Bookmarks

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Learning materials (for myself)

• Evolution and genetics
  • An Owner’s Guide to the Human Genome by Jonathan Pritchard, Stanford University; see this Twitter thread
  • Shiny pop-gene course apps and resources by Silas Tittes
• Genomics and bioinformatics
  • Machine learning for genomics, 2020 Fall by Prof. Manolis Kellis
  • Intro. to bioninformatics and computational biology, 2020 Spring by Prof. Xiaole Shirley Liu
• Math
  • Linear algebra by Prof. Gilbert Strang
  • Multi-variable calculus by Prof. Denis Auroux
  • Statistics 110: Probability by Prof. Joe Blitzstein
• Machine learning, etc.
  • The Mechanics of Machine Learning by Terence Parr and Jeremy Howard
  • Awesome Diffusion Models, collection by heejkoo
  • Deep Learning Course by François Fleuret

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Readings potentially relevant to Random Questions

• Computationally less expensive alternative repeat-masking options

• Orthology application stories

• Conservation, etc. of promoters and enhancers

• Methods and examples of exploring evolution of GRNs

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Whole Genome Alignment (WGA)

• Tools: Progressive cactus (2020), SibeliaZ (2020), AnchorWave (2021)

• UCSC resources and tools
  • MultiZ alignments
  • Whole genome alignment howto
  • DoBlastzChainNet.pl

• make_lastz_chains: a NextFlow pipeline to run lastz in multiple threads.

• WGA / graph genome application stories, benchmarks, reviews, etc. (to be added…)

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Orthology inference

• Tools: OrthoFinder (2019, 2015), PANTHER (2019), …

• Benchmarks, reviews, etc.

  • Quest for Orthologs in the Era of Biodiversity Genomics (2024) - a comprehensive review of current states and challenges
  • DRSC integrative ortholog prediction tool (DIOPT) - includes links to other tools
  • Quest for Orthologs (QfO)
  • How are orthologs calculated by NCBI Orthologs

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Data visualization

• Genomics
  • Chromosome visualization with ideogram.js
  • Colin’s curated list of “awesome genome visualization” tools.
  • GenoCAT.tools
• Generic
  • Create/share beautiful images of your source code using carbon.
  • Chenxin Li’s “Friends don’t let friends …” series
  • The “30-Day Chart Challenge” GitHub #30DayChartChallenge @30DayChartChallenge

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Random but cool encounters

• On “Mutationism”
  • What on earch is mutationism
  • Is the growing relevance of SV, WGD, and gene duplication a resurgence of a softer form of mutationism? A Twitter thread

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