Curriculum Vitae

Department of Mathematics Physics Building Duke University Durham, NC 27708

(919)-660-2845 (office) (email)

Education

PhD	University of California, Berkeley	1979
BS	Haverford College	1974

Areas of Research

Computational Topology, Computational Geometry, Computational Biology, Algorithms

Areas of Interest

Computational Biology
Computational Topology
Algorithms

Professional Experience / Employment History

Duke University

Director, Center for Computational Science, Engineering and Medicine, , 2002 - 2007

Professor of Computer Science, Computer Science, 2001 - present

Secondary Appointment

Vice-Provost for Acdemic Affairs, , July 01, 1999 - December 31, 2004

Professor of Mathematics, Mathematics, 1993 - present

Washington and Lee University

Professor and Chair, Mathematics, 1991 - 1992

University of Michigan

Professor, Mathematics, 1989 - 1991

Associate Professor, Mathematics, 1985 - 1989

University of Maryland

Assistant Professor, Mathematics, 1983 - 1985

Columbia University

Ritt Assistant Professor, Mathematics, 1979 - 1983

Visiting Positions

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

• 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.      
• Topological Methods for the Analysis of High-dimensional Data Sets and 3D Object Recognition, DARPA, 2005/01-2008/12.      
• STTR Phase I: Representation and Visualization of Plant Genotypic, Phenotypic,and Environmental Relationships, NSF IIP, 0637869, 2007/01-2007/12.      
• Genomic Approaches to Identify Genes for Root System Architecture Traits, NSF DBI, 0606873, 2006/08-2007/07.      
• Reference structure tomography for ubiquitous and efficient human tracking and identification, Army Research Office, 2003/09-2006/12.      
• SBIR: Advanced Computer-Aided Inspection Research, NIST Advanced Technology Program, 2003/07-2006/06.      

Professional Service

A&S Council

Associate Director, Center for Systems Biology Steering Committee, 2006 - 2007  

University Committee

Bioinformatics and Computational Biology PhD Program Steering Committee, 2003 - present  

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  

Mathematical Biology Search Commitee, 2004 - 2005  

Papers Refereed

Refereed numerous papers, 1993 - present  

NSF Reviews And Panels

Participant, NSF Workshop in Mathematics and Robotics, 2000  

Univ Services

SAMSI Scienctific Advisory Committee, 2004 - present  

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

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  

Extreme elevation on a 2-manifold, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004  

Time-varying Contour Trees for Continuous Space-Time Data, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004  

HPRM: A Hierarchical PRM, International Conference on Robotics and Automation, 2003  

Loops in Reeb Graphs of 2-Manifolds, 19th ACM Symposium on Computational Geometry, 2003  

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  

Combinatorial Morse Theory and Persistence, with Applications to Distinguishing Noise from Feature, Lawrence Livermore National Labs, Feb, 2001  

Conference on Algebraic Topological Methods in Computer Science, Stanford University, 2001  

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

Books

1. H. Edelsbrunner and J. Harer, Computational Topology, An Introduction (2007)
2. Penner, R. C. and Harer, J. L., Combinatorics of train tracks, pp. xii+216, 1992, Princeton University Press, Princeton, NJ

