The trend towards very large DNA sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NP-hard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates and list a series of alternate solutions in the event that several appear equally good. Moreover it uses a limited form ...

Research article Genetic association study of selected candidate genes (ApoB, LPL, Leptin) and telomere length in obese and hypertensive individuals

My family iii lowed me to clarify several important aspects of the thesis for the general reader. I thank Professor Michael Schatz for making sure that the theoretical framework presented in the dissertation was correctly presented and related to the relevant prior art extensively. I also express my thanks to Professor Alan Siegel for improving the presentation and stile of the thesis. He has been not just a scientific mentor but also a tutoring figure in virtue of his high commitment to the value of education. Finally, I would like to thank Professor Raul Rabadan for suggesting many areas of application of the tools developed in this thesis. One of the contributions of the dissertation (TotalReCaller) is the result of the joint work with Fabian Menges. I am particularly grateful to him for such collaboration as well as for all the valuable and energetic discussions that we had on many of the topics presented in this thesis. I also would like to thank all the members of the NYU Bioinformatics Group for creating a unique and