bookmarks.md

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Bookmarks

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Learning materials (for myself)

• Evolution and genetics

  • An Owner's Guide to the Human Genome{:target="_blank"} by Jonathan Pritchard, Stanford University; see this Twitter thread{:target="_blank"}
  • Shiny pop-gene course apps and resources{:target="_blank"} by Silas Tittes

• Genomics and bioinformatics

  • Machine learning for genomics, 2020 Fall{:target="_blank"} by Prof. Manolis Kellis
  • Intro. to bioninformatics and computational biology, 2020 Spring{:target="_blank"} by Prof. Xiaole Shirley Liu

• Math

  • Linear algebra{:target="_blank"} by Prof. Gilbert Strang
  • Multi-variable calculus{:target="_blank"} by Prof. Denis Auroux
  • Statistics 110: Probability{:target="_blank"} by Prof. Joe Blitzstein

• Machine learning, etc.

  • The Mechanics of Machine Learning{:target="_blank"} by Terence Parr and Jeremy Howard
  • Awesome Diffusion Models, collection by heejkoo

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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{:target="_blank"} (2020{:target="_blank"}), SibeliaZ{:target="_blank"} (2020{:target="_blank"}), AnchorWave{:target="_blank"} (2021{:target="_blank"})

• UCSC resources and tools

  • MultiZ alignments{:target="_blank"}
  • Whole genome alignment howto{:target="_blank"}
  • DoBlastzChainNet.pl{:target="_blank"}

• make_lastz_chains{:target="_blank"}: 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{:target="_blank"} (2019{:target="_blank"}, 2015{:target="_blank"}), PANTHER{:target="_blank"} (2019{:target="_blank"}), ...

• Benchmarks, reviews, etc.

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

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Data visualization

• Genomics

  • Chromosome visualization with ideogram.js{:target="_blank"}
  • Colin's curated list of "awesome genome visualization{:target="_blank"}" tools.
  • GenoCAT.tools{:target="_blank"}

• Generic

  • Create/share beautiful images of your source code using carbon{:target="_blank"}.
  • Chenxin Li's "Friends don't let friends ..." series
  • The "30-Day Chart Challenge" GitHub{:target="_blank"} #30DayChartChallenge{:target="_blank"} @30DayChartChallenge{:target="_blank"}

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Random but cool encounters

• On "Mutationism"
  • What on earch is mutationism{:target="_blank"}
  • Is the growing relevance of SV, WGD, and gene duplication a resurgence of a softer form of mutationism? A Twitter thread{:target="_blank"}

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