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Math @ Duke
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Curriculum Vitae
John HarerClick here for a printer-ready version, or
download as a PDF or Word file.-
Department of Mathematics
Physics Building
Duke University
Durham, NC 27708
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(919) 660-2845 (office)
 (email)
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- Education
| PhD | University of California, Berkeley | 1979 |
| BS | Haverford College | 1974 |
- Areas of Research
Computational Topology, Computational Biology, Algorithms
- Areas of Interest
- Computational Biology
Computational Topology
Dynamics on Networks
Algorithms
- Professional Experience / Employment History
- Duke University
- Professor of Electrical and Computer Engineering, 2011 - present
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- Director, Computational Biology and Bioinformatics Program, Institute for Genome Sciences and Policy, 2008 - present
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- Director, Center for Computational Science, Engineering and Medicine, 2002 - 2007
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- Professor of Computer Science, Computer Science, 2001 - present
- Secondary Appointment
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- Vice-Provost for Acdemic Affairs, July 01, 1999 - December 31, 2004
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- Department Chair, Mathematics, July 01, 1994 - June 30, 1999
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- Professor of Mathematics, Mathematics, 1993 - present
- Washington and Lee University
- Professor, Mathematics Chair, Rupert Distinguished Professor, Mathematics, 1991 - 1992
- University of Michigan
- Professor, Mathematics, 1989 - 1991
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- Associate Professor, Mathematics, 1985 - 1989
- University of Maryland
- Assistant Professor, Mathematics, 1983 - 1985
- Columbia University
- Ritt Assistant Professor, Mathematics, 1979 - 1983
- Visiting Positions
- Visitor, Institute Curie, July 01, 2007 - June 30, 2008
- Professor, Scuola Normale Superiore, 1997 - 1998
- Professor, Duke University, 1992 - 1993
- Awards, Honors, and Distinctions
Henry Russell Award, University of Michigan, July, 1988
Faculty Recognition Award, University of Michigan, July, 1987
Fellowship, Sloane Foundation, July, 1987
Postdoctoral Fellowship, NSF, July, 1983
- Recent Grant Support
- Foundations of Information Systems, Johns Hopkins University Applied Physics Laboratory, 108852, 2012/04-2017/03.
- ATD: Online Multiscale Algorithms for Geometric Density Estimation in High-Dimensions and Persistent Homology of Data for Improved Threat, National Science Foundation, DMS-1222567, 2012/09-2016/08.
- EMSW21-RTG: Geometric, Topological and Statistical Methods for Analyzing Massive Datasets, National Science Foundation, DMS-1045153, 2011/08-2016/07.
- Bioinformatics and Computational Biology Training Program, National Institutes of Health, 5T32-GM071340-05, 2005/07-2016/06.
- Biochronicity: Time, Evolution, Networks, and Function, Defense Advanced Research Projects Agency, D12AP00025-0002, 2012/03-2016/03.
- Biochronicity: Time, Evolution Networks, Defense Advanced Research Projects Agency, D12AP00001, 2011/12-2015/12.
- Inferring Network Controls from Topology Using the CHomP Database, Air Force Office of Scientific Research, FA9550-10-1-0436, 2010/09-2015/09.
- Designing Networks that are Capable of Self-Healing and Adapting, Defense Threat Reduction Agency, 2010/11-2013/11.
- Knowledge Enhanced Exapixel Photography, Defense Advanced Research Projects Agency, N66001-11-1-4002-P00005, 2012/10-2013/09.
- OASIS: Operationally Aware Sensing thru Information Scaling, Johns Hopkins University Applied Physics Laboratory, 110279, 2012/10-2013/09.
- A Multidimensional Imaging Platform to Analyze Crop Root System Dynamics in Response to Changing Environments, Department of Agriculture, 2011-67012-30773, 2011/09-2013/08.
- GEPR: Genome-wide analysis of root traits, National Science Foundation, NSF-DBI-0820624, 2008/09-2012/08.
- Conference: Foundational Mathematics for Understanding Security, Air Force Office of Scientific Research, AFOSR-FA9550-10-1-0436, 2012/07-2012/07.
- Duke Center for Systems Biology, NIH, 2007/07-2012/06.
- Data Acquisition, Processing and Modeling of Morphogenesis in 4D, NSF, 0714796, 2006/07-2012/06.
- Biochronicity: Time, Network, Evolution and Function, Defense Advanced Research Projects Agency, D12AP00001, 2011/11-2012/04.
- Predictive Biology: Adaptability, Robustness and the Fundamental Laws of Biology, Princeton University, 00001744, 2009/09-2011/09.
- Duke on Network Security, Air Force Office of Scientific Research, FA9550-10-1-0465, 2010/09-2011/08.
