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Colby T. Ford

@colby.tuple.xyz

#MoML @ MIT just kicked off. It’s cool to see so many people excited about #ML and #molecularmodeling. Let’s see what un-“folds” next!

Our 🦋 #peleke-1 paper was accepted this year and the poster is in spot #13.

#molecules #ai #llm #plm #bioinformatics #computationalbiology #biochemistry

October 22, 2025 at 2:09 PM

Colby T. Ford

@colby.tuple.xyz

New paper! peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation 🦋

Link: www.biorxiv.org/content/10.1...

peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation

The discovery of therapeutic antibodies is a traditionally arduous process. Today, the lab-based process of antibody discovery consists of several time-consuming steps that involve live animal immuniz...

www.biorxiv.org

October 17, 2025 at 3:23 PM

Reposted by Colby T. Ford

Boston Protein Design and Modeling Club

@bpdmc.org

If you missed seeing @colby.tuple.xyz's excellent talk back in July, you can now check out the recording 👇 youtu.be/k63Xh-oJMs0

Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability

YouTube video by Boston Protein Design and Modeling Club

youtu.be

September 9, 2025 at 9:53 PM

Colby T. Ford

@colby.tuple.xyz

5 Tips for Fine-Tuning Protein Language Models (PLMs) on Azure Machine Learning

blog.colbyford.com/5-tips-for-f...

5 Tips for Fine-Tuning Protein Language Models (PLMs) on Azure Machine Learning

Protein Language Models (PLMs) are ramping up as the next frontier in AI-assisted drug design. We have seen the utility of models like…

blog.colbyford.com

August 27, 2025 at 2:10 PM

Colby T. Ford

@colby.tuple.xyz

Our new research shows how bird flu is evolving:
www.wbtv.com/video/2025/0...

New research shows how bird flu is evolving

It is evolving and researchers at UNC Charlotte have discovered that could be a problem

www.wbtv.com

July 25, 2025 at 1:35 PM

Reposted by Colby T. Ford

Boston Protein Design and Modeling Club

@bpdmc.org

quick reminder to join us tonight at @harvardmed.bsky.social for a great talk by Colby Ford @colby.tuple.xyz

Boston Protein Design and Modeling Club @bpdmc.org · Jul 2

Come learn about how to run the computational infrastructure that's powering the protein design revolution

July 9th 2025 at 7pm EDT in TMEC250 @harvardmed.bsky.social

"Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability"

Colby Ford @colby.tuple.xyz

bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

July 9, 2025 at 1:01 PM

Colby T. Ford

@colby.tuple.xyz

H5N1 Adapts for a Human Host youtu.be/FNWdzaZCemk?... via
@YouTube

H5N1 Adapts for a Human Host

YouTube video by UNC Charlotte

youtu.be

June 4, 2025 at 2:46 PM

Colby T. Ford

@colby.tuple.xyz

New paper: #AI -Based #Antibody Design Targeting Recent #H5N1 Avian Influenza Strains

www.biorxiv.org/content/10.1...

AI-Based Antibody Design Targeting Recent H5N1 Avian Influenza Strains

In 2025 alone, H5N1 avian influenza is responsible for thousands of infections across various animal species, including avian and mammalian livestock such as chickens and cows, and poses a threat to h...

www.biorxiv.org

April 25, 2025 at 11:18 AM

Colby T. Ford

@colby.tuple.xyz

New avian #influenza (H5N1) paper: Large-scale computational modelling of H5 influenza variants against HA1-neutralising antibodies!

We used #AI- and #physics-based modeling of over 18k H5N1 isolates.

Paper: lnkd.in/ekikJrE9
Code: lnkd.in/eY8Y4vmt

#bioinformatics #genomics #computationalbiology

March 20, 2025 at 7:27 AM

Colby T. Ford

@colby.tuple.xyz

New paper! Transcriptomic analyses in bioinformatics are only as good as the data we give them. In this article, we outline some best practices for QC in sequencing and bioinformatics in RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, and a ton more.

Read the article: www.sciencedirect.com/science/arti...

Comprehensive guide for epigenetics and transcriptomics data quality control

Host response to environmental exposures such as pathogens and chemicals can include modifications to the epigenome and transcriptome. Improved signat…

www.sciencedirect.com

February 2, 2025 at 6:29 PM

Colby T. Ford

@colby.tuple.xyz

I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...

#ai #proteinfolding #alphafold

December 13, 2024 at 1:46 PM

Colby T. Ford

@colby.tuple.xyz

New Paper Alert! We're very excited that our SARS-CoV-2 N <> cytokine modeling paper has been accepted in Frontiers in Bioinformatics. In this work, we showcase the use of high-performance computing for large-scale molecular modeling.

Give it a read: www.frontiersin.org/articles/10....

Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

Understanding the interactions between SARS-CoV-2 and the human immune system is paramount to the characterization of novel variants as the virus co-evolves with the human host. In this study, we empl...

www.frontiersin.org

June 1, 2024 at 3:13 PM

Colby T. Ford

@colby.tuple.xyz

Our consortium paper for CAGI: The Critical Assessment of Genome Interpretation was just released.

Read the paper in Genome Biology here: genomebiology.biomedcentral.com/articles/10....

#bioinformatics #genomics #genetics #computationalbiology #machinelearning #ai #datascience #rarediseases

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods - Genome Biology

Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. ...

genomebiology.biomedcentral.com

February 25, 2024 at 2:54 PM

Colby T. Ford

@colby.tuple.xyz

I'm very excited to present some exciting research that I've been working on. PD-1 is a very important target in cancer therapeutics, so using AI to speed up the drug discovery process is certainly of interest.

AI-designed anti-PD-1 antibodies - bioRvix preprint (www.biorxiv.org/content/10.1...)

PD-1 Targeted Antibody Discovery Using AI Protein Diffusion

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

January 24, 2024 at 7:37 PM

Colby T. Ford

@colby.tuple.xyz

I'm very excited to share this collaborative research project that included myself and researchers from MIT Lincoln Lab where we showcased the utility of high-performance computing to scale molecular modeling in SARS-CoV-2 research.

Read the preprint here: www.biorxiv.org/content/10.1...