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chemoautotroph/README.md

Kaiyu Nie

Computational Biology & ML Researcher | RNA/DNA Design 路 Evolutionary Optimization 路 AI for Science

I build computational systems for biomolecular sequence design, combining evolutionary optimization, machine learning, multi-tool validation, and reproducible scientific software.

  • Completing an MASc in Computer Engineering at Concordia University
  • Research focus: RNA/DNA sequence design, inverse folding, and evolutionary optimization
  • First-authored and presented an RNA inverse-folding paper at IEEE CEC / WCCI 2026
  • Open to Computational Scientist, Research Engineer, and ML-for-Biology roles across Canada

Featured Work

馃К cFold

A multi-tool evolutionary framework for designing RNA sequences under structural and IUPAC constraints, presented at IEEE CEC / WCCI 2026.

Current Research

  • DNA aptamer design: Optimizing multivalent fluorescent aptamer architectures with oxDNA simulations; eight candidates selected for experimental validation.
  • RNA and ribozyme design: Extending cFold to additional predictors and pseudoknotted targets, with selected designs undergoing experimental validation.

Selected Tools

Python 路 PyTorch 路 Evolutionary Algorithms 路 ViennaRNA 路 MXFold2 路 oxDNA 路 Linux 路 Docker 路 Git 路 SLURM

Links

Website 路 LinkedIn 路 Email

Pinned Loading

  1. cfold cfold Public

    cFold: a modular multi-tool evolutionary algorithm framework for RNA inverse folding (IEEE WCCI 2026)

    Python 1