Coding Sequences as Executable Functions
A Type-Theoretic Framework for the Central Dogma
Formalizes the central dogma (DNA→mRNA→Protein) as a typed compilation pipeline. Codons as opcodes, alternative splicing as dependent types, mutations as type errors.
Regulatory Sequences as Control Flow
A Type-Theoretic Framework for Gene Expression
Promoters as function entry points, enhancers as environment variables, silencers as access control. Gene regulatory networks as typed dataflow graphs.
Non-Coding RNAs as Signals and Middleware
A Type-Theoretic Framework for Post-Transcriptional Control
miRNA as guard clauses, siRNA as exception handlers, lncRNA as middleware scaffolds, tRNA as natural transformations between codon and amino acid functors.
Structural DNA as Memory Architecture
A Type-Theoretic Framework for Genome Organization
Telomeres as linear resources, centromeres as synchronization primitives, TADs as memory segments, chromatin loops as pointers.
Repetitive Elements as Self-Modifying Code
A Type-Theoretic Framework for Genome Plasticity
Transposons as endofunctors on the genome category. Cut-and-paste as move semantics, copy-and-paste as template instantiation.
Epigenetic Marks as Runtime State
A Type-Theoretic Framework for Chromatin Accessibility
DNA methylation as monadic configuration, histone modifications as access permissions, chromatin remodeling as garbage collection.
Developmental Programs as Orchestration
A Type-Theoretic Framework for Morphogenesis
Hox genes as the main module, morphogen gradients as distributed config, cell fate as refinement type narrowing.
DNA-Lang: A Typed Orchestration Language
For Biological Programming
Synthesizes all 7 types into a unified language specification with parser, type checker, compiler (4 targets), and runtime.