CURRICULUM VITAE
`
`Name: John Quackenbush, Ph.D.
`
`Date: November 14, 2022
`
`Office Address: Department of Biostatistics, 677 Huntington Avenue, Building II,
`Room 421, Boston, MA 02115
`
`Home Address: 86 Walpole Street, Dover, MA 02030, USA
`
`Work e-mail: johnq@hsph.harvard.edu
`
`Work Phone: +1.617.432.9028
`
`Work FAX +1.617.432.5619
`
`Mobile Phone: +1.301.526.1740
`
`Date & Place of Birth: January 4, 1962 Kingston, PA, USA
`
`Education:
`
`1983 Physics
`
`California Institute of Technology,
`Pasadena, CA
`M.S. University of California, Los Angeles, CA
`1984 Physics
`1990 Theoretical Particle Physics Ph.D. University of California, Los Angeles, CA
`
`B.S.
`
`Postdoctoral Training:
`
`1990-1992
`
`Postdoctoral Fellow, Experimental Particle Physics,
`University of California, Los Angeles, CA
`
`1992-1994
`
`Staff Scientist, Molecular Genetics and Genomics,
`The Salk Institute for Biological Studies, La Jolla, CA
`
`1994-1996
`
`Research Associate, Genomics and Bioinformatics,
`Stanford Human Genome Center, Palo Alto, CA
`
`Academic Appointments:
`
`2018- present Henry Pickering Walcott Professor of Computational Biology and
`Bioinformatics; Chair, Department of Biostatistics; Director, Harvard
`Health Data Science Center, Harvard TH Chan School of Public Health
`Research Activities: Development of methods in network medicine and
`systems biology aimed at understanding the multifactorial drivers of
`human health and disease, identifying disease subtypes and new
`therapeutic interventions, and exploring differences between the sexes in
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`disease etiology and response to therapy; development of open-source
`software tools supporting research and clinical applications.
`Activities: Founding Director/Co-Director, SM Program in
`Computational Biology and Quantitative Genetics (CBQG); Director,
`BD2K T32 Training Grant; Director T32 Cancer Training Grant;
`Founding Co-Director and Executive Committee, Joint Biostatistics and
`Bioinformatics T32 Training Grant; Director, Harvard Quantitative
`Biomedical Research Center.
`
`2005- present Professor of Biostatistics and Computational Biology,
`Department of Data Science, Division of Computational Biology,
`Dana-Farber Cancer Institute;
`Professor of Cancer Biology, Department of Cancer Biology,
`Dana-Farber Cancer Institute
`Research Activities: Application of genomic technologies and
`integrative computational analysis to model cellular systems with an
`emphasis on understanding of human cancers and other diseases;
`development of open-source software tools supporting research and
`clinical applications.
`
`2005- 2018
`
`2008- 2018
`
`Professor of Computational Biology and Bioinformatics,
`Department of Biostatistics, Harvard TH Chan School of Public Health
`Research Activities: Application of genomic technologies and
`integrative computational analysis to model cellular systems with an
`emphasis on understanding of human cancers and other diseases;
`development of open-source software tools supporting research and
`clinical applications.
`Activities: Founding Director, SM Program in Computational Biology
`and Quantitative Genetics (CBQG); Director, BD2K T32 Training
`Grant; Founding Co-Director and Executive Committee, Joint
`Biostatistics and Bioinformatics T32 Training Grant.
`
`Director, Canter for Cancer Computational Biology,
`Dana-Farber Cancer Institute
`Research Activities: Integrative approaches to data analysis focused on
`clinical and translational applications and linking clinical and laboratory
`data in support of basic research; creation of software tools and systems
`to support research; overall analytical support for investigative research
`activities for all Dana-Farber Investigators.
`
`2007 – present Adjunct Professor of Bioinformatics, Boston University
`Activities: Mentoring PhD student thesis research.
`
`2003- 2005
`
`Professor, Chemical Engineering, University of Maryland
`Activities: Mentoring PhD student thesis research.
