Michael Waterman

Brief Biography

Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after 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 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 University of Montreal.

Michael Waterman was named a Guggenheim Fellow (1995). He is an elected member of the American Academy of Arts and Sciences (1995), the National Academy of Sciences (2001) and the National Academy of Engineering (2012). Also he is a elected Fellow of the American Association for the Advancement of Science (1990), Institute of Mathematical Statistics (1991), Society of Industrial and Applied Mathematics (2009) and International Society of Computational Biology (2009). In fall 2000 he became the first Fellow of Celera Genomics. Waterman received a Gairdner Foundation International Award (2002), the Friendship Award from the Chinese government (2013) and the Dan David Prize (2015). He is an elected Foreign Member of the French Académie des Sciences (2005) and the Chinese Academy of Sciences (2013). He received Doctor Philosophiae Honors Causia from Tel Aviv University (2011) and Southern Denmark University (2013).

During 2003-2008, Professor Waterman held a 5-year term as Faculty Master of Parkside International Residence College at USC. 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.

From May 2008 to May 2014, in addition to his USC appointment Michael Waterman became Chair Professor at Tsinghua University in Beijing.  He led a team of distinguished scientists which collectively worked to enhance Tsinghua's programs in bioinformatics and computational biology. Currently he is Cao Xingcheng Chair Professor at Tsinghua University and Distinguished Professor at Fudan University in Shanghai.

Michael Waterman is a founding editor of Journal of Computational Biology and is on the editorial board of several journals. He is the author of Introduction to Computational Biology: Maps, Sequences and Genomes and is a co-author of the text Computational Genome Analysis: An Introduction. Also with Istrail and Pevzner in 1997 he began the international conference Research in Computational Biology (RECOMB).

Professor Waterman works in the area of Computational Biology and Bioinformatics, 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. His paper with Idury in 1995 introduced the use of Eulerian and De Bruijn graphs for sequence assembly.

Statistical Issues of Sequence Comparison: Analysis by Position and Analysis by Pattern​


Comparison of DNA and protein sequences is often done by calculation of an optimal alignment between two sequences. This talk will briefly survey statistical issues for global and local alignment, including Smith-Waterman and BLAST. In the last few years analysis by pattern or word counts has become important. A careful analysis of the relevant count summaries is crucial to increasing the statistical power of this approach.​