DNA ​

ASML of DNA Sequencing is nice watch.

Assembly of proteins is like a programming language. However we barely understand how it works. DNA to amino acids is just a dictionary lookup.

Notes ​

• Is DNA compressed?
• One of the potential "limits" to DNA size is that everything has to be copied whenever a cell divides, which takes both time and energy to do, so there is selective pressure to keep it relatively efficient. A second limiting factor is that the DNA copying machinery isn't 100% accurate, so you end up with errors whenever DNA is copied despite the presence of error-checking processes (better in some organisms than others). So the with longer DNA you also end with more potential for errors. Cancer is primarily caused by this buildup of errors (though it's also the basis of evolution)
• DNA is copied by a protein machine 10 nanometers in size. In bacteria, it produces 1,000 DNA bases per second. Scaled to daily-life proportions, this would be equivalent to a FedEx truck going at the speed of sound, delivering the correct package every 30 centimetres.

Links ​

• mosdepth - Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
• Four new DNA letters double life’s alphabet (2019)
• Deep Genomics - AI-Powered Discovery Platform.
• DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction (2019)
• Algorithms for DNA Sequencing course
• The structure of DNA (2019)
• DIY Bacterial Gene Engineering CRISPR Kit
• seqviz - Framework agnostic DNA viewer for sequences or files (gb, fasta, etc) with auto-feature annotation.
• STRBase - Short Tandem Repeat DNA Internet DataBase.
• Sarek - Workflow designed to run analyses on whole genome or targeted sequencing data from regular samples or tumour / normal pairs and could include additional relapses.
• The structure of DNA by direct imaging (2015)
• Direct imaging of single DNA molecules (2016)
• How DNA goes to RNA and how RNA goes to proteins
• How to turn DNA into Music (2020) (Code)
• CoverM - Aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.
• Samtools org - Several groups working on formats and tools for next-generation sequencing.
• Samtools tools - Tools (written in C using htslib) for manipulating next-generation sequencing data.
• Specifications of SAM/BAM and related high-throughput sequencing file formats (Code)
• Research into single-molecule fluorescence and protein-DNA interactions
• How do Genes know when to Turn On and Off? (2020)
• Cosmic Rays May Explain Life’s Bias for Right-Handed DNA (2020) (HN)
• Allostery through DNA drives phenotype switching (2020)
• Manolis Kellis: Human Genome and Evolutionary Dynamics (2020)
• Two female CRISPR scientists make history, winning Nobel in chemistry (2020)
• Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks (2020) - How do precise boundaries of gene expression form in developing tissues? (Tweet)
• PanglaoDB - Single Cell Sequencing Resource For Gene Expression Data.
• scRNAseq analysis notes from Ming Tang
• Brain Cell DNA Refolds Itself to Aid Memory Recall (2020)
• SingleCellNet - Classify single cells across species and platforms.
• CellNet - Network biology applied to stem cell engineering.
• Molecular lithography: Making 3D nanosuperconductors with DNA (2020)
• cube3d.dna - 3D engine implementation in DNA code. (Tweet)
• clinker - Gene cluster comparison figure generator.
• Codex DNA - Automated gene synthesis. DNA Printer.
• DNA seen through the eyes of a coder (HN)
• 30 years since the Human Genome Project began – what's next? (2020) (HN)
• DNA synthesis for true random number generation (2020)
• An Onion's Genome Has Five Times More DNA Than Humans (2019) (HN)
• Sequencing your DNA with a USB dongle and open source code (2021) (HN)
• DNA Repair Mechanisms (2020)
• Could DNA have a form of primitive "password protection"? (2021)
• DNA Features Viewer - Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.
• FabricNano - DNA Nanotechnology. Revolutionary new cell-free approach to producing chemicals.
• Rosalind Franklin - Wikipedia (Tweet)
• Biology brief: How DNA and proteins work (2021)
• Mirror image DNA polymerase has been engineered (2021) (HN)
• ENSnano - 3D graphical application for DNA nanostructures.
• Brain Cells Break Their DNA to Learn More Quickly (2021)
• The Complex Truth About ‘Junk DNA’ (HN)
• The Technology of Life. A DNA-centric tour of biology. (Tweet)
• Your DNA is in a database (2021)
• Rosalind Franklin's X-ray photo of DNA as an undergraduate optical diffraction experiment (2013) (Tweet)
• Is DNA append only?
• MetaGraph - Tool for scalable construction of annotated genome graphs and sequence-to-graph alignment.
• SNAP (Scalable Nucleotide Alignment Program)
• wfmash - DNA sequence read mapper based on mash distances and the wavefront alignment algorithm.
• Sequencing your DNA with a USB dongle and open source code (2021) (HN)
• fastq.bio - Quickly generate data quality reports for FASTQ files. (Code)
• A centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles (2022) (Tweet)
• basicsynbio - Open-source Python package to facilitate BASIC DNA assembly workflows.
• REPP - Tool for DNA assembly.
• DNA Analysis in Rust (2022)
• Patchwork - Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data.
• MeConcord - Read-level DNA methylation analyses and visualization.
• GeneSpeak - Library to encode text as DNA and decode DNA to text.
• Quantum tunneling makes DNA more unstable (2022) (HN)
• DHA: nature's favorite semiconductor (2020)
• Quickdna - Fast DNA manipulation for Rust and Python.
• RNA Sequencing - Your own pipeline from scratch (2022)
• Understanding the code of life: generative models of regulatory DNA sequences based on diffusion models
• Mutato - Toolkit for mutation analysis using DNA sequencing data.
• Breakfast - Software for detecting genomic structural variants from DNA sequencing data.
• RegTools - Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
• We're wasting money by only supporting gzip for raw DNA files (2023) (HN)
• The ASML of DNA Sequencing (2023)
• VarFish - Comprehensive DNA variant analysis for diagnostics and research.
• RNA-FM - RNA foundation model.