How to find us
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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.
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.
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
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
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
- 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