Since 2011 together with Dr. Andrew Groover at the US Forest Service and our students and colleagues: Llijun Liu, Matt Zinkgraf, Trevor Ramsay, Victor Missirian, and Suzane Gertulla, we have been working on deciphering key gene regulatory relationships effecting secondary tree growth in poplar trees. We are grateful to the USDA AFRI (grant 2011-67013-30062) for their support of this project. This page is dedicated to the software we and others have written and a virtual machine we have compiled for running the studies reported in our publications.
We have put together a virtual machine, available for download here, VM. It comprises of all the necessary software to be able to reproduce the results from our publications below. We have also uploaded it into iPlant, under the name Populus_ChIPseq_VM_1.0 .
The scripts we used to process the data are available here, and are described in the above README file.
A resource for characterizing genome-wide binding and putative target
genes of transcription factors expressed during secondary growth in Populus
Lijun Liu, Trevor Ramsay, Matthew Zinkgraf, David Sundell, Nathaniel Robert Street, Vladimir Filkov, and Andrew Groover