Bookmarks
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
Readings potentially relevant to Random Questions
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Computationally less expensive alternative repeat-masking options
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Orthology application stories
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Conservation, etc. of promoters and enhancers
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Methods and examples of exploring evolution of GRNs
Whole Genome Alignment (WGA)
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Tools: Progressive cactus (2020), SibeliaZ (2020), AnchorWave (2021)
- UCSC resource and tools
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make_lastz_chains: a NextFlow pipeline to run
lastzin multiple threads. - WGA / graph genome application stories, benchmarks, reviews, etc. (to be added…)
Orthology inference
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Tools: OrthoFinder (2019, 2015), PANTHER (2019), …
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Benchmarks, reviews, etc.
- DRSC integrative ortholog prediction tool (DIOPT) - includes links to other tools
- Quest for Orthologs (QfO)
- How are orthologs calculated by NCBI Orthologs
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
Learning materials (for myself)
- 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
- 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
- Evolution and genetics
- Shiny pop-gene course apps and resources by Silas Tittes
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