Molecular Information Systems Spring 2020

CSE 599x

Introduction to basic concepts - DNA/proteins basics, PCR, sequencing, synthesis, etc. - Paper presentation assignments - Project ideas/brainstorming

• Slides

• None

Project pitches + team formation

• None

Paper discussion - DNA data storage overview and foundational papers (Matt and Lee)

• Molecular digital data storage using DNA (Ceze et al. - Nature Reviews Genetics)

• Next-Generation Digital Information Storage in DNA (Church et al. - Science)

• Toward practical high-capacity low-maintenance storage of digital information in synthesised DNA (Goldman et al. - Nature)

• Slides

• Readings

Paper discussion - DNA data random access (Lee and JeffM)

• Random access in large-scale DNA data storage (Organick et al. - Nature Biotechnology)

• Driving the Scalability of DNA-Based Information Storage Systems (Tomek et al. - ACS Synthetic Biology)

• A Rewritable Random-Access DNA-Based Storage System (Yazdi et al. - Nat Sci Rep)

• Slides

• Readings

Paper discussion - DNA data storage encoding (Melissa and Ashley)

• DNA Fountain enables a robust and efficient storage architecture (Erlich and Zielinski - Science)

• Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes (Grass et al. - Angewandte Communications)

• Readings

Paper discussion - DNA near-data computing (Callie)

• DNA data storage and hybrid molecular electronic computing (Carmean et al. - IEEE)

• A content-addressable DNA database with learned sequence encodings (Bee et al. - DNA24)

• Building an associative memory vastly larger than the brain (Baum - Science technical comment)

• Readings

Paper discussion - DNA computing with strand displacement overview (Nick)

• Dynamic DNA nanotechnology using strand displacement reactions (Zhang and Seelig - Nature Chemistry)

• DNA-based Molecular Architecture with Spatially Localized Components (Muscat et al. - ISCA)

• Readings

Project midterm update # 1

• Project update

Paper discussion - DNA DSD computing neural networks (Aishwarya)

• Neural network computation with DNA strand displacement cascades (Qian - Nature)

• Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks (Cherry et al. - Nature)

• Slides

• Readings

Paper discussion - DNA DSD computing for data (Gus and Jason)

• SIMD-DNA Single Instruction Multiple Data Computation with DNA Strand Displacement (Wang et al. - DNA25)

• Programmable chemical controllers made from DNA (Chen et al. - Nature Nano)

• SIMD-DNA slides

• Programable Chemical Controlers slides

• Readings

Paper discussion - Wetlab Automation + Programming Languages (Ashley and JeffM)

• Puddle-A Dynamic Error-Correcting Full-Stack Microfluidics Platform (Willsey et al. - ASPLOS’19)

• Harnessing QbD Programming Languages and Automation for Reproducible Biology (Sadowski et al. - Cell)

• Readings

Paper discussion - Nanopore sensing overview (Justin)

• Terminator-free template-independent enzymatic DNA synthesis for digital information storage (Lee et al. - Nature Comms)

• Readings

Midterm project updates 2

• Project updates

Midterm project updates 2

• Project updates

Paper discussion - Nanopore Sequencing Basecalling + optimizing DNA data storage for nanopore (Matt)

• Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy (Chandak et al. - preprint)

• Nanocall- An Open Source Basecaller for Oxford Nanopore Sequencing Data (David et al. - Bioinformatics)

• Chiron- translating nanopore raw signal directly into nucleotide sequence using deep learning (Teng et al. - GigaScience)

• Readings

Paper discussion - Nanopore Molecular Apps (Katie and Jessica)

• Porcupine-Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands (Doroschak et al. - preprint)

• Multiplexed direct detection of barcoded protein reporters on a nanopore array (Cardozo et al. - preprint)

• Readings

Paper discussion - DNA-of-things (Fanny)

• A DNA-of-things storage architecture to create materials with embedded memory (Koch et al. - Nature Biotechnology)

• Readings

Paper discussion - CyBio security (Melissa)

• Computer Security Privacy and DNA Sequencing-Compromising Computers with Synthesized DNA Privacy Leaks and More (Ney et al. - USENIX)

• Exploiting Index Cross-Talk to Modify Variant Calls (Ney et al. - BioRxiv)

• Readings

Project presentations

• Presentation

Project presentations

• Presentation