`
`2002 - 2006
`
` Investigator, The Institute for Genomic Research
`Research Activities: Development and implementation of technology
`and strategies, including computational methods and software tools,
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`necessary for functional analysis of the human and other genomes.
`Analysis of human gene expression in colon tumors using microarrays,
`rodent models of heart, lung, blood and sleep disorders and gene
`expression in Arabidopsis. Director of the TIGR Gene Index Project,
`providing freely available databases and software to estimate gene
`content in more than 100 organisms.
`
`2000- 2005
`
`Professor, Department of Biochemistry,
`The George Washington University
`Activities: Instructor in various courses, curriculum committee for
`Genomics.
`
`1998 – 2005 Lecturer, The Department of Biostatistics,
`The Johns Hopkins University
`Activities: Instructor in the Masters In Biotechnology Program
`
`1997 - 2001 Associate Investigator, The Institute for Genomic Research
`Research Activities: Development and implementation of technology
`and strategies, including computational methods and software tools,
`necessary for functional analysis of the human and other genomes.
`Analysis of human gene expression in colon tumors using microarrays,
`rodent models of heart, lung, blood and sleep disorders and gene
`expression in Arabidopsis. Director of the TIGR Gene Index Project,
`providing freely available databases and software to estimate gene
`content in more than 50 organisms.
`
`1997
`
`Assistant Investigator, The Institute for Genomic Research
`Research Activities: Development and implementation of technology and
`strategies, including analytical methods and software tools, necessary for
`functional analysis of the human and other genomes.
`
`1994 - 1997 Research Associate, Stanford Human Genome Center
`Stanford University
`Research Activities: Project leader for development and implementation
`of a transposon-mediated strategy for large-scale genomic DNA
`sequencing including development and implementation of laboratory
`protocols, analytical methods, computer software, and instrumentation.
`Mapping, sequencing, and annotating regions of human chromosomes 4
`and 21.
`
`1992 - 1994 Staff Scientist, The Salk Institute for Biological Studies
`Research Activities: Development of improved methods for DNA
`sequencing, combinatoric strategies and devices for screening large
`libraries, simulation and optimization of single pass sequencing
`strategies including genome sequence sampling. Project director for the
`STS content mapping of chromosome 11. Development of methods and
`software tools to support genome mapping.
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`John Quackenbush
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`1990 - 1992 Postdoctoral Fellow, Department of Physics
`University of California, Los Angeles
`Research Activities: Research in particle physics, field theory and
`phenomenology. Founding member of the Antiproton Experiment
`(APEX) collaboration that set the world’s best experimental limit on the
`lifetime of the antiproton.
`
`1987 - 1992 Visiting Lecturer, Department of Physics
`University of California, Los Angeles
`
`1984 - 1996 Physics Instructor, Southern California Science Institute
`New College of California
`
`1983 – 1990 Teaching Fellow, Department of Physics
`University of California, Los Angeles
`
`1983 - 1990 Research Fellow, Department of Physics
`University of California, Los Angeles
`Thesis Supervisor: E.T. Tomboulis
`Research Activities: Research in elementary particle physics,
`mathematical physics, field theory focusing on the development of two-
`dimensional gauge field theory models and the construction of
`associated string theory models.
`
`Nonacademic Employment
`
`2011-2014
`
`2014-2017
`
`Co-Founder, CEO and Board Chairman, Genospace LLC
`Activities: Genospace provides software solutions to operationalize
`precision medicine through the integration of clinical and genomic data
`and its presentation to clinical and research users in an intuitive format.
`
`Co-Founder and Board Chairman, Genospace LLC
`Activities: Genospace provides software solutions to operationalize
`precision medicine through the integration of clinical and genomic data
`and its presentation to clinical and research users in an intuitive format.
`In January 2017, Genospace was sold to the Hospital Corporation of
`America to support research and to acquire our world-leading solution
`for clinical trials matching.
