Yang Lab of Plant Evolution @ University of Minnesota
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How to find us

SHIPPING ADDRESS
For temperature sensitive packages:
University of Minnesota
NAME OF RECIPIENT (Yang Lab)
Suite 140, 1479 Gortner Ave
St. Paul, MN 55108
USA

Regular packages: 
University of Minnesota
NAME OF RECIPIENT (Yang Lab)
712 Biological Sciences Center
1445 Gortner Ave
Saint Paul, MN 55108
​USA
​MAILING ADDRESS
​
NAME OF RECIPIENT (Yang Lab)
​
714 Biological Sciences Center
1445 Gortner Avenue
Saint Paul, MN 55108-1095
​USA

General lab expectations

General lab expectations can be found here

Lab meeting

We meet to talk about papers related to lab members' specific projects. Here is the schedule. 

Field and Lab Protocols

Our phylotranscriptomic field and lab protocols are published here. Updates are posted here.
Guideline for collecting tissues and vouchers: protocol and training materials. 

Data Analysis Work Flow

Our untargeted phylotranscriptomic data analysis workflow is published here, with updated code on bitbucket.

Here are some scripts for carrying out baited homology inference starting from one or more "baits" and search genomes and/or transcriptomes to construct homologous gene trees. Scripts are written for doing the search either one at a time or 30,000 genes at a time https://bitbucket.org/yangya/adh_2016. It takes top hits per taxon, estimate alignments and trees, and resolve the tree topology. Therefore it much more robust to transcriptome data sets that have isoforms and incomplete sequences.

Facilities

Molecular lab: 705 and 713 Biological Sciences Center
Computational lab and office: 712 Biological Sciences Center
On-site (one floor up) collection facilities: University of Minnesota Herbarium (MIN)
On-site (5 min walk) greenhouse and growth chambers: Plant Growth Facilities
On-site (downstairs) sequencing core facilities: University of Minnesota Genomics Center
On-site (downstairs) microscopy and imaging facilities: University Imaging Center

Useful links

Seminars
  • Seminars on campus. We attend seminars by College of Biological Sciences (EEB and PMB) regularly. We occasionally also go to those by College of Food, Agricultural and Natural Resource Sciences. 
  • Online seminars on phylogenetics: phyloseminar
  • Biocomputing Discussion Group by Peter Morrell Lab
​
Phylogenetic Comparative methods:
Harmon's intro book https://lukejharmon.github.io/pcm/

Misc how-to guides
How to plot a phylogeny in R http://lebeagle.qcbs.ca/post/172412130928/r-toolbox-how-to-plot-a-phylogeny-using-phytools
How to peer review http://reviewers.plos.org/resources/#how-to-review
How to give presentations https://www.youtube.com/watch?v=Yis6mAnMjTc&feature=youtu.be