Synopsis: In this project, we develop computational tools to infer regulatory regions in noncoding DNA, based on conservation over evolutionary time, and including biochemical data from the ENCODE project.
Current and recent collaborators: Leif Oxburgh, Carol Kim, Jim Coffman
Current staff and students: Craig Lessard, Sam McFarland, Brenna Gardner, Naomi Heuer, Amanda Castonguay, Ben Congdon-Jones
- With Carol Kim's lab at the University of Maine, we have computationally identified regulatory elements for CFTR, the gene responsible for cystic fibrosis, and completed preliminary biological validations of these.
- With Jim Coffman's lab at the Mount Desert Island Biological Lab, we have computationally identified regulatory regions for FOXJ1, a gene important in cilia development, and completed preliminary biological validations of these.
- With Leif Oxburgh's lab at the Maine Medical Center Research Institute, we have computationally identified regulatory regions for PDGFRb, a gene critical to kidney development, and completed preliminary biological validations of these.
Synopsis: In this project, we develop computational tools that identify genes that might be influenced by specific regulatory factors (specified by the user).
Collaborators: Leif Oxburgh, Mary Ann Asson-Batres
Staff and students: Sam McFarland, Craig Lessard, Jen Fetting
- With Leif Oxburgh's lab at the Maine Medical Center Research Institute, we are working to identify genes that might be regulated by FOXD1.
- With Mary Ann Asson-Batres of Tennessee State University and Doug Sawyer of the Maine Medical Center Research Institute, we are working to identify genes that might be regulated by the presence of Vitamin A.
Synopsis: Find the most plausible evolutionary relationships among species
Staff and students: Emily Greenfest, Josh Ladieu, Kevin Septor, Lunn Sawyer
