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Colby T. Ford

@colby.tuple.xyz
61 followers 8 following 33 posts

Computational Biologist & Cloud AI Architect. 4x Microsoft MVP Awardee in AI and Azure. Currently at Tuple and UNC Charlotte's CIPHER center. 🧬 colbyford.com | tuple.xyz

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Colby T. Ford @colby.tuple.xyz · 21/09/2026
It seems everyone has found fun use cases for #Jev. Well, how about Jev for protein binder classification? ➡Give the blog a read: blog.colbyford.com/zero-shot-cl... #zeroshotclassification #proteinbinders #proteindesign #bindingassay @adaptyvbio @TwistBioscience
blog.colbyford.com
Zero-Shot Classification of Protein Binders with Jev
Jev, a zero-shot classification model by TypeSafe AI, popped up last week and it has taken over my LinkedIn feed. People have already been…
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Colby T. Ford @colby.tuple.xyz · 27/08/2026
Ever wonder if a BitNet-style 1.58-bit LLM would work for generating antibodies? New blog post: blog.colbyford.com/evaluating-a... #drugdesign #bioai #antibody #structuralbiology
blog.colbyford.com
Evaluating a Ternary Protein Language Model Architecture for Rapid Antibody Sequence Generation
A couple years ago, Microsoft Research released a novel approach for large language models that use a 1.58-bit architecture, resulting in a…
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Colby T. Ford @colby.tuple.xyz · 06/08/2026
New preprint! Our new project at Silico Biosciences, called #Hoike, provides a #JEPA and #diffusion framework for synthetic generation of gene expression data. www.biorxiv.org/content/10.6... #biomarkerdiscovery #geneexpression #transcriptomics #computationalbiology #bioinformatics #genomics
biorxiv.org
Hoike: A Joint-Embedding Predictive Architecture for Transcriptome Data Generation with Diffusion Models
In biomarker discovery, access to sufficient quantities of condition-specific transcriptomic data is often limited by cohort size, privacy concerns, and domain shift between normal and condition popul...
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Colby T. Ford @colby.tuple.xyz · 06/08/2026
I need this video as a remake of the 3D pipes screensaver from Windows 98.
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Colby T. Ford @colby.tuple.xyz · 04/08/2026
New preprint! Our latest project at Silico Biosciences, called #Kukulu, uses a novel Joint Embedding Predictive Architecture (JEPA) for diffusion-based reconstruction of antibody CDR loops. www.biorxiv.org/content/10.6... #AI #antibodydesign #drugdiscovery #jepa #diffusion
biorxiv.org
Kukulu: Diffusion-Based Reconstruction of Antibody CDR Loops using a Structure-Aware Joint Embedding Predictive Architecture
Antibody complementarity-determining regions (CDRs), especially CDR-H3, are a dominant source of binding specificity but remain difficult to design due to coupled sequence-structure constraints and lo...
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Colby T. Ford @colby.tuple.xyz · 04/08/2026
New research from the #UNCC #CIPHER Center: A map of the historical spread of #Cyclospora cayetanensis with a focus on the United States of America (USA) Preprint: www.medrxiv.org/content/10.6...
medrxiv.org
A map of the historical spread of Cyclospora cayetanensis with a focus on the United States of America (USA)
Cyclospora cayetanensis causes significant seasonal foodborne illness, characterized by recent large-scale nationwide outbreaks. We are currently experiencing the largest recorded outbreak in USA hist...
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Colby T. Ford @colby.tuple.xyz · 28/05/2026
New blog post! "Building Multi-agentic Bioworkflows with Microsoft Foundry and Nextflow" Give it a read: medium.com/p/building-m... #nextflow #cloud #azure #microsoftfoundry #agenticai #workflows
medium.com
Building Multi-agentic Bioworkflows with Microsoft Foundry and Nextflow
As bioinformatics workflows grow in scale and complexity, automating the data retrieval, analysis, and interpretation is imperative for…
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Colby T. Ford @colby.tuple.xyz · 21/05/2026
🦟📄 New preprint: "Stage-aware transcriptomics reveals selective haplotype persistence in short-term ex vivo cultured Plasmodium vivax" Read it here: www.biorxiv.org/content/10.6... #malaria #research #preprint #plasmodium #transcriptomics #RNAseq #haplotyping #tropicaldiseases
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Colby T. Ford @colby.tuple.xyz · 14/05/2026
Computational Structural Analysis Predicts Host-Range Promiscuity and Antiviral Resistance in North American H5N1 Lineages | Computational and Structural Biotechnology Journal spj.science.org/doi/10.34133...
