About

Relevant books, papers, lectures and other learning materials online, mostly authored by others but compiled & curated by us.

Books

Text books

• Statistics backgroud most relevant to our research.
• Computational biology.

Popular science books

• Book club 2015, a list compiled by Xin He in 2015.
• CSG book club.

Other useful books

• Writing and scientific writing

Papers

Keep up with literature

• A list of relevant journals.
• How to keep up with the scientific literature (a 2016 blogpost).
  • A distilled version by Gao Wang.

General collections

• Nature’s Scitable.
• PLoS Compbio Education collection.
• Nature Biotech Computational Biology collection.
• Computational genomics papers, a list compiled by Xin He in 2016.
• Matthew Stephens lab reading list, papers from the lab.

Statistical genetics

• NRG GWAS collection.
• Statistical genetics papers.
• Statistical Genetics Resources by @sinarueeger

Transcriptome computational biology

• RNA-seq papers.

Online courses & tutorials

Statistics

• 5 minutes statistics by Matthew Stephens, with some additional material.
  • highly recommended if you already know some statistics.
• Statistics in action with R
• Bayesian Data Analysis by Aki Vehtari
• Statistical Rethinking Youtube video by Richard McElreath
  • highly recommended if you need an introduction to Bayesian statistics
• Misc. material:
  • PCA tutorial Lior Pachter.
  • PCA with bigsnpr
  • Variational Inference by David Blei.
  • A primer on variational inference
  • Explaining variational inference
  • p-value and Bayes Factor
  • Bayesian FDR

Machine learning

• Deep learning for computer vision, Stanford
• Misc. material:
  • Math for machine learning, a note from UC Berkeley CS 189/289A.
  • Matrix calculus for deep learning.
  • Toturial on Generative Adversarial Networks

Statistical genetics

• A practical introduction to statistical genetics by Robert Maier.
  • highly recommended, even if you are already savvy in statistical genetics.
• GWAS course by Matti Pirinen
• Statistical genetics short courses by Suzanne Leal
• Misc. material:
  • LD clumping vs pruning

Programing

• Software Carpentry tutorials, the “Core Lessons” on Unix Shell, git, Python and R.