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lindsey guan

@lindseyguan.bsky.social
704 followers 170 following 10 posts

she/her | PhD student in the Keating Lab @MIT | Bio & CS @UCBerkeley

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Reposted by lindsey guan
Jody Mou @moujo.bsky.social · 29/09/2026
Excited to share a preprint of my main PhD work in @nickpolizzi.bsky.social's lab - introducing LUCI-tag, a new orthogonal self-labeling protein tag based on K-Ras(G12C) and its covalent inhibitors! www.biorxiv.org/content/10.6... (1/16)
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Reposted by lindsey guan
Keating Lab @keatinglab.bsky.social · 18/01/2026
Here’s a preprint from the Keating Lab: www.biorxiv.org/content/10.6.... Foster Birnbaum and Amy E. Keating demonstrate that sequence design models, such as ProteinMPNN, are limited because they were trained only on native sequences.
biorxiv.org
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lindsey guan @lindseyguan.bsky.social · 14/10/2025
now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Training bias and sequence alignments shape protein–peptide docking by AlphaFold and related methods
Protein-peptide interactions mediate many biological processes. Accurate structural models of protein-peptide complexes, determined by experiment or computational prediction, are essential for unders...
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Reposted by lindsey guan
Nature @nature.com · 25/09/2025
We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US NIH grants to reveal the broad-reaching consequences go.nature.com/4pBArFH
go.nature.com
What research might be lost after the NIH’s cuts? Nature trained a bot to find out
We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US National Institutes of Health grants to reveal the broad-reaching consequences of such action.
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Reposted by lindsey guan
Eli Lipsitz @eli.lipsitz.net · 21/08/2025
The Game Bub Crowd Supply campaign is live! And it's been redesigned with a new horizontal design. You can now back the campaign to get your very own pre-assembled Game Bub! www.crowdsupply.com/second-bedro...
crowdsupply.com
Game Bub
An open-source FPGA retro-emulation handheld
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Reposted by lindsey guan
Yo Akiyama @yoakiyama.bsky.social · 05/08/2025
Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
biorxiv.org
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
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lindsey guan @lindseyguan.bsky.social · 24/06/2025
preprint is out for the first project of my phd! we investigated how structure prediction models work for protein-peptide complexes, where the peptide often doesn’t have a deep MSA / there’s no good paired MSA 🧵 (1/5) www.biorxiv.org/content/10.1...
biorxiv.org
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/06/2025
How AlphaFold and related models predict protein-peptide complex structures www.biorxiv.org/content/10.1101/202…
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Reposted by lindsey guan
David Pfau @davidpfau.com · 28/05/2025
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
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Eli Lipsitz @eli.lipsitz.net · 05/05/2025
There’s been a lot of interest in Game Bub, so I’m going to be launching a crowdfunding campaign through @crowdsupply.bsky.social! Sign up for updates and to hear when the campaign goes live: www.crowdsupply.com/second-bedro... This will be an assembled product, not just a kit!
crowdsupply.com
Game Bub
An open-source FPGA retro-emulation handheld
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Reposted by lindsey guan
@LaBonneLaB @labonnelab.bsky.social · 04/03/2025
Published in the Chicago Sun Times today
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Reposted by lindsey guan
Eli Lipsitz @eli.lipsitz.net · 12/02/2025
I’m excited to announce Game Bub, an open-source FPGA emulation handheld with support for Game Boy and Game Boy Advance cartridges: eli.lipsitz.net/posts/introd...
eli.lipsitz.net
Game Bub: open-source FPGA retro emulation handheld
I’m excited to announce the project I’ve been working on for the last year and a half: Game Bub, an open-source FPGA based retro emulation handheld, with support for Game Boy, Game Boy Color, and Game...
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Reposted by lindsey guan
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 08/02/2025
Another assault on US competitiveness at a time when biomedicine is roaring with innovation, an own-goal in a high-stakes international tournament. Of course the real losers are American people needing medicines and cures. www.washingtonpost.com/health/2025/...
washingtonpost.com
NIH cuts billions of dollars in biomedical funding, effective immediately
The move halts a large slice of money for most universities and research institutions virtually overnight, imperiling vital research in everything from cancer to heart disease.
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Reposted by lindsey guan
anthrofuentes.bsky.social @anthrofuentes.bsky.social · 02/02/2025
If you can, do something, speak up and act up. www.science.org/doi/10.1126/...
science.org
Scientists as political advocates
Science, both teaching and doing, is under attack. The recent US presidential election of a person and platform with anti-science bias exemplifies this. The study of climate processes and patterns and...
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Reposted by lindsey guan
Simon Mathis @simonmathis.bsky.social · 25/11/2024
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely. I use it a lot for my protein design workflows together with @biotite.bsky.social. Just `pip install pymol-remote`
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lindsey guan @lindseyguan.bsky.social · 27/11/2024
✨new work from our lab!✨ RLA is a contrastive-learning approach that assesses sequence-structure compatibility by aligning sequence and structure machine learning representations! RLA can successfully filter protein binder designs. 1/3 🧶 journals.aps.org/prxlife/abst...
journals.aps.org
Jointly Embedding Protein Structures and Sequences through Residue Level Alignment
Residue Level Alignment integrates protein sequence and structure information in a self-supervised model, improving speed and precision in predicting protein binding and structural stability.
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