spj.science.org
Computational Structural Analysis Predicts Host-Range Promiscuity and Antiviral Resistance in North American H5N1 Lineages | Computational and Structural Biotechnology Journal
Influenza A virus has been circulating in birds in Eurasia for more than 146 years, but human infection has been sporadic. H5N1 (clade 2.3.4.4b) has recently infected hundreds of species of wild and d...
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Colby T. Ford @colby.tuple.xyz · 14/05/2026
In case you missed my talk on "Building Multi-agentic Bioworkflows with Microsoft Foundry and Nextflow" a couple weeks ago at #NextflowSummit in Boston, you're in luck! You can now watch all of the sessions on YouTube. Watch here: youtu.be/oxhXGVFUZvQ?...
youtu.be
Colby Ford: Building Multi-agentic Bioworkflows with Microsoft Foundry and Nextflow
YouTube video by Nextflow
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Colby T. Ford @colby.tuple.xyz · 12/05/2026
"Building Agentic Solutions with Microsoft Foundry" is now available for pre-order on Amazon! Pre-order your copy here: a.co/d/0h4441jD #MicrosoftFoundry #agenticai #book #author #cloud #ai #azure #foundry #agents #generativeai
a.co
Building Agentic Solutions with Microsoft Foundry: Patterns, Workflows, and Best Practices for Intelligent Agents
Building Agentic Solutions with Microsoft Foundry: Patterns, Workflows, and Best Practices for Intelligent Agents [Ford, Colby T.] on Amazon.com. *FREE* shipping on qualifying offers. Building Agentic Solutions with Microsoft Foundry: Patterns, Workflows, and Best Practices for Intelligent Agents
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Colby T. Ford @colby.tuple.xyz · 19/04/2026
Join me at the Nextflow Summit in Boston on May 1st to learn about "Building Multi-agentic Bioworkflows with Microsoft Foundry and Nextflow". Link: summit.nextflow.io/2026/boston/... #bioinformatics #genomics #microsoftfoundry #ai #agents #nextflow
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Colby T. Ford @colby.tuple.xyz · 06/04/2026
🦞 New blog post ⤑ Connect #OpenClaw to #AI models deployed in your own private Microsoft Foundry project. Link: medium.com/@colbyford/c...
medium.com
Connecting OpenClaw to Models in Microsoft Foundry
OpenClaw has taken the AI world by storm as it enables users to build local, personal AI agents to perform various tasks. Some people are…
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Colby T. Ford @colby.tuple.xyz · 19/03/2026
New blog post! Structuring #Proteomics Data from Multiple Lab Vendors in #Cloud Data Warehouses medium.com/@colbyford/s...
medium.com
Structuring Proteomics Data from Multiple Lab Vendors in Cloud Data Warehouses
When dealing with genomics and transcriptomics data, the bioinformatics community has mostly settled on a few file formats (e.g., BAM, VCF…
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Colby T. Ford @colby.tuple.xyz · 03/03/2026
🐿 Feeling squirrely about #AI #agents? I have a new O'Reilly book coming out that might help! "Building Agentic Solutions with Microsoft Foundry" comes out in a few months, but you can read chapters 1-3 today! 🔗: www.oreilly.com/library/view... #microsoftfoundry #azure #finetuning #knowledgebases 🌰
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Colby T. Ford @colby.tuple.xyz · 26/01/2026
🧬 New Blog Post: Building Data-Heavy Bioinformatics APIs using Serverless Azure Functions and Cosmos DB medium.com/p/building-d...
medium.com
Building Data-Heavy Bioinformatics APIs using Serverless Azure Functions and Cosmos DB
I’ve been using Azure Functions and Cosmos DB for years across various clients and use cases. However, it was only recently that I…
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Colby T. Ford @colby.tuple.xyz · 15/12/2025
Today seemed like a good day to open-source some AI antibody design code! Using our 🦋 peleke-1 antibody languages models, we generated many antibody sequences that target Nipah virus with decent affinity. Repo: github.com/silicobio/Ni...
