Difference between revisions of "Tracy Heath"

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[[File:thsquare.jpg|right]]
 
[[File:thsquare.jpg|right]]
Current: <br/>
 
Postdoctoral Researcher<br/>
 
University of Kansas and University of California, Berkeley
 
 
In January 2015:<br/>
 
 
Assistant Professor<br/>
 
Assistant Professor<br/>
 
Dept. Ecology, Evolution, & Organismal Biology<br/>
 
Dept. Ecology, Evolution, & Organismal Biology<br/>
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== Contact Information ==
 
== Contact Information ==
  
*Institutional web pages:
+
*Web page: http://phyloworks.org/
**http://phylo.bio.ku.edu/content/tracy-heath
 
**http://cteg.berkeley.edu/members/heath.html
 
*Blog: http://treethinkers.org/blog
 
 
*Twitter: [https://twitter.com/trayc7 @trayc7]
 
*Twitter: [https://twitter.com/trayc7 @trayc7]
*Email: tracyh "at" berkeley "dot" edu
+
*Email: phylo "at" iastate "dot" edu
 
 
  
 
== Research ==
 
== Research ==
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== Time at MBL ==
 
== Time at MBL ==
Sunday July 27 - Wednesday August 6
+
Thursday August 1 - Sunday August 11
  
 +
== 2019 Course ==
  
== 2014 Course ==
+
Divergence Time Estimation in RevBayes - August 4 & 5
  
* Phylogenetic Inference using [[RevBayes]] (with [[Michael Landis]])
+
All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html
* [[Bayesian inference of species divergence times in BEAST2]]
 
  
  
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Graphical Models
 
Graphical Models
* Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, in press. doi: 10.1093/sysbio/syu039.
+
* Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. ([http://sysbio.oxfordjournals.org/content/63/5/753 doi: 10.1093/sysbio/syu039]).
  
Reviews on Divergence-Time Estimation
+
Divergence-Time Estimation
* Thorne JL, Kishino H. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. ([ftp://statgen.ncsu.edu/pub/thorne/mypapers/clockreview1215wfigs.pdf PDF])
+
* 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. ([ftp://statgen.ncsu.edu/pub/thorne/mypapers/clockreview1215wfigs.pdf 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)
 
* 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 [http://treethinkers.org/wp-content/uploads/2014/08/DivTime_BEAST2_tutorial_2014.pdf divergence-time tutorial]
 +
 +
== Additional Tutorials ==
 +
 +
* More tutorials on divergence time estimation in RevBayes and BEAST2 ([http://phyloworks.org/workshops/divtime.html link])
 +
* Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics ([https://www.bsse.ethz.ch/cevo/taming-the-beast/materials.html link])
 +
 +
== 2016 Course ==
 +
 +
* Phylogenetic Inference using [[RevBayes]] (with [[Michael Landis]])
 +
* [http://phyloworks.org/workshops/divtime.html Bayesian Divergence Time Estimation in BEAST2] ([http://phyloworks.org/workshops/WH_2015_divtime_lec_d.pdf slides])
 +
 +
== 2017 Course ==
 +
 +
 +
Morning lecture slides and example scripts
 +
* Hierarchical models and integrative Bayesian analysis ([https://www.slideshare.net/trayc7/integrative-bayesian-analysis-in-revbayes slides])
 +
** RevBayes archery model demo ([[:File:Archery_model.zip|files]])
 +
** RevBayes GTR demo ([https://github.com/revbayes/revbayes_tutorial/tree/master/RB_CTMC_Tutorial files])
 +
* Bayesian divergence-time estimation ([https://www.slideshare.net/trayc7/bayesian-divergence-time-estimation-lecture-at-bodega-2014-workshop slides])
 +
 +
Afternoon tutorial
 +
* [[Total-evidence analysis in RevBayes]]

Latest revision as of 15:31, 3 August 2019

Thsquare.jpg

Assistant Professor
Dept. Ecology, Evolution, & Organismal Biology
Iowa State University


Contact Information

Research

Heath.jpg

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

Thursday August 1 - Sunday August 11

2019 Course

Divergence Time Estimation in RevBayes - August 4 & 5

All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html


Suggested Reading

Graphical Models

  • Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. (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

Additional Tutorials

  • More tutorials on divergence time estimation in RevBayes and BEAST2 (link)
  • Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics (link)

2016 Course

2017 Course

Morning lecture slides and example scripts

  • Hierarchical models and integrative Bayesian analysis (slides)
    • RevBayes archery model demo (files)
    • RevBayes GTR demo (files)
  • Bayesian divergence-time estimation (slides)

Afternoon tutorial