John Quackenbush

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John Quackenbush
JohnQuackenbush.jpg
Born (1962-01-04) January 4, 1962 (age 53)
Kingston, Pennsylvania, United States
Institutions Harvard University
Dana-Farber Cancer Institute
Institute for Molecular Bioscience, (University of Queensland)
Alma mater California Institute of Technology (B.S.)
University of California, Los Angeles (Ph.D.)
Known for bioinformatics, computational biology, microarray analysis, genomics, functional genomics

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),[1][2][3] as well as the director of its Center for Cancer Computational Biology (CCCB).[4] 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).[5][6][7][8][9]

Education and early life[edit]

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.

Career and Research[edit]

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),[10] 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.[11]

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.[12][13] 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.

In 2011, Quackenbush published The Human Genome: Book of Essential Knowledge (Imagine Publishing, U.S.), which outlines the history, science, and implications behind the Human Genome Project. He was also awarded with a $4 million-dollar fellowship bestowed by Australia's National Health and Medical Research Council to study chemotherapy resistant ovarian cancers in collaboration with colleagues at the University of Queensland's Institute for Molecular Bioscience.[14]

Quackenbush currently serves on the editorial boards of five major journals and is editor-in-chief at Genomics. He has served on several committees at the National Academies and the Institute of Medicine, including the Committee on Validation of Toxicogenomic Technologies: A Focus on Chemical Classification Strategies,[15][16] the Panel on Collecting, Storing, Accessing, and Protecting Biological Specimens and Biodata Social Science Surveys,[17] and the Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials.[18] He is currently a member of scientific advisory boards at St. Jude Children’s Research Hospital, at the Lovelace Respiratory Research Institute, The Hope Funds for Cancer Research. and for the National Institute for Health's Roadmap Epigenomics Project. Quackenbush is also a member of the scientific advisory boards of a number of biotech and precision medicine companies, including Caris Life Sciences, SynapDx, Perthera, and NABsys.

In 2012, Quackenbush, along with partner Mick Correll, founded GenoSpace, a software company focused on developing tools to enable precision genomic medicine. In the summer of 2013, Quackenbush was honored as a White House Open Science Champion of Change.

Awards and honors[edit]

Publications[edit]

Books[edit]

  • Author, The Human Genome: Book of Essential Knowledge (Imagine Publishing, U.S., 2011)
  • Contributor, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (Wiley Interscience, 2004)
  • Coauthor, Microarray Gene Expression Data Analysis: A Beginner's Guide (Wiley-Blackwell, 2003)

Journals[edit]

His research has been widely published in peer reviewed scientific journals.[1][19][20][21][22][23][24][25][26][27][28][29]

References[edit]

