Mihai's homepage

Curriculum Vitae
Commentary on Open-Access/Open-Source

Research interests

Genome assembly
Metagenomics: sequencing of organisms directly from an environment (without culturing).
Novel sequencing technologies and their impact on assembly and analysis
Development of algorithms for pathogen detection. Project sponsored by the Homeland Security Advanced Research Projects Agency.
High throughput genome finishing.
Systems biology. Under this broad category I am particularly interested in leveraging the information obtained through environmental sequencing to understand the interactions between organisms within an environment as well as the interactions between a community of organisms and their host (e.g. interactions between oral bacteria and the human mouth)

E. Ghedin et al. Draft genome of the filarial nematode parasite Brugia malayi. Science 317 :1756-1760, 2007.
Clark, A. G., M. B. Eisen, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18, 2007.
D.D. Sommer, A.L. Delcher, S.L. Salzberg, M. Pop. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics, 8:64, 2007.
S.R. Gill, M. Pop, R.T. DeBoy, P. Eckburg, I. Hance, B. Samuel, J. Gordon, D. Relman, C.M. Fraser, K.E. Nelson. Metagenomic analysis of the human distal gut microbiome. Science 312, pp. 1355-1359, 2006
S.L. Salzberg, J.D. Hotopp, A.L. Delcher, M. Pop, M.B. Eisen, W.C. Nelson. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology 6(3), pp. R23, 2005
M. Pop, A. Phillippy, A.L. Delcher and S.L. Salzberg. Comparative genome assembly. Briefings in Bioinformatics. 5(3), pp. 237-248, 2004.
M. Pop. Shotgun sequence assembly. Advances in Computers vol. 60, M. Zelkowitz ed. pp. 193-248, June 2004.
M. Pop, S. L. Salzberg, M. Shumway. Genome Sequence Assembly: Algorithms and Issues. IEEE Computer 35(7) 2002, pp. 47-54. Copyright 2002 IEEE. Reproduced with permission from IEEE.
T.D. Read, S.L.Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. Busch, K.L. Smith, J.M. Schupp, D. Solomon, P. Keim, C.M. Fraser. Comparative genome sequencing as a method for discovery of novel polymorphisms in Bacillus anthracis. Science 296, pp. 2028-2033, 2002