`
`Hospital or Affiliated Institution Appointments:
`
`2003 – 2005 Adjunct Professor, Department of Biostatistics
`Bloomberg School of Public Health, The Johns Hopkins University
`
`
`2005- present Professor, Department of Biostatistics and Computational Biology
`Dana-Farber Cancer Institute
`
`
`2014- present Professor, Channing Division of Network Medicine, Brigham and
`Women’s Hospital
`
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`Hospital and Health Care Organization Service Responsibilities:
`
`John Quackenbush
`
`2005- present Primary research areas are computational and system biology focused on
`the integration of diverse data types to provide insight into biological
`processes that drive human disease phenotypes.
`Department of Data Science, Division of Computational Biology,
`Dana-Farber Cancer Institute
`
`
`2014- present Research at the interface of systems biology and pulmonary disease,
`exploration of how sex and gender affect disease risk, development of
`methods to better handle sex differences in systems approaches, and
`advising faculty in their research and the Director in setting directions
`for future work.
`Channing Division of Network Medicine, Brigham and Women’s
`Hospital
`
`
`
`Major Committee Assignments:
`
`1998
`1998
`1998
`
`National Laboratory Genome Project Visit Review Panel, DOE
`1994
`Caltech/BAC Library Construction Site Visit Review Panel, DOE
`1995
`Bioinformatics Grant Review Panel, DOE
`1996-1998
`1997-2001 Grant Review Panel, DOE
`1997
`Hollander Fellowship Review Panel, DOE
`1997
`Five-Year Program Advisory Committee, NCRR
`1997
`Cancer Chromosome Anatomy Project program Steering Committee, NCI
`1998
`National Laboratory Functional Genomic Review Panel, DOE
`1998
`Full-Length cDNA Library Construction and Sequencing Advisory,
`Committee, NCI
`Functional Genomics Panel, Welcome Trust
`Genomics Grant Review Panel, NSF SBIR
`Special Program in Tropical Disease Research Review, UNDP/World
`Bank/WHO
`Low-Dosage radiation Grant Review Panel, DOE
`1999-2000
`Bioinformatics Review Panel, NSF
`1999
`Special Emphasis Review Panel, NHLBI
`1999
`Microarray Working Group Advisory Panel, NIDCR
`1999
`Special Emphasis Review Panel, NIMH
`1999
`Plant Biology Review Panel, NSF
`1999
`Board of Directors, MGED
`1999-2007
`Grant Review Panel, NIDA SBIR
`2000
`Plant Biology Review Panel, USDA
`2000
`Plant Biology Review Panel, NSF
`2000
`Exceptional Chromosome Regions Working Group, DOE
`2000
`Working Group on US Scientific Interactions, NSF
`2000
`2000-2006 Genome/GCAT study section, NIH
`2000-2003
`PGA Coordinating Committee, HHLBI
`2000-2003
`PGA Bioinformatics Committee, NHLBI
`
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`2000-2003
`2000
`2001
`
`PGA Microarray Committee, NHLBI
`Working Group on Australia Scientific Interactions, NSF
`Review Meeting RFP ES-01-01 National Center for Toxicogenomics
`(NCT) Microarray Resource, HIEHS
`Plant Genome Scientific Advisory Board, University of Georgia
`2001-2003
`Innovative Technology Review Panel, NCI
`2001-2003
`2001-2002 Genome Study Section, NIH
`2002-2006 GCAT Study Section, NIH
`2001
`Bioinformatics in Neuroscience and Sleep Research Workshop, NIDDK
`2001
`Plant Genome Site Visit Panel, NSF
`2001-2003
`BISTI Review Panel, NIH
`2001-2005 Grant Review Panel, NCI
`2002
`Microarray Supplement Review Panel, NHLBI
`2002-2006
`Panel on Emerging Issues in Toxicogenomics, NRC
`2004-2006
`Panel on Applications of Toxicogenomics, NRC
`2003-2010 Genome British Columbia Scientific Advisory Board
`2005-2014
`EPA Board of Scientific Counselors
`2005-2011
`St. Jude’s Children’s Research Hospital Scientific Advisory Board
`2006-2007 Harvard School of Public Health, Lefkopoulou Award Committee
`Member
`Dana Farber Cancer Institute, Computational Biology Search Chair
`2006
`EU FP6 Grant Review Panel
`2005
`2006-2007 Harvard School of Public Health, Seminar Committee Member
`2006-2019 Harvard School of Public Health, Curriculum Committee Member
