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More info on the "problem space" as a concept.

One Cell, Three Genomes Problem Solving Space

Session #3 Studying One Cell with Three Genomes

Data for Workbench Practice
Rearranging the Branches on a New Tree of Life - A New York Times article describing the role of molecular data in figuring out the phylogenetic relationships between groups of organisms. Here is a very small dataset to look at the relationship between plants animals and fungi. [enolase dataset]

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:

Description of sequences
Rubisco large subunit
Rubisco small subunit

Developing phylogenies from 3-genomes

Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ, Moore G, Wolfe AD, dePamphilis CW.
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny.
Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13166-71.
PMID: 11069280      PubMed Abstract

Sequences studied for the paper:
http://depcla4.bio.psu.edu/basals/taxon.list.suppmaterial2.html

Support materials for the paper:
http://depcla4.bio.psu.edu/basals

The Barkman dataset:
Sequences in Fasta format

Chaw SM, Parkinson CL, Cheng Y, Vincent TM, Palmer JD.
Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4086-91.
PMID: 10760277     PubMed Abstrat

Chaw dataset:
Sequences in Fasta format

Popset:
http://www.ncbi.nlm.nih.gov:80/cgi-bin/Entrez/PopSet/wwwddv.cgi?gi=7546769

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.

Additional Resources

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)