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  1. 14-Pure-Education
  2. My Knowledge Wiki 🌿
  3. biology
  4. genomics

DNA

PreviousgenomicsNextGenomics

Last updated 4 years ago

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Notes

  • 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)

Links

  • - Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

  • - AI-Powered Discovery Platform.

  • [DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction (2019)]()

  • - Framework agnostic DNA viewer for sequences or files (gb, fasta, etc) with auto-feature annotation.

  • - Short Tandem Repeat DNA Internet DataBase.

  • - Workflow designed to run analyses on whole genome or targeted sequencing data from regular samples or tumour / normal pairs and could include additional relapses.

  • ()

  • - Aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.

  • - Several groups working on formats and tools for next-generation sequencing.

  • - Tools (written in C using htslib) for manipulating next-generation sequencing data.

  • ()

  • ()

  • - How do precise boundaries of gene expression form in developing tissues? ()

  • - Single Cell Sequencing Resource For Gene Expression Data.

  • - Classify single cells across species and platforms.

  • - Network biology applied to stem cell engineering.

  • - 3D engine implementation in DNA code. ()

  • - Gene cluster comparison figure generator.

  • - Automated gene synthesis. DNA Printer.

  • ()

  • ()

  • ()

Is DNA compressed?
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.
mosdepth
Four new DNA letters double life’s alphabet (2019)
Deep Genomics
https://www.cell.com/cell/fulltext/S0092-8674(19)30547-1
Algorithms for DNA Sequencing course
The structure of DNA (2019)
DIY Bacterial Gene Engineering CRISPR Kit
seqviz
STRBase
Sarek
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
Samtools org
Samtools tools
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)
Tweet
PanglaoDB
scRNAseq analysis notes from Ming Tang
Brain Cell DNA Refolds Itself to Aid Memory Recall (2020)
SingleCellNet
CellNet
Molecular lithography: Making 3D nanosuperconductors with DNA (2020)
cube3d.dna
Tweet
clinker
Codex DNA
DNA seen through the eyes of a coder
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