  1. ^ a b John Quackenbush's publications indexed by Google Scholar, a free service provided by Google
  2. ^ John Quackenbush's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  3. ^ "Researcher Profile, John Quackenbush, PhD". Dana Farber Cancer Institute. Archived from the original on 2015-04-07. 
  4. ^ "Computational Biology and Functional Genomics Laboratory - John Quackenbush". Harvard University. Archived from the original on 2015-01-25. 
  5. ^ "John Quackenbush, Harvard School of Public Health Bio". Harvard University. Archived from the original on 2011-02-25. 
  6. ^ Bateman, A; Quackenbush, J (2009). "Bioinformatics for next generation sequencing". Bioinformatics 25 (4): 429. doi:10.1093/bioinformatics/btp037. PMID 19202193. 
  7. ^ Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H.; Yamanaka, I.; Kiyosawa, H.; Yagi, K.; Tomaru, Y.; Hasegawa, Y.; Nogami, A.; Schönbach, C.; Gojobori, T.; Baldarelli, R.; Hill, D. P.; Bult, C.; Hume, D. A.; Quackenbush, J.; Schriml, L. M.; Kanapin, A.; Matsuda, H.; Batalov, S.; Beisel, K. W.; Blake, J. A.; Bradt, D. (2002). "Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs". Nature 420 (6915): 563–573. doi:10.1038/nature01266. PMID 12466851. 
  8. ^ Fantom, Consortium; Suzuki, H; Forrest, A. R.; Van Nimwegen, E; Daub, C. O.; Balwierz, P. J.; Irvine, K. M.; Lassmann, T; Ravasi, T; Hasegawa, Y; De Hoon, M. J.; Katayama, S; Schroder, K; Carninci, P; Tomaru, Y; Kanamori-Katayama, M; Kubosaki, A; Akalin, A; Ando, Y; Arner, E; Asada, M; Asahara, H; Bailey, T; Bajic, V. B.; Bauer, D; Beckhouse, A. G.; Bertin, N; Björkegren, J; Brombacher, F et al. (2009). "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line". Nature Genetics 41 (5): 553–62. doi:10.1038/ng.375. PMID 19377474. 
  9. ^ Carninci, P; Kasukawa, T; Katayama, S; Gough, J; Frith, M. C.; Maeda, N; Oyama, R; Ravasi, T; Lenhard, B; Wells, C; Kodzius, R; Shimokawa, K; Bajic, V. B.; Brenner, S. E.; Batalov, S; Forrest, A. R.; Zavolan, M; Davis, M. J.; Wilming, L. G.; Aidinis, V; Allen, J. E.; Ambesi-Impiombato, A; Apweiler, R; Aturaliya, R. N.; Bailey, T. L.; Bansal, M; Baxter, L; Beisel, K. W.; Bersano, T et al. (2005). "The transcriptional landscape of the mammalian genome". Science 309 (5740): 1559–63. doi:10.1126/science.1112014. PMID 16141072. 
  10. ^ Dublin, Matthew. "Dana-Farber, Quackenbush Launch Analysis Consultancy Center | Genome Technology | Informatics". GenomeWeb. Retrieved 2012-05-07. 
  11. ^ "Integrating Clinical and Genomics Data". Bio-IT World. Retrieved 2012-05-07. 
  12. ^ "John Quackenbush, Lung Genomics Research Consortium Investigator Bio". lung-genomics.org. Archived from the original on 2012-03-19. 
  13. ^ "Lung Genomics Research Consortium Launches Website". National Jewish Organization. Retrieved 2013-04-04. 
  14. ^ "Industry-News.net - Home". Biotechnologynews.net. Retrieved 2012-05-07. 
  15. ^ "Validation of Toxicogenomic Technologies". National Academies Press. Retrieved 2013-04-04. 
  16. ^ "Validation of Toxicogenomic Technologies". National Academies Press. Retrieved 2013-04-04. 
  17. ^ "Conducting Biosocial Surveys: Collecting, Storing, Accessing, and Protecting Biospecimens and Biodata". National Academies Press. Retrieved 2013-04-04. 
  18. ^ "Evolution of Translational Omics". National Academies Press. Retrieved 2013-04-04. 
  19. ^ Mar, J. C.; Wells, C. A.; Quackenbush, J. (2011). "Defining an informativeness metric for clustering gene expression data". Bioinformatics 27 (8): 1094–1100. doi:10.1093/bioinformatics/btr074. PMC 3072547. PMID 21330289. 
  20. ^ Culhane, A. C.; Schwarzl, T.; Sultana, R.; Picard, K. C.; Picard, S. C.; Lu, T. H.; Franklin, K. R.; French, S. J.; Papenhausen, G.; Correll, M.; Quackenbush, J. (2009). "GeneSigDB--a curated database of gene expression signatures". Nucleic Acids Research 38 (Database issue): D716–D725. doi:10.1093/nar/gkp1015. PMC 2808880. PMID 19934259. 
  21. ^ Mar, J. C.; Quackenbush, J. (2009). Papin, Jason A., ed. "Decomposition of Gene Expression State Space Trajectories". PLoS Computational Biology 5 (12): e1000626. doi:10.1371/journal.pcbi.1000626. PMC 2791157. PMID 20041215. 
  22. ^ Djebbari, A.; Quackenbush, J. (2008). "Seeded Bayesian Networks: Constructing genetic networks from microarray data". BMC Systems Biology 2: 57. doi:10.1186/1752-0509-2-57. PMC 2474592. PMID 18601736. 
  23. ^ Mar, J. C.; Rubio, R.; Quackenbush, J. (2006). "Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples". Genome Biology 7 (12): R119. doi:10.1186/gb-2006-7-12-r119. PMC 1794432. PMID 17169148.  open access publication - free to read
  24. ^ Larkin, J. E.; Frank, B. C.; Gavras, H.; Sultana, R.; Quackenbush, J. (2005). "Independence and reproducibility across microarray platforms". Nature Methods 2 (5): 337–344. doi:10.1038/nmeth757. PMID 15846360. 
  25. ^ Eschrich, S.; Yang, I.; Bloom, G.; Kwong, K.; Boulware, D.; Cantor, A.; Coppola, D.; Kruhøffer, M.; Aaltonen, L.; Orntoft, T. F.; Quackenbush, J.; Yeatman, T. J. (2005). "Molecular Staging for Survival Prediction of Colorectal Cancer Patients". Journal of Clinical Oncology 23 (15): 3526–3535. doi:10.1200/JCO.2005.00.695. PMID 15908663. 
  26. ^ Whitelaw, C. A.; Barbazuk, W.; Pertea, G.; Chan, A.; Cheung, F.; Lee, Y.; Zheng, L.; Van Heeringen, S.; Karamycheva, S.; Bennetzen, J. L.; Sanmiguel, P.; Lakey, N.; Bedell, J.; Yuan, Y.; Budiman, M. A.; Resnick, A.; Van Aken, S.; Utterback, T.; Riedmuller, S.; Williams, M.; Feldblyum, T.; Schubert, K.; Beachy, R.; Fraser, C. M.; Quackenbush, J. (2003). "Enrichment of Gene-Coding Sequences in Maize by Genome Filtration". Science 302 (5653): 2118–2120. doi:10.1126/science.1090047. PMID 14684821. 
  27. ^ Saeed, A.; 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.; Vinsavich, A.; Trush, V.; Quackenbush, J. (2003). "TM4: A free, open-source system for microarray data management and analysis". BioTechniques 34 (2): 374–378. PMID 12613259. 
  28. ^ Brazma, A.; Hingamp, P.; Quackenbush, J.; Sherlock, G.; Spellman, P.; Stoeckert, C.; Aach, J.; Ansorge, W.; Ball, C. A.; Causton, H. C.; Gaasterland, T.; Glenisson, P.; Holstege, F. C. P.; Kim, I. F.; Markowitz, V.; Matese, J. C.; Parkinson, H.; Robinson, A.; Sarkans, U.; Schulze-Kremer, S.; Stewart, J.; Taylor, R.; Vilo, J.; Vingron, M. (2001). "Minimum information about a microarray experiment (MIAME)-toward standards for microarray data". Nature Genetics 29 (4): 365–371. doi:10.1038/ng1201-365. PMID 11726920. 
  29. ^ Dublin, Matthew (1 June 2009), "Dana Farber, Quackenbush Launch Analysis Consultancy Center", GenomeWeb, retrieved 18 May 2011