lindsey guan
@lindseyguan.bsky.social
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she/her | PhD student in the Keating Lab @MIT | Bio & CS @UCBerkeley
now out in Protein Science!
onlinelibrary.wiley.com/doi/10.1002/...
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Training bias and sequence alignments shape proteināpeptide 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...
https://onlinelibrary.wiley.com/doi/10.1002/pro.70331
29 days ago
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lindsey guan
Nature
about 2 months ago
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
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What research might be lost after the NIHās 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.
https://go.nature.com/4pBArFH
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lindsey guan
Eli Lipsitz
3 months ago
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...
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Game Bub
An open-source FPGA retro-emulation handheld
https://www.crowdsupply.com/second-bedroom/game-bub
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lindsey guan
Yo Akiyama
3 months ago
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 modelingš§µ
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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 ...
https://biorxiv.org/content/10.1101/2025.08.02.668173v1
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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 doesnāt have a deep MSA / thereās no good paired MSA š§µĀ (1/5)
www.biorxiv.org/content/10.1...
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https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1
5 months ago
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lindsey guan
bioRxiv Bioinfo
5 months ago
How AlphaFold and related models predict protein-peptide complex structures
https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1
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lindsey guan
David Pfau
6 months ago
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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lindsey guan
Eli Lipsitz
6 months ago
Thereās been a lot of interest in Game Bub, so Iām 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!
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Game Bub
An open-source FPGA retro-emulation handheld
https://www.crowdsupply.com/second-bedroom/game-bub
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lindsey guan
@LaBonneLaB
8 months ago
Published in the Chicago Sun Times today
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lindsey guan
Eli Lipsitz
9 months ago
Iām 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...
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Game Bub: open-source FPGA retro emulation handheld
Iām excited to announce the project Iāve 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...
https://eli.lipsitz.net/posts/introducing-gamebub/
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lindsey guan
Carolyn Bertozzi
9 months ago
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/...
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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.
https://www.washingtonpost.com/health/2025/02/08/nih-cuts-billions-dollars-biomedical-funding-effective-immediately/
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Anne Carpenter
9 months ago
So one approach is to omit these words from your research. The other is for all of us to double down on including these words in EVERYTHING.
add a skeleton here at some point
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reposted by
lindsey guan
9 months ago
If you can, do something, speak up and act up.
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.adt7194
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lindsey guan
Simon Mathis
12 months ago
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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āØnew 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 š§¶
journals.aps.org/prxlife/abst...
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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.
https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.2.043013
12 months ago
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