`2006-2009 Harvard School of Public Health, Computational Biology Search Chair
`2007-present EU FP7 Genomics Grant Review Panel
`2008-present Lovelace Respiratory Research Institute, Scientific Advisory Board
`2008-2010 NAS Panel on Collecting, Storing, and Distributing Biodata linked to
`Social Science Surveys
`RC1 Grant Review “Editorial Review” Panel
`2009
`RC2 Genomic Science Grant Review
`2009
`Epigenomics Roadmap Grant Review Panel
`2009
`Epigenomics Roadmap Advisory Board
`2009-2014
`NCI EUREKA Grant Review Panel
`2010
`Chair, NCRR S10 Grant Review Panel
`2010
`NASA ISS Genomic Applications Study Section
`2016
`NASA Human Research Program Long-Duration Flight Advisory Panel
`2019
`21st Century Cures Act Biomarker Advisory Group
`2016
`Research Oversight Committed, Genome British Columbia
`2012-2019
`2014-present Shriner’s Hospital standing review panel
`2005-present Various NIH grant review panels, either as an ad hoc member or as an ad
`hoc reviewer. I typically serve on at least six per year and can provide a
`more detailed list on request.
`2005-present Various EU and Canadian grant review panels, either as an ad hoc
`member or as an ad hoc reviewer. I can assemble a detailed list on request.
`2017-present Research Foundation Flanders (FWO) standing review panel.
`2018-present Chair, Department of Biostatistics, Harvard T.H. Chan School of Public
`Health
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`John Quackenbush
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`Nonacademic Board and Advisory Board Positions (active or past five years):
`
`2005-2016 Nabsys Inc., Scientific Advisory Board
`2010-2017
`Lovelace Respiratory Research Institute, Scientific Advisory Board
`2012-2016
`SynapDx, Scientific Advisory Board
`2012-2017 Genospace LLC, Founder, CEO, Board of Directors; Chairman of the
`Board
`Blueprint Genomics, Scientific Advisory Board
`2012-2020
`Thomson-Reuters, Genomics Advisory Board
`2013-2017
`2013-present Caris Life Sciences, Scientific Advisory Board
`2020-present Caris Life Sciences, Data Science Advisory Board
`2014-present Shriner’s Hospitals, Scientific Advisory Board
`2014-present Olema Pharmaceuticals, Scientific Advisory Board
`2015-present Haymakers for Hope, Board of Directors
`2015-present Lacriscience, Scientific Advisory Board
`2017-present Merck KGaA, Precision Medicine Advisory Board
`2018-present Renalytix AI, Advisory Board
`2018-present Dover, MA, Capital Budget Committee
`2019-present StitchBio, Scientific Advisory Board
`2020-present Charles River School Health and Safety Committee (COVID Advisory
`Board)
`2020-present Boston University Academy Health and Safety Committee (COVID
`Advisory Board)
`2021-present Dover, MA, Board of Health Special Advisor
`2021-present Congreso Futuro International Advisory Board, Chile
`
`
`Professional Societies:
`
`Member
`Member
`Member
`Member
`Member
`
`1988 American Physical Society
`1988 APS Biophysics Division
`1988 APS International Physics Group
`1988 APS Division of Particles and Fields
`1988 World Federation of Scientists
`1990 Microarray Gene Expression Data Society (MGED)/
`Member
`Functional Genomics Data Society (FGED)
`Board Member
`
`President
`(2011-2014)
`Member
`1995 The Human Genome Organization (HUGO)
`Member
`1996 Association of Science Professionals (ASP)
`1998 American Association for the Advancement of Science (AAAS) Member
`1999 Center for the Study of the Evolution of Life (CSEOL)
`Member
`2005 American Association for Cancer Research
`Member
`
`Community Service Related to Professional Work:
`
`I have presented more than 350 talks, courses, and workshops since joining Dana-Farber
`and the Harvard T.H. Chan School of Public Health in 2005; detailed lists will be
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`provided upon request. I have also taught numerous courses and workshops on the
`analysis of genomic data and have served as an organizer of the EMBO course on DNA
`microarray analysis for more than five years.