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Colby T. Ford @colby.tuple.xyz · 22/10/2025
#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
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Colby T. Ford @colby.tuple.xyz · 17/10/2025
New paper! peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation 🦋 Link: www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Reposted by Colby T. Ford
Boston Protein Design and Modeling Club @bpdmc.org · 09/09/2025
If you missed seeing @colby.tuple.xyz's excellent talk back in July, you can now check out the recording 👇 youtu.be/k63Xh-oJMs0
youtu.be
Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability
YouTube video by Boston Protein Design and Modeling Club
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Colby T. Ford @colby.tuple.xyz · 27/08/2025
5 Tips for Fine-Tuning Protein Language Models (PLMs) on Azure Machine Learning blog.colbyford.com/5-tips-for-f...
blog.colbyford.com
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…
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Colby T. Ford @colby.tuple.xyz · 25/07/2025
Our new research shows how bird flu is evolving: www.wbtv.com/video/2025/0...
wbtv.com
New research shows how bird flu is evolving
It is evolving and researchers at UNC Charlotte have discovered that could be a problem
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Reposted by Colby T. Ford
Boston Protein Design and Modeling Club @bpdmc.org · 09/07/2025
quick reminder to join us tonight at @harvardmed.bsky.social for a great talk by Colby Ford @colby.tuple.xyz
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Colby T. Ford @colby.tuple.xyz · 04/06/2025
H5N1 Adapts for a Human Host youtu.be/FNWdzaZCemk?... via @YouTube
youtu.be
H5N1 Adapts for a Human Host
YouTube video by UNC Charlotte
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Colby T. Ford @colby.tuple.xyz · 25/04/2025
New paper: #AI -Based #Antibody Design Targeting Recent #H5N1 Avian Influenza Strains www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Colby T. Ford @colby.tuple.xyz · 20/03/2025
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
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Colby T. Ford @colby.tuple.xyz · 02/02/2025
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...
sciencedirect.com
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…
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Colby T. Ford @colby.tuple.xyz · 13/12/2024
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
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Colby T. Ford @colby.tuple.xyz · 01/06/2024
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....
frontiersin.org
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...
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Colby T. Ford @colby.tuple.xyz · 25/02/2024
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
genomebiology.biomedcentral.com
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. ...
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Colby T. Ford @colby.tuple.xyz · 24/01/2024
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...)
biorxiv.org
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
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Colby T. Ford @colby.tuple.xyz · 04/12/2023
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...
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Colby T. Ford @colby.tuple.xyz · 15/10/2023
Hello!
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Colby T. Ford @colby.tuple.xyz · 15/10/2023
Protein Sequence Generation with EvoDiff: colbyford.medium.com/exploring-ai... #proteins #diffusion #ai #computationalbiology #bioinformatics #rfdiffusion #alphafold #colabfold
colbyford.medium.com
Exploring AI-Based Protein Sequence Generation with EvoDiff from Microsoft Research
EvoDiff is a new, state-of-the-art protein sequence generation system from Microsoft Research. How well does it work?
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Colby T. Ford @colby.tuple.xyz · 15/10/2023
Hello, BlueSky. ☁️
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Reposted by Colby T. Ford
bioRxiv Genetics @biorxiv-genetic.bsky.social · 16/09/2023
Behavioral and transcriptomic analyses of mecp2 function in zebrafish www.biorxiv.org/content/10.1101/202…
biorxiv.org
Behavioral and transcriptomic analyses of mecp2 function in zebrafish https://www.biorxiv.org/content/10.1101/2023.09.13.557635v1
Rett Syndrome (RTT), a human neurodevelopmental disorder characterized by severe cognitive and motor
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