- Professional Service
- A&S Council
- APT, 2008-2009
- Review Committee for Dean of Engineering, 2011 - 2012
- CBB Admissions Committee, 2008 - 2012
- CBB Advisory Comittee, 2008 - 2012
- Director, Computational Biology and Bioinformatics PhD Program, 2008 - 2012
- Director and DUS, Modeling Biological Systems Undergraduate Certificate, 2008 - 2011
- Thesis Committee - Jacob Frelinger - CBB, December 2010
- Thesis Committee - Ying Zheng- CS, December 2010
- Thesis Committee - Andreas Pfenning - CBB, December 2010
- Co-PI and Member of Steering Committee, Center for Systems Biology, December 2010
- Director of International Relations, Center for Systems Biology Steering Committee, December 2008
- Nescent Director Search Committee, October 2008
- Associate Director, Center for Systems Biology Steering Committee, 2006 - 2007
- University Committee
- Review Committee for Brittany Fasy, October 2008
- Computational Biology Section Proposal, December 2007
- AP&T, September 1, 2005 - June 30, 2007
- Departmental Computing Support, September, 2005 - May, 2006
- Chair, Strategic Planning for Research Computing, August, 2005 - May, 2006
- Chair, Task Force for Computation and Data Analysis in the Social Sciences, January 01, 2005 - July 01, 2005
- B&B Chair Search Committee, 1999 - July 01, 2005
- Research Committee, September, 2005 - May, 2005
- Academic Space Committee, 2003 - December 31, 2004
- Global Change Steering Committee, 2000 - December 31, 2004
- Member, Academic Priorities Committee, 1999 - December 31, 2004
- Provost's Inner Staff, 1999 - December 31, 2004
- Duke Forest Advisory Committee, 1999 - December 31, 2004
- Project Advisory Committee for French Science Center, 2003 - 2004
- Materials Science Governance Committee, 2000 - 2004
- Review Committee for Dean of Pratt School of Engineering, 2002 - 2003
- IGSP Director Search, 1999 - 2003
- IGSP Leadership Committee, July 01, 1999 - July 01, 2003
- Search Committee for Dean of the Nicholas School of the Environment, 2000 - 2001
- Chair, CBCB Director Search Committee, 2000 - 2001
- Strategic Planning Oversight Committee, 1999 - 2001
- Chair, Science and Engineering Working Group, 1999 - 2001
- Dept Committee
- Appointments Committee, 1993 - present
- Committee to write basic linear algebra exam, 2011 - 2012
- Chair, A. Layton Tenure Committee, December 2011
- Paul Magwene Tenure Committee, December 2011
- Applied ARP, 2010-2011
- Applied ARP, 2009-2010
- Maggioni Promotion Committee, December 2009
- Renewal for Mauro Maggioni, October 2008
- Mathematical Biology Search Commitee, 2004 - 2005
- Papers Refereed
- Consultant to US Government on Classified Matters, 2005 - present
- Refereed numerous papers, 1993 - present
- Panel Member, NSF Review Panel - CDS&E program, December 2012
- Consultant to ARGON ST, 2011 - 2012
- Consultant to Grassroots Technology, 2009 - 2011
- NSF Reviews And Panels
- Participant, NSF Workshop in Mathematics and Robotics, 2000
- Univ Services
- SAMSI Scienctific Advisory Committee, 2004 - 2010
- Director, Center for Computational Science, Engineering and Medicine, 2001 - 2007
- Search Committee for A&S IT director, December 2005
- Board Member, NISS Board of Trustees, 2002 - 2005
- Reviewer for Research Day, March 30, 2005
- Vice-Provost for Academic Affairs, Provost's Office:, July 01, 1999 - February 28, 2005
- TUCASI, July 1, 1999 - January 01, 2005
- Member, SAMSII Board of Govenors, 2003 - December 31, 2004
- Chief Staff, Academic Affairs Committee - Duke Board of Trustees, July 01, 1999 - December 31, 2004
- Chair, DFELL Advisory Committee, 1999 - 2004
- Reviewer for Research Day, March, 2004
- Search Committee for Neural Analysis Faculty - BME, 2002
- Search Committee for Vice-Provost for Research, 2001
- Chair, Committee on Academic Practices and Policies, North Carolina School of Science and Math Board of Trustees, 1999 - 2001
- Strategic Planning Process Coordinator, 1999 - 2001
- Selected Recent Invited Talks
- Inferring Control from Topology & Data, AFOSR Annual Review, DC, December 21, 2012
- Building Regulatory Networks for Periodic Procceses, Duke Systems Biology Seminar, November, 2012
- Frechet means for persistence diagrams and vineyads, BIRS, October, 2012
- Mathematical Ideas in the Life Sciences Modeling Cellular Clocks, DIMACS (Rutgers), September, 2012
- Topological Data Analysis, Applied Communication Sciences, September, 2012
- Building Gene Regulatory Networks for Periodic Processes, Duke CBB, August, 2012
- DARPA Biochronicity: Toward Building a Unified Biological Clock and Understanding its Response to External Factors, Seattle, August, 2012
- DARPA BIochronicity: Biochronicity: Time, evolution, networks, and function, Duke University, May 08, 2012
- DARPA Biochronicity Kick-Off: Biochronicity: Time, evolution, networks, and function, San Diego, February, 2012