`
`In addition, I have served on the Scientific Advisory Board of the St. Jude’s Children’s
`Research Hospital, the Scientific Advisory Board for the Lovelace Respiratory Research
`Institute, Research Oversight Committees for various Genome Canada programs, and the
`Board of Scientific Counselors of the Environmental Protection Agency. I have also been
`a member of advisory boards for a number of NIH initiatives, including the Roadmap
`Epigenome Project, the Extracellular RNA Communication Consortium, the Atopic
`Dermatitis Research Network (ADRN), and the Trans-Omics for Precision Medicine
`(TOPMed) program.
`
`Since the onset of the COVID19 pandemic, I have served numerous local school and
`community groups by advising these on policy and practice. I am particularly proud that
`the two schools I advised instituted a series of policies addressing air quality, masking,
`distancing, hygiene, and vaccination that allowed them to remain open without any
`documented cases of in-school transmission during the 2020-2021 and 2021-2022
`academic years. I have also become a special advisor to the Dover, MA Board of Health
`and provide advice to the Dover-Sherborn Regional School District on COVID and other
`heath-related matters.
`
`(Peer Review for Scientific Journals)
`
`1994-2016 Genomics
`1994-2009
`BioTechniques
`1996-2010 Genome Research
`2000-2010 Genome Biology
`1997-1998
`Analytical Biochemistry
`1997-present Nature
`1997-2010
`Nucleic Acids Research
`1999-2010
`Nature Genetics
`1999-2009
`EMBO Reports
`1999-2017
`Nature Biotechnology
`1999-present Science
`2000-2016
`Bioinformatics
`2000-2009
`Journal of Theoretical Biology
`2000-2009 Mammalian Genomics
`2000-2006 Gene
`2000-2016
`BMC Genomics, BMC Bioinformatics
`2001-2009
`Structural and Functional Genomics
`2001-2010
`Nature Reviews Genetics
`2001-2006
`American Journal of Applied Statistics
`2009-present PLoS Computational Biology
`2015-present Proceedings of the National Academy of Sciences
`2017-present Molecular Systems Biology
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`Editorial Boards:
`
`Editorial Board
`2000-2009
`2000-2012 Associate Editor
`2000-present Editorial Board
`2000-2006
`Editorial Board
`2006-2017
`Editor-in-Chief
`2018-present Editorial Board
`2022-present Editorial Board
`
`Awards and Honors:
`
`BioTechniques
`Bioinformatics
`BMC Genomics
`Genomics
`Genomics
`Cancer Research
`GEN Biotechnology
`
`1987
`
`1987
`
`2007
`
`2007
`2007
`
`2008
`2010
`2010
`
`2010
`2010
`
`1985 - 1991 Outstanding Teaching Award (7), UCLA Physics Department
`Jun John Sakurai Scholarship, 24th International School of
`1986
`Subnuclear Physics, Ettore Majorana Centre for Scientific Culture,
`Erice, Italy
`UCLA Distinguished Teaching Assistant Award, UCLA Academic
`Senate
`Prize for Best Student and Prize for Best Scientific Secretary,
`25th International School of Subnuclear Physics, Ettore Majorana Centre
`for Scientific Culture, Erice, Italy
`Graduate Distinguished Scholar Award, UCLA Alumni Association
`1988
`1992 - 1997 SERCA Fellow, National Human Genome Research Institute
`George D. Wilbanks Lectureship in Gynecological Oncology,
`2006
`University of South Florida College of Medicine
`President’s Distinguished Lectureship, American Society of
`Reproductive Medicine
`Leopold G. Koss Lectureship, Universität Bern, Switzerland
`Distinguished International Advisors at IEE BIBE, the original and the
`oldest IEEE flagship international conference in Bioinformatics and
`Bioengineering.
