Subsections of Greg — HTGAA Spring 2026

Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Does the option: Option 1 Option 2 Option 3 Enhance Biosecurity • By preventing incidents • By helping respond Foster Lab Safety • By preventing incident • By helping respond Protect the environment • By preventing incidents • By helping respond Other considerations • Minimizing costs and burdens to stakeholders • Feasibility? • Not impede research • Promote constructive applications

  • Week 2 HW: DNA r/w/e

    My homework DNA! graph LR; DNA–>RNA–>proteins

Subsections of Homework

Week 1 HW: Principles and Practices

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Does the option:Option 1Option 2Option 3
Enhance Biosecurity
• By preventing incidents
• By helping respond
Foster Lab Safety
• By preventing incident
• By helping respond
Protect the environment
• By preventing incidents
• By helping respond
Other considerations
• Minimizing costs and burdens to stakeholders
• Feasibility?
• Not impede research
• Promote constructive applications

Week 2 HW: DNA r/w/e

My homework

DNA!

graph LR;
DNA-->RNA-->proteins

Subsections of Labs

Week 1 Lab: Pipetting

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Projects

Final projects:

  • Mindmap mindmap root((HTGAA 2025)) AI + Computational Bio Multi-omics → LLM orchestration Genomics / Transcriptomics / Proteomics / Metabolomics Indirect pulls from DBs; NCBI, UniProt, KEGG, Reactome AI protein/peptide design PepMLM from HuggingFace for peptide generation Structure prediction + docking/MD Binder design: AfDesign / RFdiffusion / EvoBind / BindCraft Automation & coding Google Colab protocols → Opentrons robots Scale experiments, iterate fast Protein Science & Design Amino acids & stereochemistry L vs D amino acids, helix handedness Secondary structure α-helices & variants, β-sheets → aggregation Amyloids as stable materials Model protein eGFP: primary→tertiary structure characterization Genetic Engineering Methods DNA read/write/edit basics Gel electrophoresis, Benchling workflows PCR chemistry Phusion HF Master Mix components/purpose Assembly Gibson Assembly Cloning & expression Vector design → E. coli expression Regulatory Logic & Circuits Post-transcriptional vs post-translational control Endoribonucleases for RNA cleavage vs proteases for protein degradation Cell-Free Systems Why cell-free? Speed - no culturing! Open control of DNA, amino acids, energy, enzymes Toxic proteins OK; supports UAAs Bioproduction & Pathways Carotenoids in E. coli crtE + crtI + crtB → lycopene + crtY → β-carotene Automation mindset What new questions when everything is automated? Phage Engineering: MS2 Lysis protein L N- vs C-terminal roles; C-term TM drives lysis 33-nt non-overlapping window Introduce stop codon to split N from C → DnaJ-independent lysis Preserve overlaps with cp/rep genes Mitochondrial Therapeutics Target: Cyclophilin D “CypD” Block mPTP opening in I/R injury Design peptide inhibitor; plan in vitro/in vivo validation Knowledge Sources NCBI GenBank • UniProt • KEGG • Reactome

Subsections of Projects

Individual Final Project

Mindmap

mindmap
  root((HTGAA 2025))
    AI + Computational Bio
      Multi-omics → LLM orchestration
        Genomics / Transcriptomics / Proteomics / Metabolomics
        Indirect pulls from DBs; NCBI, UniProt, KEGG, Reactome
      AI protein/peptide design
        PepMLM from HuggingFace for peptide generation
        Structure prediction + docking/MD
        Binder design: AfDesign / RFdiffusion / EvoBind / BindCraft
      Automation & coding
        Google Colab protocols → Opentrons robots
        Scale experiments, iterate fast
    Protein Science & Design
      Amino acids & stereochemistry
        L vs D amino acids, helix handedness
      Secondary structure
	        α-helices & variants, β-sheets → aggregation
        Amyloids as stable materials
      Model protein
        eGFP: primary→tertiary structure characterization
    Genetic Engineering Methods
      DNA read/write/edit basics
        Gel electrophoresis, Benchling workflows
      PCR chemistry
        Phusion HF Master Mix components/purpose
      Assembly
        Gibson Assembly
      Cloning & expression
        Vector design → E. coli expression
    Regulatory Logic & Circuits
      Post-transcriptional vs post-translational control
        Endoribonucleases for RNA cleavage vs proteases for protein degradation
    Cell-Free Systems
      Why cell-free?
        Speed - no culturing!
        Open control of DNA, amino acids, energy, enzymes
        Toxic proteins OK; supports UAAs
    Bioproduction & Pathways
      Carotenoids in E. coli
        crtE + crtI + crtB → lycopene
        + crtY → β-carotene
      Automation mindset
        What new questions when everything is automated?
    Phage Engineering: MS2
      Lysis protein L
        N- vs C-terminal roles; C-term TM drives lysis
        33-nt non-overlapping window
        Introduce stop codon to split N from C → DnaJ-independent lysis
        Preserve overlaps with cp/rep genes
    Mitochondrial Therapeutics
      Target: Cyclophilin D "CypD"
        Block mPTP opening in I/R injury
        Design peptide inhibitor; plan in vitro/in vivo validation
    Knowledge Sources
      NCBI GenBank • UniProt • KEGG • Reactome

Group Final Project

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