DNA Sequencing in the 21st Century: Algorithms and Estimation

2014 ISIT Plenary Lecture
DNA Sequencing in the 21st Century: Algorithms and Estimation
Michael S. Waterman
University of Southern California



The ability to produce DNA sequence has dramatically increased since the 2001 announcement of the human genome sequence. This lecture will survey a few of the algorithmic and statistical estimation issues in this area. The volume of raw sequence reads from which genomes must be estimated has caused a shift from the computational methods used in the Human Genome Project. Those methods have been used and improved since the mid 1970s. A new approach reduced computation time, but required much more memory. This result brought about new memory reduction techniques. At the same time, traditional sequence comparison methods used since the early 1970s have in part been replaced by so-called alignment-free methods.



Michael Waterman, PhD, University Professor, University of Southern California. Professor of Biological Sciences, Computer Science and Mathematics. Prof. Waterman also holds an Endowed Associates Chair at USC. Prior to his arrival at USC in 1982, Prof. Waterman held positions at Los Alamos National Laboratory and Idaho State University. He has a bachelor's degree in Mathematics from Oregon State University, and a PhD in Statistics and Probability from Michigan State University. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Arts and Sciences (1995), and was elected to the National Academy of Sciences (2001). Also, Prof. Waterman is a Fellow of the American Association for the Advancement of Science, Fellow of the Institute of Mathematical Statistics and Fellow of the Society of Industrial and Applied Mathematics. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at the University of Montreal. In fall 2000 he became the first Fellow of Celera Genomics. In 2002 he received a Gairdner Foundation International Award and in 2005 he was elected to the French Académie des Sciences.

During 2003-2008, Professor Waterman held a 5-year term as Faculty Master of Parkside International Residence College. PIRC is a residential college that is home to over 600 undergraduates and serves as a center for internationally oriented cultural, academic and social events. Beginning May 2008, in addition to his USC appointment, Michael Waterman became Chair Professor at Tsinghua University in Beijing. He leads a team of distinguished scientists who will collectively work to enhance Tsinghua's programs in bioinformatics and computational biology.

Professor Waterman works in the area of Computational Biology, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a founding editor of the Journal of Computational Biology, is on the editorial board of seven journals and the author of Introduction to Computational Biology: Maps, Sequences and Genomes and is a co-author of the text Computational Genome Analysis: An Introduction.