`Distinguished Lecture in Computer Science, Wayne State University
`IPM Distinguished Lecture, Mt. Sinai Medical School, New York
`The Ian Lawson Van Toch Memorial Seminar Series in
`Computational Biology, Ontario Cancer Institute
`Harvard-Australia Foundation Fellowship
`Bancroft Fellow-in-Residence, Queensland Institute for Medical
`Research, Queensland, Australia
`Jackson Memorial Fellowship, Griffith University, Queensland,
`Australia
`Australia Fellow, National Health and Medical Research Council,
`Australia
`White House Open Science Champion of Change, Office of the
`President of the United States of America
`
`
`2010
`
`2011
`
`2013
`
`
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`John Quackenbush
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`Mentor of the Year Award, Postdoc and Graduate Student Organization,
`Dana-Farber Cancer Institute
`National Cancer Institute Outstanding Investigator Award (R35)
`National Academy of Medicine, National Academies of Science,
`Medicine, and Engineering
`
`2016
`
`2018
`2022
`
`
`
`Part II: Research, Teaching, and Clinical Contributions
`
`A. Narrative report (700 words or less) of Research, Teaching, and Clinical
`Contributions. Please focus primarily on the areas in which most of your time and
`effort is spent.
`
`My current research involves development of new analytical methods for the integrated
`analysis of large-scale biomedical data, including genomic data, to better understand the
`nature of human diseases, including cancer and pulmonary diseases, with the goal of
`developing better methods for diagnosis and treatment. Two defining characteristics of
`my work are a commitment to reproducible research through development of open-source
`software implementations of analytical methods, and an emphasis on studying sexual
`dimorphism in health and disease.
`
`A longstanding component of my work is methods development for robust biomarkers.
`We have applied this to identifying reproducible predictive biomarkers in cancer and
`have explored reproducibility in large, published data sets, demonstrating that many are
`inconsistent. In collaboration with Hugo Aerts, I have been working to extend our
`methods to the analysis of quantitative feature data extracted from radiographic images
`(an emerging field called “radiomics”), to use these to identify predictive biomarkers, and
`to link these features to genetic mutations in cancer. I have also come to recognize that
`while individual “features” such as the expression of genes or specific mutations may not
`be sufficient on their own to identify drivers of biological states or to predict outcome or
`response to therapy in disease.
`
`I have also been developing methods for inferring gene regulatory network models using
`gene expression and other sources of data. We published a method, PANDA, that builds
`on “message passing” (an idea developed communications theory) to optimize
`information flow through a gene regulatory network model, allowing us to infer
`condition-specific networks and to compare these between phenotypes. We have
`developed many extensions of PANDA that incorporate other data types and have applied
`these to the study of diseases, including ovarian cancer, colorectal cancer, chronic
`obstructive pulmonary disease, asthma, and Alzheimer’s disease, as well as to the
`investigation of sexual dimorphism. Consistent with our commitment to open and
`reproducible science, we have collected these methods (all named for animals) with
`standardized source code in R, C, Matlab, and Python, into the “Network Zoo”
`(https://netzoo.github.io/). To support the widespread use of these methods, we developed
`“netBooks” (http://netbooks.networkmedicine.org/), a collection of online tutorials that
`use Jupyter notebooks to introduce the use of our methods and, increasingly, to allow all
`of our published analyses to be rerun by those interested in the analyses.