- DARPA Biochronicity: Algorithms and methods of discovering periodicity in biological datasets, San Diego, February, 2012
- Time Series, Time Varying Data, Geometry and Topology, Incline Village, Nevada, February, 2012
- Topological & Geometric Structure in Noisy Data, Incline Village, Nevada, February, 2012
- Inferring Control from Topology & Data, AFOSR Annual Review, November 29, 2011
- Structure in Noisy Data, Siam Conference NCState University, October 7, 2011
- Structure in Data, Duke RTG Seminar, September 8, 2011
- Modeling Gene Networks, DARPA Fun Bio Final Review, August 29, 2011
- Networks That Self-Heal: Slime Molds in Action, Duke RTG Seminar, May 19, 2011
- Structure in Data, Johns Hopkins Advanced Physics Laboratory, May 17, 2011
- Statistics on Persistence Diagrams, Ohio State Computatiional Geometry Seminar, April 09, 2011
- Structure in Data, Ohio State Colloquium, April 8, 2011
- Structure in Data, Virginia Tech Colloquium, April 1, 2011
- Community Network - Biological Inspiration, Princeton University, 17 December 2010
- Computational Topology Methods for Dimension Reduction, Duke Univesity, 17 December 2010
- Control of the Yeast Cell Cycle, DARPA FunBio Annual Review -Dana Point California, 17 December 2010
- FunBio - Biologically Inspiration for Networks, Princeton University, 17 December 2010
- Inferring Control from Topology and Data, AFOSR annual program review, Arlington, VA, November 29, 2010
- Self-Healing Networks, London Institute for Mathematical Sciences, June, 2010
- Network Node FunBio, DARPA FunBio Annual Review -Dana Point California, January, 2010
- Persistent Local Homology for Root Shape, Duke University Workshop on Plant Root Architecture, October 01, 2009
- Dynamics of Biological Models of Gene Regulator y Networks, Curie Institute, Paris, August 10, 2009
- Finding Cycles in Boolean Networks, London Institute of Mathematical Sciences, June 11, 2009
- Plant Root Architecture, Georgia Tech, May 27, 2009
- Dynamics on Biological Networks, Duke FunBio DARPA Meeting, April 3, 2009
- Persistence, Point Clouds and Local Homology, George Washington University, March 23, 2009
- Gene Regulatory Network Clocks., Duke University Systems Biology Seminar, March 18, 2009
- Persistence, Point Clouds and Local Homology, Rutgers - IAS Workshop, March 04, 2009
- Persistent Homology and Applications, Dept of Mathematics, UNCG, November 10, 2008
- How do Biological Networks Keep Time, CBB Retreat, Sept, 2008
- Persistence, Point Clouds and Local Homology, Ecole Normale Superior, March, 2008
- Persistent Intersection Homology, INRIA - Sophia Antipolis, June, 2008
- Persistent Homology for root shape description, DARPA TDA meeting - San Diego, December, 2007
- Topology and Biology, DARPA FunBio meeting - San Diego, December, 2007
- Topological Persistence, Rutgers University, November, 2006
- Persistence for Image Analysis, MSRI, October, 2006
- Extended Persistence with Applications, MSRI, September, 2006
- Discovering Stratified Structures in Datasets, DARPA meeting - Santa Barbara, May, 2006
- Discovering stratified structure using local homology, DARPA meeting, Duke University, December 15, 2005
- Using flattening for surface comparison, NIST site review, Geomagic, RTP, November 29, 2005
- Extended Persistence and Intersection Homology, DARPA meeting, San Raphael, California, October 30, 2005
- 2004 IMA New Directions Short Course in Computational Topology, Institute for Mathematics and its Applications, July 6-16, 2004 [available here]
- Extreme elevation on a 2-manifold, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004 [htm]
- Time-varying Contour Trees for Continuous Space-Time Data, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004 [htm]
- HPRM: A Hierarchical PRM, International Conference on Robotics and Automation, 2003 [available here]
- Loops in Reeb Graphs of 2-Manifolds, 19th ACM Symposium on Computational Geometry, 2003 [html]
- Morse Complexes for Piecewise Linear 3-Manifolds, 19th ACM Symposium on Computational Geometry, 2003
- Workshop on Computaional Topology, INRIA Sophia Antipolis, Oct 21-25, 2002 [available here]
- Combinatorial Morse Theory and Persistence, with Applications to Distinguishing Noise from Feature, Lawrence Livermore National Labs, Feb, 2001 [html]
- Conference on Algebraic Topological Methods in Computer Science, Stanford University, 2001 [html]
- Minimal Trap Design, ICRA 2001 , Seoul, 2001
- Doctoral Theses Directed
- Anne Collins, Configuration Spaces in Robotic Manipulation and Motion Planning, (2002)
- Chris Odden, (1997)
- Joel Foisy, (1996)
- Publications (listed separately)
Last modified: 2012/12/18 |
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dept@math.duke.edu 
ph: 919.660.2800
fax: 919.660.2821
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 Mathematics Department
Duke University, Box 90320
Durham, NC 27708-0320
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