Curriculum Vitae

John Harer

Department of Mathematics
Physics Building
Duke University
Durham, NC 27708 		(919) 660-2845 (office)
(email)
Education

PhDUniversity of California, Berkeley1979
BSHaverford College1974
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
Director, Computational Biology and Bioinformatics Program, Institute for Genome Sciences and Policy, 2008 - present
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
Department Chair, Mathematics, July 01, 1994 - June 30, 1999
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
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

Professional Service

A&S Council
Review Committee for Dean of Engineering, 2011 - present  
APT, 2008-2009  
CBB Admissions Committee, 2008 - present  
CBB Advisory Comittee, 2008 - present  
Director, Computational Biology and Bioinformatics PhD Program, 2008 - present  
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  
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 Grassroots Technology, 2009 - present  
Consultant to US Government on Classified Matters, 2005 - present  
Refereed numerous papers, 1993 - present  
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, 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  
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 (January 13, 2010), American Mathematical Society, ISBN 0-8218-4925-5 (http://www.ams.org/bookstore-getitem/item=mbk-69.)
  2. Penner, R. C. and Harer, J. L., Combinatorics of train tracks, pp. xii+216, 1992, Princeton University Press, Princeton, NJ

Papers Published

  1. with Yuriy Mileyko, Sayan Mukherjee, Probability measures on the space of persistence diagrams, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 25
  2. with Paul Bendich, Taras Galkovskyi, Improving Homology Estimates with Random Walks, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 16
  3. with Anjali S. Iyer-Pascuzzi, Christopher N. Topp, Jill T. Anderson, Cheng-Ruei Lee, Olga Symonova, Yuriy Mileyko, Taras Galkovsky, Ying Zheng, Randy Clark, Leon Kochian, Herbert Edelsbrunner, Joshua S. Weitz, Thomas Mitchell-Olds and Philip N. Benfey, Quantitative Genetic Analysis of Root System Architecture in Rice Plant and Animal Genomes, XX Genome Conference (2011)
  4. with Gilberto Bini, Euler characteristics of moduli spaces of curves, Journal of the European Mathematical Society, vol. 13 no. 2 (2011), pp. 487-512
  5. with Paul Bendich, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (2011), pp. 305-336
  6. Anjali Iyer-Pascuzzi, Joshua S. Weitz, Olga Symonova,Yuriy Mileyko, Yueling Hao, Heather Belcher, John Harer, and Philip N. Benfey, Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems, Plant Physiology, vol. 152 (2010), pp. 1148-1157
  7. D. Cohen-Steiner, H. Edelsbrunner, J. Harer and Y. Mileyko., Lipschitz functions have L_p-stable persistence., Foundations of Computional Mathematics, vol. 10 no. 2 (2010), pp. 127-139
  8. D. Cohen-Steiner, H. Edelsbrunner and J. Harer., Extending persistence using Poincare and Lefschetz duality, Found. Comput. Math., vol. p (2009), pp. 79-103, Erratum 133-134.
  9. H. Edelsbrunner and J. Harer, The persistent Morse complex segmentation of a 3-manifold., in 3D Physiological Human Workshop, 2009, Lecture Notes Comp. Sci., edited by N. Magnenat-Thalmann, vol. 5903 (2009), pp. 36-50, Springer-Verlag, Berlin
  10. D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov., Persistent homology for kernels, images, and cokernels., Proc. Sympos. Discret Alg. (2009)
  11. P. Bendich, D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov., Inferring local homology from sampled stratified spaces., Proc. 48th Ann. Sympos. Found. Comput. Sci. (2008), pp. 536-546
  12. H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci and J. Snoeyink, Time-varying Reeb graphs for continuous space-time data., Comput. Geom. Theory Appl., vol. 41 (2008), pp. 149-166.
  13. D. Cohen-Steiner, H. Edelsbrunner and J. Harer., Stability of persistence diagrams., Discrete Comput. Geom., vol. 37 (2007), pp. 103-120
  14. H. Edelsbrunner and J. Harer, Persistent homology --- a survey., In Twenty Years After, eds. J. E. Goodman, J. Pach and R. Pollack, AMS. (2007)
  15. 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)
  16. 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
  17. 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
  18. 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.
  19. 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.
  20. with P. Agarwal and A. Collins, HPRM: A Hierarchical PRM, Proc. Intl. Conf. Robotics and Automation (2003)
  21. 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.
  22. 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
  23. P. Agarwal, A. Collins and J. Harer, Minimal Trap Design, Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA), (2001)
  24. H. Edelsbrunner, J. Harer and A. Zomorodian, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proc. 17th Sympos. Comput. Geom. 2001, 70-79.
  25. 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
  26. 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
  27. Harer, John, The third homology group of the moduli space of curves, Duke Math. J., vol. 63, no. 1, pp. 25--55, 1991
  28. 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
  29. Harer, John L., The cohomology of the moduli space of curves, Theory of moduli (Montecatini Terme, 1985), pp. 138--221, 1988, Springer, Berlin
  30. 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
  31. Harer, J. and Zagier, D., The Euler characteristic of the moduli space of curves, Invent. Math., vol. 85, no. 3, pp. 457--485, 1986
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. Harer, John, Representing elements of pi1(M3) by fibred knots, Math. Proc. Cambridge Philos. Soc., vol. 92, no. 1, pp. 133--138, 1982
  38. Harer, John, How to construct all fibered knots and links, Topology, vol. 21, no. 3, pp. 263--280, 1982
  39. 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
  40. Harer, John, On handlebody structures for hypersurfaces in C3 and CP3, Math. Ann., vol. 238, no. 1, pp. 51--58, 1978

