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Michael Molla, Ph.D.

Dr. Molla has 18 years of professional experience in computer science; 13 applying computer science to problems in biology and medicine. His focus is on computational analysis of large biomedical datasets, and his research makes use of machine learning and other computational methods to perform central tasks in high-throughput biology.

Dr. Molla began his career in bioinformatcs as an undergraduate with summer internships at the Roswell Park Cancer Institute and the National Library of Medicine.  He received his undergraduate degree from Brandeis University in December 1992 and went to work at IBM as a software engineer.  In 1997, having received two IBM informal awards for technical achievement, he left IBM to work at the MIT/Whitehead Institute Center for Genome Sequencing.  As a member of the center's sequencing informatics team, Dr. Molla designed and implemented algorithms and created custom software to support the rapid growth of the Human Genome Project and the first phase of what became the SNP Consortium project.  During this time, he also completed a Master of Engineering degree from the University of Colorado with classes taken at MIT.

In 1999, Dr. Molla left the Genome Center to complete a Ph.D. in computer science (with genetics minor) at the University of Wisconsin.  There he worked with his advisor, Jude Shavlik, my minor advisor Frederick Blattner, and Nimblegen Systems (now Roche Nimblegen) to apply machine-learning techniques to the design of gene chips and the interpretation of microarray data.  At the same time, he worked as a consultant for Nimblegen, helping to develop their bioinformatics capability as they grew from a small startup company into a leading gene-chip manufacturer.

Among Dr. Molla's algorithmic contributions to Nimblegen, he created a neural-network-based algorithm for designing gene-chip probes, a dynamic-programming approach to DNA copy-number segmentation and a method for SNP identification based on machine learning’s K-Nearest Neighbors algorithm.  He also helped to develop the method of directly selecting DNA for sequencing using a gene chip to capture the sequences.

From 2007 to 2010, Dr. Molla worked as a research fellow in the Biomedical Engineering Department of Boston University.  There he collaborated primarily with James Collins and Simon Kasif.  Dr. Molla helped to lead the first ever study of the complete human “repeatome”: all of the length-3 tandem-repeats in the human genome and supervised graduate students in ground-breaking studies of antibiotic resistance in bacteria.

Page last updated: July 24, 2014