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`We have also been exploring the connection between genotype and phenotype, using
`gene expression as a surrogate for phenotype. We have developed a new approach,
`CONDOR, to the analysis of expression quantitative trait loci that uses a bi-partite graph
`to represent associations between gene expression levels and both local (cis-acting) and
`distant (trans-acting) significant genetic variants. We find that the overall structure of the
`graph provides insight not only into how genetic variants work together to influence
`phenotype, but also into evolutionary constraints on the genetic variants themselves. This
`has given us new insight into how many genetic variants of small effect-size can
`collectively exert strong influence on phenotype.
`
`More recently, we have been asking whether how one can model regulatory networks in
`the context of genetic background, recognizing that an individual’s genotype will
`manifest its effects through alterations of patterns of gene expression that ultimately will
`influence the functional processes active in individuals. That method, EGRET, represents
`an important step forward in the analysis of the link between genotype and phenotype and
`is the first method for linking genetic cause and phenotypic effect through the action of
`individual regulatory processes.
`
`Our group also builds and maintains a variety of software tools to support genomic
`analysis. the TM4 suite of open-source software tools for the analysis of DNA microarray
`data. The most widely used of these, MeV, is a powerful data mining software tool, that
`places sophisticated analytical tools behind an intuitive graphical user interface.
`Developed to be accessible to laboratory biologists, MeV has more than 260,000 users
`worldwide. We recently transitioned MeV to a cloud-based platform, WebMeV
`(http://mev.tm4.org) to take advantage of cloud scalability to better handle large
`sequence-based data. WebMeV now has 3000 registered users and provides more than
`100 analysis sessions per day.
`
`I am also very involved in teaching and mentoring. I developed, launched, and direct the
`Computational Biology and Quantitative Genetics (CBQG) master’s degree program, I
`was co-PI and co-director of the first joint Biostatistics and Bioinformatics training grant
`in the US and recently stepped down to develop and direct a training grant program as
`part of the NIH’s Big Data to Knowledge (BD2K) program. I also developed and teach
`an introductory genomics tools and methods course and have co-taught an online course
`on reproducible research through HarvardX (https://www.edx.org/course/principles-
`statistical-computational-harvardx-ph527x).
`
`I have trained more than 80 postdoctoral fellows and graduate students (including MS
`and PhD students whom I have mentored for their thesis projects) and have mentored a
`number of junior faculty members since joining the Harvard TH Chan School of Public
`Health and Dana-Farber Cancer Institute in 2005. I have emphasized diversity in hiring
`postdocs; more than half of my trainees have been female and four of the five postdocs
`from my group who have moved onto faculty positions in the past year have been female.
`I also maintain an extensive network of former trainees (and their current trainees) which
`meets weekly as we continue to work collaboratively in the development and application
`of network methods.
`
`
`
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`John Quackenbush
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`B. Funding Information
`
` I
`
` have had more than twenty-five years of continuous grant support from the NIH and
`other organizations. My current support includes:
`
`Active Research Support
`3/1/2017 – 2/28/2022
`5R01CA205406-03 (Ng, K.)
`
`
`NIH/NCI
`Novel Randomized Controlled Trials of Vitamin D Supplementation in Patients
`with Colorectal Cancer: Impact on Survival and Biology
`This project is exploring the biology underlying the effects of vitamin D on survival of
`colorectal patients.
`Role: Co-Investigator
`1R35CA220523 (Quackenbush, J.)
`NIH/NCI
`Unraveling the Complexities of Risk and Mechanism in Cancer
`This NCI Career Award supports Dr. Quackenbush’s ongoing work to model genetic
`processes in cancer and to elucidate the link between genotype and phenotype so as to
`better understand the drivers of cancer and to identify potential targets for therapeutic
`intervention, with a particular emphasis on understanding differences between men and
`women. Role: Principal Investigator
`1R01HG011393 (DeMeo, D / Quackenbush, J.)
`NIH/NCI
`Network Tools to Understand Sex- and Gender-Specific Drivers of Disease
`This project will develop robust methods for handling male and female multi-omic data,
`with an emphasis on applying these to the inference of gene regulatory network models
`and the use of such models for gaining insight into the regulatory processes that drive
`clinical differences in human health and disease. Role: co-Principal Investigator
`1U24CA231846-01A1 (Quackenbush, J.)
