Useful links

Reprodubility and data science

• My notes on mindful programming
• Karl Broman’s notes on reproducible research
• Version control: notes from Software Carpentry at UW-Madison (there might be more recent notes out there)
• Tukey (1962) The future of data analysis
• R Markdown: The Definite Guide
• Rich Edwards (2015) Bioinformatics is just like bench science and should be treated as such

Learning Julia

• Learn X in Y minutes: julia
• Julia for R programmmers: cheatsheet
• Julia for Python/Matlab programmers: cheatsheet

Recent courses

• 2019: Faculty member of the Marine Biological Laboratory workshop on Molecular Evolution. Lecture and tutorial on phylogenetic networks. Woods Hole, USA.
  • slides
  • wiki
• 2016: Botany 563 Guest lecture: Introduction to phylogenetic networks
  • slides
  • code

Tutorials

Nantucket developR 2019

Tutorial on best computing practices using R: mindful programming. Notes from other instructors here.

Molecular Evolution Workshop at Woods Hole 2019

Tutorial on inference of phylogenetic networks using Julia package: PhyloNetworks

Instituto de Biología - UNAM

Introduction to PhyloNetworks and SNaQ: Same tutorial as in Evolution 2016, links below.

Evolution 2016

Phylogenomics symposium and software school: Introduction to PhyloNetworks and SNaQ

• wiki
• julia code
• R code

Other teaching experience

Teaching Assistant (UW-Madison)

• Summer 2014 PhD qualifier Summer camp
• Spring 2013 Introduction to Biostatistics for Population Health II (BIOSTAT 552) (professor Ron Gangnon)
• Fall 2012 Introduction to Biostatistics for Population Health I (BIOSTAT 551) (professor Ron Gangnon)
• Spring 2012 Introduction to Biostatistics for Population Health II (BIOSTAT 552) (professor Ron Gangnon)
• Fall 2011 Introduction to Biostatistics for Population Health I (BIOSTAT 551) (professor Ron Gangnon)
• Summer 2011 Introduction to Statistical Methods (STAT 301) (professor Kam Wah Tsui)
• Spring 2011 Introduction to Statistical Methods (STAT 301) (professor Kevin Packard)
• Fall 2010 Introduction to Theory and Methods of Mathematical Statistics I (STAT 311) (professor Zhengjun Zhang)

Instructor (ITAM)

• Summer 2010 Advanced Algebra
• Spring 2010 Calculus II
• Fall 2009 Calculus III
• Fall 2009 Actuarial Mathematics I
• Spring 2010 Actuarial Mathematics I
• Fall 2009 Actuarial Mathematics III
• Spring 2010 Actuarial Mathematics III

Mentoring experience

2019

• Software Development Project, Fast reconstruction and visualization of phylogenetic networks, Harnoor Singh and Naman Kanwar – Georgia State University.

2018

• Software Development Project, Julia package for GAMuT test, Anna Voss - Emory University
• Statistics Senior Honors Thesis, GWAS data analysis for epilepsy, Mengtong Hu - Emory University

2016

• Software Development Project, Parallelization of SNaQ in PhyloNetworks, Josh McGrath - University of Wisconsin-Madison
• Undergraduate Research Scholar, Computing tools for bayesian phylogenetic inference, Jordan Vonderwell - University of Wisconsin-Madison
• Statistics Senior Honors Thesis, Computing tools and performance of PhyloNetworks, Nan Ji - University of Wisconsin-Madison

2015

• Statistics Senior Honors Thesis, Inconsistency of species-tree methods under gene flow, Mengyao Yang – University of Wisconsin-Madison
• Integrated Biological Sciences Summer Research Program, Visualizing inferred phylogenetic networks in Julia, John Spaw – University of Wisconsin-Madison

2014

• Integrated Biological Sciences Summer Research Program, Using quartets to estimate phylogenetic networks, John Malloy – University of Wisconsin-Madison.