Professor of Biostatistics and Computational Biology
Director, Center for Cancer Computational Biology
Dana-Farber Cancer Institute
Quackenbush’s route to a career in genomics has been, in a word, unconventional; the result of both redirection due to decreased funding for basic research in physics, as well as “being in the right place at the right time” to work instead on the Human Genome Project. Throughout his career, he has pioneered many advances in genomics and bioinformatics. His move to DFCI in 2005 fulfilled a youthful dream—a Harvard professorship—albeit in a very different field from his early fantasies.
One of Quackenbush's major accomplishments at DFCI has been to design and implement an “integrated clinical and research data warehouse.” This is a savvy way to merge information from multiple sources and make it readily accessible, while reducing human error and bypassing problems inherent in linking together different types of data. Oracle and InforSense, two software companies that promote the integration of information, played key roles in the success of this project.
Not long after the data warehouse came to life in 2008, Quackenbush was asked, “What’s next?” His reply: “I don’t know where this [integration system] will go next, to be honest, but it’s likely to go somewhere.” Two years later, “somewhere” definitely includes the LGRC, where he and Mick Correll are leading efforts to collect, manage, and analyze the data produced by the consortium and make it available to other scientists who are studying lung disease.
• Ph.D., theoretical particle physics, University of California, Los Angeles (UCLA, 1990).
• Postdoctoral Fellow, experimental high energy physics, UCLA (1990–1992).
• National Center for Human Genome Research SERCA Fellow, the Salk Institute (1992–1994), Stanford University (1994–1996), and The Institute for Genomic Research (TIGR, 1997).
• Investigator, TIGR (1997–2005).
• Professor of Biostatistics and Computational Biology, Dana-Farber Cancer Institute (DFCI); Professor of Cancer Biology, DFCI; and Professor of Computational Biology and Bioinformatics, Harvard School of Public Health (2005–present).
• Director, Center for Cancer Computational Biology, DFCI.
• Serves on the editorial boards of five major journals (including Editor-in-Chief at Genomics) and has served on numerous government review panels.
• More than 167 publications (as of April 2010).
The following select publications by Dr. Quackenbush relate to his work in the LGRC:
Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J. GeneSigDB—a curated database of gene expression signatures. Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25.
Chen DT, Nasir A, Culhane A, Venkataramu C, Fulp W, Rubio R, Wang T, Agrawal D, McCarthy SM, Gruidl M, Bloom G, Anderson T, White J, Quackenbush J, Yeatman T. Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Res Treat. 2010 Jan;119(2):335-46.
Antonescu C, Antonescu V, Sultana R, Quackenbush J. Using the DFCI gene index databases for biological discovery. Curr Protoc Bioinformatics. 2010 Mar;Chapter 1:Unit1.6.1-36.
Mar JC, Quackenbush J. Decomposition of gene expression state space trajectories. PLoS Comput Biol. 2009 Dec;5(12):e1000626.
Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009 May;41(5):553-62.
Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Brown P. Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clin Cancer Res. 2009 Oct 15;15(20):6327-40.
Djebbari A, Quackenbush J. Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol. 2008 Jul 4;2:57.
Walker JK, Ahumada A, Frank B, Gaspard R, Berman K, Quackenbush J, Schwarz DA. Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness. Am J Respir Cell Mol Biol. 2006 Jun;34(6):711-8.
Cook DN, Wang S, Wang Y, Howles GP, Whitehead GS, Berman KG, Church TD, Frank BC, Gaspard RM, Yu Y, Quackenbush J, Schwartz DA. Genetic regulation of endotoxin-induced airway disease. Genomics. 2004 Jun;83(6):961-9.
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinasavic A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.
As a preschooler, I was fascinated by road construction and its equipment, particularly the steamroller. I demanded that my family call me “Roadmaker” and would answer to nothing else. But once I started school, there was only one career for me: scientist. I loved watching television shows with scientist-type characters—the “Professor” on Gilligan’s Island, for one. And I loved the idea that science was the future.
I think “hero” is an overused word, and I don’t have any. But I do admire people like Richard Feynman and Carl Sagan—successful scientists who were equally good at communicating what they did to the broader public.
There’s nothing in science quite like discovering something new. It’s pretty close to what Neil Armstrong and Buzz Aldrin must have felt, being the first to walk on the moon. Only nobody will watch me on TV or remember most of my little “moon landings.”
The constant pursuit of funding. In the past few years, science has changed in that we are spending more of our time applying for grants and less time actually doing science.
On airplanes. For just a few hours—ignoring the can-of-sardines-like atmosphere—I’m free of disturbances, phone calls, or people knocking on my office door.
Nothing in the past; but I’d love to live long enough to see my first grandchild (who probably won’t be born for another 30 years) graduate from college and start life.
I’d play myself—and win the Oscar for best actor, to boot, before heading off to pick up my Nobel Prize!
Red Hot Chili Peppers (Greatest Hits); the Pixies (Death to the Pixies); Neil Young’s Live Rust, among others. If entertaining my four-year-old son, then it would be the soundtrack to Oh Brother, Where Art Thou?
I would spend an extra day each week playing with my son and that evening cooking a nice dinner for my wife.