Papers Published

1. D. Cohen-Steiner, H. Edelsbrunner and J. Harer., Stability of persistence diagrams., Discrete Comput. Geom., vol. 37 (2007), pp. 103-120
2. H. Edelsbrunner and J. Harer, Persistent homology --- a survey., In Twenty Years After, eds. J. E. Goodman, J. Pach and R. Pollack, AMS. (2007)
3. D. Attali, H. Edelsbrunner, J. Harer, Y. Milokov, Alpha-beta witness complexes, Proc. 10th Workshop Algor. Data Struct., 2007, Springer LNCS 4619, 386-397. (2007)
4. with H. Edelsbrunner, V. Natarajan, V. Pascucci., Local and Global Comparison of Continuous Functions, Proc. IEEE Conf. Visualization, 2004, 275-280. (2004), pp. 275-280
5. with P. K. Agarwal, H. Edelsbrunner, and Y. Wang, Extreme elevation on a 2-manifold., Proc. 20th Ann. Sympos. Comput. Geom. (2004), pp. 357-365
6. with H. Edelsbrunner, A. Mascarenhas and V. Pascucci, Time-varying Reeb graphs for continuous space-time data., Proc. 20th Ann. Sympos. Comput. Geom. (2004), pp. 366-372.
7. with K. Cole-McLaughlin, H. Edelsbrunner, V. Natarajan and V. Pascucci, Loops in Reeb graphs of 2-manifolds., Discrete Comput. Geom., vol. 32 (2004), pp. 231-244.
8. with P. Agarwal and A. Collins, HPRM: A Hierarchical PRM, Proc. Intl. Conf. Robotics and Automation (2003)
9. with H. Edelsbrunner, V. Natarajan and V. Pascucci., Morse-Smale complexes for piecewise linear 3-manifolds., Proc. 19th Ann. Sympos. Comput. Geom. (2003), pp. 361-370.
10. with H. Edelsbrunner., Jacobi sets of multiple Morse functions., Foundations of Computational Mathematics, Minneapolis, eds. F. Cucker, R. DeVore, P. Olver and E. Sueli, Cambridge Univ. Press, England, (2002), pp. 37-57
11. P. Agarwal, A. Collins and J. Harer, Minimal Trap Design, Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA), (2001)
12. H. Edelsbrunner, J. Harer and A. Zomorodian, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proc. 17th Sympos. Comput. Geom. 2001, 70-79.
13. Goulden, I. P. and Harer, J. L. and Jackson, D. M., A geometric parametrization for the virtual Euler characteristics of the moduli spaces of real and complex algebraic curves, Trans. Amer. Math. Soc., vol. 353, no. 11, pp. 4405--4427 (electronic), 2001
14. Harer, John L., The rational Picard group of the moduli space of Riemann surfaces with spin structure, Mapping class groups and moduli spaces of Riemann surfaces (Gottingen, 1991/Seattle, WA, 1991), pp. 107--136, 1993, Amer. Math. Soc., Providence, RI
15. Harer, John, The third homology group of the moduli space of curves, Duke Math. J., vol. 63, no. 1, pp. 25--55, 1991
16. Harer, John L., Stability of the homology of the moduli spaces of Riemann surfaces with spin structure, Math. Ann., vol. 287, no. 2, pp. 323--334, 1990
17. Harer, John L., The cohomology of the moduli space of curves, Theory of moduli (Montecatini Terme, 1985), pp. 138--221, 1988, Springer, Berlin
18. Harer, John and Kas, Arnold and Kirby, Robion, Handlebody decompositions of complex surfaces, Mem. Amer. Math. Soc., vol. 62, no. 350, pp. iv+102, 1986
19. Harer, J. and Zagier, D., The Euler characteristic of the moduli space of curves, Invent. Math., vol. 85, no. 3, pp. 457--485, 1986
20. Harer, John L., The virtual cohomological dimension of the mapping class group of an orientable surface, Invent. Math., vol. 84, no. 1, pp. 157--176, 1986
21. Harer, John L., Stability of the homology of the mapping class groups of orientable surfaces, Ann. of Math. (2), vol. 121, no. 2, pp. 215--249, 1985
22. Geometry and topology, Proceedings of the special year held at the University of Maryland, College Park, Md., 1983/84, edited by Alexander, J. and Harer, J., pp. vi+292, 1985, Springer-Verlag, Berlin
23. Harer, John, The homology of the mapping class group and its connection to surface bundles over surfaces, Four-manifold theory (Durham, N.H., 1982), pp. 311--314, 1984, Amer. Math. Soc., Providence, RI
24. Harer, John, The second homology group of the mapping class group of an orientable surface, Invent. Math., vol. 72, no. 2, pp. 221--239, 1983
25. Harer, John, Representing elements of pi₁(M³) by fibred knots, Math. Proc. Cambridge Philos. Soc., vol. 92, no. 1, pp. 133--138, 1982
26. Harer, John, How to construct all fibered knots and links, Topology, vol. 21, no. 3, pp. 263--280, 1982
27. Casson, Andrew J. and Harer, John L., Some homology lens spaces which bound rational homology balls, Pacific J. Math., vol. 96, no. 1, pp. 23--36, 1981
28. Harer, John, On handlebody structures for hypersurfaces in C³ and CP³, Math. Ann., vol. 238, no. 1, pp. 51--58, 1978

Papers Accepted

1. P. Bendich, D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov, Inferring Local Homology from Sampled Stratified Spaces, Foundations of Computational Science (2007)
2. David Cohen-Steiner, Herbert Edelsbrunner, J. Harer, Extending Persistence Using Poincare' Duality, Foundations of Computational Mathematics (2007)

Papers Submitted

1. D. Cohen-Steiner, H. Edelsbrunner, J . Harer, and Yuriy Mileyko, Lipschitz functions have Lp-stable persistence, Foundations of Computational Mathematics (2007)
2. D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov, Persistent Homology for Kernels and Images, Society of Computational Geometry (2007)
3. G. Bini, J. Harer, The Regular and Orbifold Euler Characteristics of the Compactified Moduli Space of Curves, Topology (2005)

Preprints

1. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2007)
2. H. Edelsbrunner, J. Harer and A. Patel, Reeb Surfaces (2006)
3. P. Bendich, J. Harer and H. King, Persistence for Intersection Homology (2006)
4. John Harer, Algorithms for Enumerating Triangulations and Other Maps in Surfaces, 1998 , preprint 1998
5. John Harer, An Alternative Approach to Trap Design for Vibratory Bowl Feeders, 1998 , preprint 1998
6. John Harer, The Euler Characteristic of the Deligne-Mumford Compactification of the Moduli Space of Curves, 1996 , preprint 1996

Other

1. with H. Edelsbrunner, Persistent Morse Complex Segmentation of a 3-Manifold, Raindrop Geomagic Technical Report, vol. 066 (2004)