John Harer | Scholars@Duke

John Harer
Professor of Mathematics

Professor Harer's primary research is in the use of geometric, combinatorial and computational techniques to study a variety of problems in data analysis, shape recognition, image segmentation, tracking, cyber security, ioT, biological networks and gene expression.

Current Appointments & Affiliations

Professor of Mathematics, Mathematics, Trinity College of Arts & Sciences 1993

Contact Information

109 Physic Bldg, Durham, NC 27708
Box 90320, Durham, NC 27708-0034
(919) 660-2845
http://cms.math.duke.edu/harer/?q=home

Background
Education, Training, & Certifications
- Ph.D., University of California at Berkeley 1979
- B.A., Haverford College 1974
Duke Appointment History
- Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2011 - 2016
- Professor in the Department of Computer Science, Computer Science, Trinity College of Arts & Sciences 2001 - 2014
- Director of the PhD Program in Computational Biology and Bioinformatics, University Institutes and Centers, Institutes and Provost's Academic Units 2010 - 2012
- Vice Provost for Academic Affairs, Duke University 1999 - 2005
- Chair, Department of Mathematics, Mathematics, Trinity College of Arts & Sciences 1994 - 1999
- Visiting Professor, Mathematics, Trinity College of Arts & Sciences 1992 - 1993
Research
Selected Grants
- Geometric and Topological Methods for Multi-Modal Data Analysis and Fusion awarded by Air Force Office of Scientific Research 2018 - 2021
- BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features awarded by National Science Foundation 2014 - 2019
- An Adaptive Pipeline from Scientific Data to Models awarded by Defense Advanced Research Projects Agency 2017 - 2019
- Quantifying Complex Spatiotemporal Systems awarded by Rutgers, The State University of New Jersey 2016 - 2018
- EMSW21-RTG: Geometric, Topological awarded by National Science Foundation 2011 - 2018
- ATD: Online Multiscale Algorithms for Geometric Density Estimation in High-Dimensions and Persistent Homology of Data fo awarded by National Science Foundation 2012 - 2017
- Foundation of Information Systems awarded by Johns Hopkins University 2012 - 2017
- Analysis of High Dimensional Complex Spatio-Temporal Data awarded by Defense Advanced Research Projects Agency 2015 - 2016
- Inferring Network Controls awarded by Air Force Office of Scientific Research 2010 - 2015
- A Multidimensional Imaging Platform to Analyze Crop Root System Dynamics in Response to Changing Environments awarded by Department of Agriculture 2011 - 2013
- GEPR: Genome-wide analysis of root traits awarded by National Science Foundation 2008 - 2012
- Duke on Network Security awarded by Air Force Office of Scientific Research 2010 - 2011
- Doctoral Program in Management and Analysis of Large Data Acquired from Sensors awarded by Department of Education 2007 - 2011
- TRPGR Genomic Approaches to Identify Genes for Root System Architecture Traits awarded by National Science Foundation 2006 - 2008
- Distributed multiscale geometric processing on real-time sensor networks on radiation fields awarded by National Science Foundation 2002 - 2004
- Persistence, Combinatorial Morse Functions awarded by National Science Foundation 2001 - 2003
- (98-0205) Computational Geometry, Robotics, and Geographic Information Systems awarded by National Science Foundation 1998 - 2000
- (96-1030) The Moduli Space of Curves; Its Level-n Covers and Torelli Space awarded by National Science Foundation 1994 - 1997
- (94-0252) The Moduli Space of Curves, its Level n Covers and Torelli Space awarded by National Science Foundation 1994 - 1996
- (95-0888) The Moduli Space of Curves, its Level-n Covers and Torelli Space awarded by National Science Foundation 1994 - 1996
- (93-0786) Mathematical Sciences Mapping Class Group & Invariants of 3-Manifolds awarded by National Science Foundation 1992 - 1994
- (92-0802) Mapping Class Group and Invariants of 3-Manifolds awarded by National Science Foundation 1992 - 1994
Publications & Artistic Works
Selected Publications
- Books
  - Edelsbrunner, H, and Harer, J. Computational Topology - an Introduction. American Mathematical Society, 2010.
- Academic Articles
