Molecular Information Engineering

Undergraduate · 15 weeks · Teaching

Materials: lab-authored slides and lab code. Cited figures and tables are credited on each slide (for teaching).

• Week 01

  History of Information Storage and the Memory Hierarchy

  Recording media · memory hierarchy · cold storage and DNA

  Lecture 1-2 · History of Information Storage, Memory Hierarchy and the DNA Storage Process (HTML slides) →
  Materials
• Week 02

  DNA Data Storage: Concepts, History and Workflow

  DNA structure · encoding → synthesis → storage → random access → sequencing → decoding

  Lecture 2-2 · Why DNA, DNA Structure and the Storage Workflow (HTML slides) →
  Materials
• Week 03

  Digital Data and DNA Encoding

  Bits · ASCII · UTF-8 · 2 bits/nt mapping · GC content · homopolymers

  Lecture 3-1 · Digital Data and DNA Encoding Theory (HTML slides) →Lecture 3-2 · Encoding Lab: Your Name in DNA — Python · MATLAB (HTML slides) →Week 3 lab code (Python · MATLAB) ↗
  Materials
• Week 04

  DNA Channel Errors and Error-Correcting Codes

  Substitution · insertion · deletion · dropout · Hamming · RS · BCH · LDPC · fountain · VT · DNA storage lab: bytes → 17-byte rows → outer XOR → fixed index → inner RS → 148 nt → file recovery

  Lecture 4-1 · Algebraic Error Correction (HTML slides) →Lecture 4-2 · Probabilistic Error Correction (HTML slides) →MATLAB labs 1–14 ↗Lab 4-3 · MATLAB DNA storage: steps 1–5 and Decoding.m →Colab notebook · DNA storage lab ↗
  Materials
• Week 05

  Hashing and High-Efficiency DNA Coding

  SHA-256 · DNA Fountain · Yin–Yang · HEDGES · k-mer · mCGR
• Week 06

  Chemical DNA Synthesis at Scale

  Phosphoramidite cycle · yield · oligo pools · microarrays

  Lecture 6-1 · Phosphoramidite chemistry: one base at a time (HTML slides) →Lecture 6-2 · Parallel synthesis on chips, oligo pools and purification (HTML slides) →Supplement · Principles of HPLC (HTML slides) →
  Materials
• Week 07

  Enzymatic Synthesis, Synthetic Biology and Xeno Nucleic Acids

  TdT · template-free synthesis · assembly · XNA

  Lecture 7-1 · Enzymatic synthesis (TdT) and gene assembly (HTML slides) →Lecture 7-2 · Xeno nucleic acids (XNAs) (HTML slides) →Lee, Kang, Yu, Haider, Lim, Song — XNAs: advances in synthesis, diagnostics, and therapeutics, Bioorg. Chem. 179 (2026) 110000 ↗
  Materials
• Week 08

  Midterm Exam

  Weeks 6–7 · 30 questions · detailed and concise versions

  Midterm questions · detailed and concise versions (HTML) →
  Materials
• Week 09

  DNA Preservation Materials and Experimental Evaluation

  DNA damage · silica · polymers · accelerated aging · file recovery

  Lecture 9-1 · Long-Term DNA Preservation (HTML slides, 75 min) →Research papers and figure credits →Previous version (2026-10-26) →
  Materials
• Week 10

  DNA File Selection and Random Access

  File addresses · selective PCR · sampling · original reuse · capsule search

  Lecture 10-1 · Random Access in DNA Data Storage (HTML slides, 75 min) →Research papers and figure credits →Previous version (2026-10-26) →
  Materials
• Week 11

  Sequencing Technologies and Nanopore Measurement

  Six core lectures + 60-minute Illumina deep dive · HGP · NGS principles · FastQC · Phred · RNA quantification · PacBio · ONT · decoding

  Lecture 11-1 · PCR, Sanger, Fluorescence and Chromatograms (HTML slides, 75 min) →Lecture 11-2 · Genome Assembly, Human History and NGS (HTML slides, 75 min) →Illumina deep dive · Chemistry, Instruments, RCA and Competitors (60 min) →NGS Experimental Principles · Diagrams and Company Videos →Lecture 11-6 · Libraries, FASTQ, FastQC and Analysis Basics (HTML slides) →Lecture 11-3 · Single-Molecule Sequencing and Roche SBX (HTML slides, 75 min) →Lecture 11-4 · Solid-State, Protein and Hybrid Nanopores, and ONT (HTML slides, 75 min) →Lecture 11-5 · Nanopore Voltage, Current, Axopatch and ADC (HTML slides, 75 min) →Photos, textbook figures and video sources →
  Materials
• Week 12

  Decoding and File Recovery

  Clustering · consensus · inner/outer ECC · hash verification

  Lab 12 · Download noisy FASTQ and recover your Week 4 file →
  Materials
• Week 13

  k-mers and Fast NGS-Based Decoding

  k-mer index · sketches · fast index scanning
• Week 14

  AI for Fast DNA Data Recovery

  ML decoding · deep-learning basecalling · iSCAN
• Week 15

  Applications, System Integration and Outlook

  Cultural heritage · medical data · DNA-of-Things · final project