One Cell, Three Genomes Problem Solving Space
Session #3 Studying One Cell with Three Genomes
Data for Workbench Practice
Phylogentic Profiling (Rubisco)
Phylogenetic profiling involves generating and comparing multiple phylogenies to look for similarities and differences across species and molecules. http://www.doe-mbi.ucla.edu/People/Yeates/Gallery/phylo_profile.html
The following datasets are available:
Developing phylogenies from 3-genomes
Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ, Moore
G, Wolfe AD, dePamphilis CW.
Chaw SM, Parkinson CL, Cheng Y, Vincent TM, Palmer JD.
Deep Green Challenges
A tradition in the computer science, information technology, and mathematical communities is to issue "challenges." Such challenges pose problems to fellow scientists, and provide an entertaining way to advance the discipline. Because the concept of challenges has not been widely applied in the life sciences, we hope that introducing them will promote additional interactions among the biological and analytical communities. http://www.life.umd.edu/labs/delwiche/deepgreen/DGchallenges.html
Origins of plastids
Collect a set of sequences to test a hypothesis about chloroplast and mitochondria evolution. We have lots of references to get you started.
Peeters_2000.pdf (1.5 mb)
Pellegrini_1999.pdf (105 kb)
Marcotte_2000.pdf (556 kb)
Grey_1999.pdf (177 kb)
Delwiche_1999.pdf (544 kb)
Delwiche_1995.pdf (2.46 mb)