John Quackenbush - American Computational Biologist And Genome Scientist

John Quackenbush (born January 4, 1962) is an American computational biologist and genome scientist. He is the Professor of Biostatistics and Computational Biology, Professor of Cancer Biology at the Dana-Farber Cancer Institute (DFCI), as well as the director of its Center for Cancer Computational Biology (CCCB). Quackenbush also holds an appointment as Professor of Computational Biology and Bioinformatics in the Department of Biostatistics at the Harvard School of Public Health (HSPH).


A native of Mountain Top, Pennsylvania, Quackenbush attended Bishop Hoban High School in Wilkes Barre, graduating in 1979, after which he attended the California Institute of Technology, where he earned a bachelor’s degree in physics. He went on to earn a doctorate in theoretical particle physics from the University of California, Los Angeles (UCLA) in 1990.

After working two years as a postdoctoral fellow in physics, Quackenbush was awarded a Special Emphasis Research Career Award from the National Center for Human Genome Research (the predecessor of the National Human Genome Research Institute), and subsequently spent the next two years at the Salk Institute working on physical maps of human chromosome 11, followed by another two years at Stanford University developing new laboratory and computational strategies for sequencing the human genome.

In 1997, Quackenbush joined the faculty of The Institute for Genomic Research (TIGR) in Rockville, Maryland, where his focus began to shift to post-genomic applications, with an emphasis on microarray analysis. Using a combination of laboratory and computational approaches, Quackenbush and his group developed analytical methods based on the integration of data across domains to derive biological meaning from high-dimensional data.

In 2005, Quackenbush was appointed to his current positions at the Dana-Farber Cancer Institute (DFCI) and the Harvard School of Public Health. Four years later, he launched the DFCI’s Center for Cancer Computational Biology (CCCB), which he directs and which provides broad-based bioinformatics and computational biology support to the research community through a collaborative consulting model, and which also performs and analyzes large-scale second-generation DNA sequencing.

A leader in the fields of genomics and computational biology, Quackenbush’s current research focuses on the analysis of human cancer using systems biology-based approaches to understanding and modeling the biological networks that underlie disease. This has led him and his colleagues to make fundamental discoveries about the role that variation in gene expression plays in defining biological phenotypes.

In 2010, Quackenbush and his colleagues at DFCI's CCCB, together with investigators at National Jewish Health's Center for Genes, Environment and Health, University of Pittsburgh's, Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Boston University's, Section for Computational Biomedicine and the Pulmonary Center, and the University of Colorado Denver, Genomics Core Facility received an $11 million grant under the American Recovery and Reinvestment Act of 2009 to launch the Lung Genomics Research Consortium. This project, funded by the National Heart Lung and Blood Institute (NHLBI), will add genetic, genomic, and epigenetic data to a collection of clinical biological samples developed by the NHLBI's Lung Tissue Research Consortium. The consortium aims to use genomic technologies and advanced data-analysis tools on available patient lung-tissue samples to gain new insights into pulmonary disease and thus develop more effective, personalized treatments.

John Quackenbush discusses creating an information ecosystem for personalized genomic medicine. 2014 Bio-IT World Keynote, John Quackenbush, Ph.D., CEO, GenoSpace; Professor, Dana-Farber Cancer Institute and Harvard School of Public Health.