https://sauravpanigrahi.com/tags/programmable-biology/Recent content in Programmable-Biology on Saurav PanigrahiHugoen-usFri, 01 May 2026 00:00:00 +0000https://sauravpanigrahi.com/reading/programmable-biology/Fri, 01 May 2026 00:00:00 +0000https://sauravpanigrahi.com/reading/programmable-biology/<p>Long-form references on biological foundation models, structure prediction, and sequence modeling.</p> <h2 id="genomic-foundation-models">Genomic Foundation Models</h2> <ul> <li> <p><a href="https://www.biorxiv.org/content/10.1101/2025.02.18.638918v1">Evo 2</a><br> Long-context genomic foundation model for sequence modeling and design.</p> </li> <li> <p><a href="https://arxiv.org/abs/2306.15794">HyenaDNA</a><br> Long-context sequence models at nucleotide resolution.</p> </li> </ul> <h2 id="structure-prediction">Structure Prediction</h2> <ul> <li> <p><a href="https://www.nature.com/articles/s41586-021-03819-2">AlphaFold</a><br> Foundational protein structure prediction paper.</p> </li> <li> <p><a href="https://www.nature.com/articles/s41586-024-07487-w">AlphaFold 3</a><br> Extends structure prediction toward biomolecular complexes and interactions.</p> </li> <li> <p><a href="https://openfold.readthedocs.io/en/latest/">OpenFold</a> Open implementation and training stack for AlphaFold-style systems.</p> </li> </ul> <h2 id="bioinformatics-practice">Bioinformatics Practice</h2> <ul> <li><a href="https://rosalind.info/problems/locations/">Rosalind</a> Bioinformatics algorithms through concrete programming problems.</li> </ul>