`9/1/2019 – 8/31/2024
`NIH/NCI
`
`MeV: A Robust Platform for Intuitive Genomic Data Analysis
`As part of the Informatics Technology for Cancer Research (ITCR) program, we will
`develop and support WebMeV, a robust, scalable data analysis software tool that uses
`intuitive visual interfaces to provide users with access to advanced data analysis methods
`for large-scale genomic data in a system that helps ensure their research is reproducible.
`Role: Principal Investigator
`2P50CA127003-11A1 (Bass, A.)
`NIH (Subcontract: Dana Farber Cancer Institute
`Dana Farber/ Harvard Cancer Center SPORE in Gastrointestinal Cancer
`The GI SPORE supports state-of-the-art investigator-initiated translational research that
`will contribute to improved prevention, early detection, diagnosis, and treatment of
`gastrointestinal cancers. Dr. Quackenbush will serve as Co-Director of the Biostatistics
`and Bioinformatics Core, which will support the quantitative needs of the investigators in
`the design of experiments and the analysis of the resulting data.
`Role: Co-Investigator/Core Co-Director
`
`9/1/2018 – 06/30/2025
`
`9/1/2018 – 8/31/2025
`
`9/1/2019 – 5/31/2024
`
` 12
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`

`John Quackenbush
`
`
`C. Report of Current Research Activities other than those mentioned above (bench
`research, clinical trials, outcome studies, efficacy studies as applicable)
`
`None to report.
`
`D. Report of Teaching (use only those categories that are applicable)
`
`1983 - 1990
`
`1984 - 1996
`
`Teaching Fellow, Department of Physics, University of California, Los
`Angeles
`Physics Instructor, Southern California Science Institute, New College
`of California
`1987 - 1992 Visiting Lecturer, Department of Physics, University of California, Los
`Angeles
`Lecturer, The Johns Hopkins University
`Instructor in the Masters in Biotechnology Program
`Professor, Department of Biochemistry, The George Washington
`University
`2003 - 2005 Adjunct Professor, Department of Biostatistics, Bloomberg School of
`Public Health, The Johns Hopkins University
`Developed program in genomics and bioinformatics; instructor in
`various courses.
`2005-present Professor, Department of Biostatistics, Harvard TH Chan School of
`Public Health
`2013-present Director, MS in Computational Biology and Quantitative Genetics
`
`
`1998 - 2005
`
`2000 - 2005
`
`E. Report of Clinical Activities
`
`1. Description of clinical practice (field, areas of major focus, site(s) of practice [private
`office, HMO, teaching hospital etc.])
`
`None
`
`2. Patient load (indicate complexity of cases, as appropriate)
`
`None
`
`3. Clinical contributions (e.g., introduction of new methods of clinical diagnosis,
`prevention, treatment, care delivery)
`
`None
`
`4. Other relevant information about clinical role (receipt of clinical awards, locally or
`nationally, invitation to participate in clinical activities at other sites, special recognition
`by peers or professional organizations as a leader in a clinical field)
`
`None
`
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`

`

`Part III: Bibliography (as of September 26, 2022)
`
`John Quackenbush
`
`Total citations: 88,598
`
`h-index: 106
`
`i10-index: 306
`
`Original Articles (325)
`
`Complete List of Published Works in MyBibliography:
`https://www.ncbi.nlm.nih.gov/myncbi/john.quackenbush.1/bibliography/public/
`
`1. Quackenbush J. Chiral anomalies in two-dimensional quantum field theory.
`Physical review D: Particles and fields. 1989;40(10):3408-14. Epub 1989/11/15.
`PubMed PMID: 10011709.
`2. Quackenbush J. Twisted world-sheet gauge fields and string models Phys Lett B.
`1990;234(3):285-91.
`3. Buchanan CD, Cousins R, Dib C, Peccei RD, Quackenbush J. Testing CP and CPT
`violation in the neutral kaon system