Papers Submitted

  1. with Taras Galkovskyi, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles A Price, Christopher Topp, Anjali Iyer-Pascuzzi, Paul Zurek, Suqin Fang, Philip N Benfey, and Joshua S Weitz, GiA Roots: Software for the High Throughput Analysis of Plant Root System Images, BMC Plant Biology (2011)
  2. with Elizabeth Munch, Michael Shapiro, Failure Filtrations for Fenced Sensor Networks, The International Journal of Robotics Research (2011), pp. 14
  3. with Michael Jenista, Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2011), pp. 12
  4. T. Fink, S. Ahnert, R. Bar-On, J. Harer, Exact dynamics of Boolean networks with connectivity one, PRL (2009)
  5. Mehak Aziz, Siobhan M. Brady, David Orlando, Appu Kuruvilla, Scott Spillias, José R. Dinneny, Terri A. Long, John Harer, Uwe Ohler, Philip N. Benfey, Gene Expression Clustering Analysis: How to Choose the Best Parameters and Clustering Algorithm (2008)

Papers In Preparation

  1. with Yuriy Mileyko, Central Sets via Persistent Homology (2011)
  2. with Paul Bendich, Jacob Harer, Estimating Intrinsic Distance Using Persistent Homology (2011)
  3. with Paul Bendich, Jacob Harer, PHIsoMap: Intrinsic Distance for Dimension Reduction Using Persistent Homology (2011)
  4. with Michael Jenista, Characterizing Realizable Boolean Cycles in Switching Networks (2011)
  5. with Anastasia Deckard, Ron Analfi, John Hogenesch, Evaluating algorithms for genome-wide data analysis of biochronicity (2011)
  6. with Elizabeth Munch, Kernel, Image, and Cokernel persistence for Relative Homology (2011)
  7. with Elizabeth Munch, Failure Filtrations for Relaxed Fence Conditions (2011)
  8. A. HB and J. Harer, Persistent Stiefel Whitney Classes (2010)
  9. Jacob Harer, Thomas Fink and John Harer, Stable Cycles Require Modular Networks (2010)
  10. T. Galkovskiy, Y. Mileyko, J. Harer, Computational Topology Tools for Images and Point Clouds (2010)
  11. Adrienne Wells, John Harer, Andrew Lyu, and Dan Kiehart, Dynamic Image Segmentation for Modelling Dorsal Closure (2009)
  12. Anjali Iyer-Pascuzzi , John Harer, Yuriy Milekov, Herbert Edelsbrunner and Philip Benfey, Persistent Local Homology for Capturing Plant Root Architecture from 2D Images (2009)
  13. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2009)

Preprints

  1. John Harer, Algorithms for Enumerating Triangulations and Other Maps in Surfaces, 1998 , preprint 1998
  2. John Harer, An Alternative Approach to Trap Design for Vibratory Bowl Feeders, 1998 , preprint 1998
  3. 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)
Last modified: 2012/03/06