# Difference between revisions of "Tracy Heath"

From MolEvol

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* Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html | * Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html | ||

* also see references in [http://treethinkers.org/wp-content/uploads/2014/08/DivTime_BEAST2_tutorial_2014.pdf divergence-time tutorial] | * also see references in [http://treethinkers.org/wp-content/uploads/2014/08/DivTime_BEAST2_tutorial_2014.pdf divergence-time tutorial] | ||

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+ | == Optional Tutorials: Phylodynamics of Infectious Diseases == | ||

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+ | Many students are interested in Bayesian methods for understanding epidemiology. There are some great tools for applying these methods, including BEAST2: | ||

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+ | * Alexei Drummand & Remco Bouckaert's [http://beast2.cs.auckland.ac.nz/index.php/Main_Page BEAST2] tutorial on: [http://beast2.googlecode.com/files/MEPsv2.0.2.pdf Measurably evolving populations, estimating rates, and Bayesian skyline plots] | ||

+ | * Trevor Bedford's tutorial on (using BEAST1): [https://github.com/trvrb/influenza-dynamics-practical Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data] |

## Revision as of 11:12, 2 August 2014

Current:

Postdoctoral Researcher

University of Kansas and University of California, Berkeley

In January 2015:

Assistant Professor

Dept. Ecology, Evolution, & Organismal Biology

Iowa State University

## Contact Information

- Institutional web pages:
- Blog: http://treethinkers.org/blog
- Twitter: @trayc7
- Email: tracyh "at" berkeley "dot" edu

## Research

I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record.

## Time at MBL

Sunday July 27 - Wednesday August 6

## 2014 Course

- Phylogenetic Inference using RevBayes (with Michael Landis)
- Bayesian inference of species divergence times in BEAST2

## Suggested Reading

Graphical Models

- Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, in press. (doi: 10.1093/sysbio/syu039).

Divergence-Time Estimation

- Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. (PDF)
- Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF)
- BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html)
- Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html
- also see references in divergence-time tutorial

## Optional Tutorials: Phylodynamics of Infectious Diseases

Many students are interested in Bayesian methods for understanding epidemiology. There are some great tools for applying these methods, including BEAST2:

- Alexei Drummand & Remco Bouckaert's BEAST2 tutorial on: Measurably evolving populations, estimating rates, and Bayesian skyline plots
- Trevor Bedford's tutorial on (using BEAST1): Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data