Predoctoral Trainee

Aaron Darling Computer Sciences Doctoral Training Program Dept. of Computer Sciences Faculty Supervisor: Nicole Perna Email: darling@cs.wisc.edu Computer Sciences web page: http://www.cs.wisc.edu/~darling/ 262-1273

Recent advances in DNA sequencing technology are yielding the entire genomic DNA sequences of many organisms. My research focuses on developing computational methods and tools for simultaneously comparing several genomes of related organisms. A comparison identifies homologous regions in all organisms under study as well as regions unique to subsets of the organisms. Points of recombination in each chromosome are also identified. The detailed comparison of genetic structure produced by these techniques creates a basis for further scientific insight into gene function, evolution, and population genomics.

CV

CV (.pdf format)

Publications

Darling ACE, Mau B, Blattner FR and Perna NT (2004). Mauve: Multiple Alignment of Conserved Genomic Sequence with Rearrangements. Genome Research, in press.

Darling AE, Mau B, Blattner FR and Perna NT (2004). GRIL: genome rearrangement and inversion locator. Bioinformatics 20(1): 122-4.

Darling AE, Carey L, and Feng W (2003). The Design, Implementation, and Performance of mpiBLAST. Proceedings of ClusterWorld Conference and Expo 2003, in press. NOTE: The mpiBLAST paper was selected for a 'best paper' award at ClusterWorld.

Darling AE, Mau B, Blattner FR, and Perna NT. Mauve: Multiple Genome Alignment. Presented at ISMB 2002, August 3-7th 2002, Edmonton AB.

Darling AE and Feng W. BLASTing away with Green Destiny. Presented at CSB2002, August 15th 2002, Palo Alto, CA.

Darling AE, Mau B, Blattner FR, and Perna NT. Mauve: Multiple Genome Alignment, Presented at the Lake Arrowhead Small Genomes Conference, September 2002, Lake Arrowhead, CA.

Darling AE and Feng W. mpiBLAST: Parallelization of BLAST for Computational Clusters, Presented at Supercomputing 2002, November 19-22nd, Baltimore, MD.

Darling AE, Carey L, and Feng W. mpiBLAST: Delivering Super-linear Speedup with an Open-Source parallelization of BLAST, Presented at Pacific Symposium on Biocomputing 2003. January 3-7th 2003, Kauai, HI.

Darling AE, Englehart A, and Feng W. An Open-Source Parallelization of BLAST. Presented at O'Reilly Bioinformatics Technology Conference (BioCon) 2003, February 2nd-4th 2003, San Diego, CA.

Glasner JD, Liss P, Plunkett III G, Darling AE, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, and Perna NT. ASAP, a systematic annotation package for community analysis of genomes. Nucl. Acids. Res., 31: 147-151, 2003.

Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett III G, Rose DJ, Darling AE, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, Schwartz DC, and Blattner FR. Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T. Infect. Immun. 71:2775-2786, 2003.

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File last modified: August 13, 2003
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