Programmable Biology

Long-form references on biological foundation models, structure prediction, and sequence modeling.

Genomic Foundation Models

• Evo 2
  Long-context genomic foundation model for sequence modeling and design.

• HyenaDNA
  Long-context sequence models at nucleotide resolution.

Structure Prediction

• AlphaFold
  Foundational protein structure prediction paper.

• AlphaFold 3
  Extends structure prediction toward biomolecular complexes and interactions.

• OpenFold Open implementation and training stack for AlphaFold-style systems.

Bioinformatics Practice

• Rosalind Bioinformatics algorithms through concrete programming problems.