Recent breakthroughs in the next-generation DNA sequencing fueled the genomics studies and revealed that some classical biological theories may be incomplete or even incorrect. I describe three controversial and hotly debated topics: Whole Genome Duplications, Random Breakage Model of Chromosome Evolution, and Mammalian Evolution, and three related challenging algorithmic problems: Genome Halving Problem, Breakpoint Re-Use Problem, and Ancestral Genome Reconstruction Problem. I further describe the Multi-Break Rearrangements framework that simplified analysis of these biological problems, led to efficient algorithmic solutions, and provided new evolutionary insights.

Second part of the presentation: http://www.slideshare.net/csclub/20101209-dnaseq-pevzner