 |
|
|
|
|
| Research |
|
|
Research projects being run on The Lattice Project Grid system are many and varied. This page lists them out and provides more information about each one.
- The Cummings Laboratory and others are using GARLI to infer evolutionary relationships based on DNA sequence data.
- The Edwards Laboratory is using the HMMPfam service to compute Pfam
assignments for all bacterial, plasmid, and virus protein sequences from
Swiss-Prot, TrEMBL, GenBank, RefSeq, and TIGR's CMR, plus an inclusive
set of all plausible Glimmer predictions from RefSeq bacterial genomes.
These protein sequences, and their Pfam assignments, are used in the
Rapid Microorganism Identification Database (www.RMIDb.org). The HMMPfam
service is also being used as a model for "data-heavy" bioinformatics
applications on the Lattice Grid infrastructure, a collaboration between
the Cummings and Edwards laboratories.
- N.J. Edwards and F. Pineda. Poster at ASMS (2006). Rapid Microorganism Identification Database (www.RMIDb.org), 2006.
- Dr. Catherine Dibble's Computational Laboratories
Group uses agent-based simulation models to study the geographic
spread of Avian Influenza across the United States, to quantify the
relative pandemic risk of US cities and determine optimal intervention
strategies. The Grid service being used is Complab.
-
Catherine Dibble, Stephen Wendel, and Kristofor Carle (University of Maryland). Simulating Pandemic Influenza Risks of U.S. Cities. In Proceedings of the 2007 Winter Simulation Conference, 2007.
- The Cummings Laboratory is using gsi to assess the performance of the statistic in a variety of situations.
- Maile Neel and Joanna Grand are using Marxan to quantify the effects of
poor and incomplete data on the ability to capture biological diversity
in nature reserves.
-
Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks.
Ecology Letters 10:364-374.
- The Laboratory of David Fushman runs protein:protein docking algorithms on Lattice. When driven by experimentally derived constraints, these will help in modeling the structures of large multi-subunit proteins, and the interactions of such proteins with various ligands. CNS is the featured Grid service in this project.
-
Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain. Mol Cell 18, 687-98 (2005).
- Floyd Reed and Holly Mortensen from the Laboratory of Sarah Tishkoff have run a number of MDIV and IM
simulations through The Lattice Project. These are studies in molecular
population genetics that seek to use DNA sequence polymorphism
to estimate the times of divergence and migration rates among
ethnically diverse human populations in Africa.
-
Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A., Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T. B., Ramakrishnan, U., Floyd A. Reed, F. A. & Mountain, J. L.
History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 24(10), 2180-2195 (2007).
NOTE: If you are a researcher using The Lattice Project for your work, please cite The Lattice Project in your papers and publications using these guidelines.
|
|
 |
