lindsey guan
@lindseyguan.bsky.social
she/her | PhD student in the Keating Lab @MIT | Bio & CS @UCBerkeley
now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...
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...
onlinelibrary.wiley.com
October 14, 2025 at 1:35 PM
now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...
Reposted by lindsey guan
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/4pBArFH
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.
go.nature.com
September 25, 2025 at 10:49 AM
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/4pBArFH
Reposted by lindsey guan
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...
You can now back the campaign to get your very own pre-assembled Game Bub!
www.crowdsupply.com/second-bedro...
Game Bub
An open-source FPGA retro-emulation handheld
www.crowdsupply.com
August 21, 2025 at 10:00 PM
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...
You can now back the campaign to get your very own pre-assembled Game Bub!
www.crowdsupply.com/second-bedro...
Reposted by lindsey guan
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🧵
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🧵
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 ...
biorxiv.org
August 5, 2025 at 6:31 AM
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🧵
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🧵
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 24, 2025 at 7:06 PM
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...
www.biorxiv.org/content/10.1...
Reposted by lindsey guan
How AlphaFold and related models predict protein-peptide complex structures https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1
June 24, 2025 at 4:46 PM
How AlphaFold and related models predict protein-peptide complex structures https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1
Reposted by lindsey guan
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.
May 28, 2025 at 10:18 AM
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.
Reposted by lindsey guan
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!
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!
Game Bub
An open-source FPGA retro-emulation handheld
www.crowdsupply.com
May 5, 2025 at 8:09 PM
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!
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!
Reposted by lindsey guan
Published in the Chicago Sun Times today
March 4, 2025 at 9:13 PM
Published in the Chicago Sun Times today
Reposted by lindsey guan
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...
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...
eli.lipsitz.net
February 12, 2025 at 5:19 PM
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...
Reposted by lindsey guan
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/...
www.washingtonpost.com/health/2025/...
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.
www.washingtonpost.com
February 8, 2025 at 5:12 PM
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/...
www.washingtonpost.com/health/2025/...
Reposted by lindsey guan
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.
This will be the biggest game of Taboo the U.S. has ever seen.
February 6, 2025 at 1:46 AM
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.
Reposted by lindsey guan
If you can, do something, speak up and act up. www.science.org/doi/10.1126/...
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...
www.science.org
February 2, 2025 at 12:56 PM
If you can, do something, speak up and act up. www.science.org/doi/10.1126/...
Reposted by lindsey guan
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`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
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`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
✨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...
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...
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.
journals.aps.org
November 27, 2024 at 9:32 PM
✨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...
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...