YuningShen1 @FeiYE00844289 @QuanquanGu

[Patrick Bryant @Patrick18287926]

I am hiring a postdoc in AI-development for protein binder design for my lab at Stockholms universitet and SciLifeLab. The environment is fantastic with many opportunities for collaboration and development of independent research directions.

Apply here: https://t.co/nNaOmosoqV

[Colin Jackson @Jackson_Lab]

https://t.co/yhMtwUzNKX Here’s a paper that was many years in the making. The idea that the climate can affect the thermodynamic mechanism of binding due to the temperature dependence of the entropy term is interesting- we see gradual shift in binding mode along evo trajectory

[Adrian Bunzel 🇪🇺🇨🇭🇩🇪🏳️‍🌈 @AdrianBunzel]

🚨 Don’t miss your chance to apply for the 3 open PhD positions in our group!
🌞 Project I : #computationaldesign of #photoenzymes for solar-driven nitrogen reduction to ammonia.
🧪 Apply now! Screening starts April 1
🔗 https://t.co/3TWmECB3GX
@mpi_marburg @maxplanckpress

[Rui Zhang @RuiZhangWUSTL]

Another wonderful collaboration with
@alanbrownhms lab. The Zhang lab together with @PolinaLishko lab (co-first author
@QingweiN) contribute the doublet microtubule structure from Crithidia fasciculata, a model organism that infects mosquitoes.

https://t.co/eDieZsYzaz

[Richard Wheeler @Zephyris]

Exciting day for parasite flagellar biology! https://t.co/r9D1O4o7FP https://t.co/WjRfupdtpO

[Hekstra Lab @HekstraLab]

Crystal structures are *not* God-given truth. They approximate, w/ flaws & errors, X-ray diffraction data. AlphaFold etc. have been trained on structures, not data. SFCalculator now differentiably connects structures to diffraction data. What does this enable? 🧵 1/4

[Yoshi__ichikawa @Yoshi__Ichikawa]

We have posted our new #preprint regarding the track recognition mechanism of dynein-2 that works in #cilia on bioRxiv @biorxivpreprint !!
https://t.co/ZRhSTnVNAS
1/8 🧵

[elevyLab @ElevyLab]

I am thrilled to say that our work is now online @CellCellPress ! I've analysed protein structures for quite some time, but @Robb_Mallik, who co-led this work, took these analyses to yet another level - 🧵👇

https://t.co/BaNJYKow4I

[Nicholas Fabiano, MD @NTFabiano]

The irony

[Patrick Bryant @Patrick18287926]

I'm hiring a new postdoc in protein design (wet lab) at Stockholm University/SciLifeLab. The work will focus on expanding our work on binder design and using new AI models that we are developing. Apply here: https://t.co/Y52eedbB0i

[Rachel Kolodny @rachelkolodny]

Our paper https://t.co/cVEnHsKk5U just came out 🥳🥳🥳
We used a deep generative network to study codon usage in two eukaryotes: S. cerevisiae and S. pombe and two bacteria: E. coli and B. subtilis. This is what we did: 🧵
@TomerSidi197763

[Tokuriki lab @tokuriki_lab]

I am very excited to share that our paper led by @erdogananisan, @PouriaDasmeh, @AdrianSerohijos is out @natcomms. It touches key dynamics to understand protein evolution"Neutral Drift" and "Phenotypic Variation" during enzyme/protein evolution.

https://t.co/EOJTGv8MNc