  - Tralie, CJ, Smith, A, Borggren, N, Hineman, J, Bendich, P, Zulch, P, and Harer, J. "Geometric cross-modal comparison of heterogeneous sensor data." 2018 Ieee Aerospace Conference (March 2018). Full Text Open Access Copy
  - Hughes, ME, Abruzzi, KC, Allada, R, Anafi, R, Arpat, AB, Asher, G, Baldi, P, de Bekker, C, Bell-Pedersen, D, Blau, J, Brown, S, Ceriani, MF, Chen, Z, Chiu, JC, Cox, J, Crowell, AM, DeBruyne, JP, Dijk, D-J, DiTacchio, L, Doyle, FJ, Duffield, GE, Dunlap, JC, Eckel-Mahan, K, Esser, KA, FitzGerald, GA, Forger, DB, Francey, LJ, Fu, Y-H, Gachon, F, Gatfield, D, de Goede, P, Golden, SS, Green, C, Harer, J, Harmer, S, Haspel, J, Hastings, MH, Herzel, H, Herzog, ED, Hoffmann, C, Hong, C, Hughey, JJ, Hurley, JM, de la Iglesia, HO, Johnson, C, Kay, SA, Koike, N, Kornacker, K, Kramer, A, Lamia, K, Leise, T, Lewis, SA, Li, J, Li, X, Liu, AC, Loros, JJ, Martino, TA, Menet, JS, Merrow, M, Millar, AJ, Mockler, T, Naef, F, Nagoshi, E, Nitabach, MN, Olmedo, M, Nusinow, DA, Ptáček, LJ, Rand, D, Reddy, AB, Robles, MS, Roenneberg, T, Rosbash, M, Ruben, MD, Rund, SSC, Sancar, A, Sassone-Corsi, P, Sehgal, A, Sherrill-Mix, S, Skene, DJ, Storch, K-F, Takahashi, JS, Ueda, HR, Wang, H, Weitz, C, Westermark, PO, Wijnen, H, Xu, Y, Wu, G, Yoo, S-H, Young, M, Zhang, EE, Zielinski, T, and Hogenesch, JB. "Guidelines for Genome-Scale Analysis of Biological Rhythms." Journal of Biological Rhythms 32, no. 5 (October 2017): 380-393. Full Text
  - Bendich, P, Chin, SP, Clark, J, Desena, J, Harer, J, Munch, E, Newman, A, Porter, D, Rouse, D, Strawn, N, and Watkins, A. "Topological and statistical behavior classifiers for tracking applications." Ieee Transactions on Aerospace and Electronic Systems 52, no. 6 (December 2016): 2644-2661. Full Text
  - McGoff, KA, Guo, X, Deckard, A, Kelliher, CM, Leman, AR, Francey, LJ, Hogenesch, JB, Haase, SB, and Harer, JL. "The Local Edge Machine: inference of dynamic models of gene regulation." Genome biology 17, no. 1 (October 19, 2016): 214-. Full Text
  - Bendich, P, Gasparovic, E, Harer, J, and Tralie, C. "Geometric Models for Musical Audio Data." Proceedings of the 32st International Symposium on Computational Geometry (SOCG) (June 2016). Link to Item
  - Perea, JA, Deckard, A, Haase, SB, and Harer, J. "SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data." BMC bioinformatics 16 (August 16, 2015): 257-. Full Text
  - Bendich, P, Gasparovic, E, Harer, J, Izmailov, R, and Ness, L. "Multi-scale local shape analysis and feature selection in machine learning applications." 2015 International Joint Conference on Neural Networks (Ijcnn) (July 2015). Full Text Open Access Copy
  - Perea, JA, and Harer, J. "Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis." Foundations of Computational Mathematics 15, no. 3 (June 2015): 799-838. Full Text
  - Munch, E, Turner, K, Bendich, P, Mukherjee, S, Mattingly, J, and Harer, J. "Probabilistic Fréchet means for time varying persistence diagrams." Electronic Journal of Statistics 9, no. 1 (2015): 1173-1204. Full Text Open Access Copy
  - Farr, RS, Harer, JL, and Fink, TMA. "Easily repairable networks: reconnecting nodes after damage." Physical review letters 113, no. 13 (September 26, 2014): 138701-. Full Text
  - Bristow, SL, Leman, AR, Simmons Kovacs, LA, Deckard, A, Harer, J, and Haase, SB. "Checkpoints couple transcription network oscillator dynamics to cell-cycle progression." Genome Biology 15, no. 9 (September 5, 2014): 446-null. Full Text
  - Turner, K, Mileyko, Y, Mukherjee, S, and Harer, J. "Fréchet Means for Distributions of Persistence Diagrams." Discrete & Computational Geometry 52, no. 1 (July 2014): 44-70. Full Text
  - Perea, JA, and Harer, J. "Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis." Foundations of Computational Mathematics 15, no. 3 (2014): 799-838. Full Text
  - Deckard, A, Anafi, RC, Hogenesch, JB, Haase, SB, and Harer, J. "Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data." Bioinformatics (Oxford, England) 29, no. 24 (December 2013): 3174-3180. Full Text
  - Topp, CN, Iyer-Pascuzzi, AS, Anderson, JT, Lee, C-R, Zurek, PR, Symonova, O, Zheng, Y, Bucksch, A, Mileyko, Y, Galkovskyi, T, Moore, BT, Harer, J, Edelsbrunner, H, Mitchell-Olds, T, Weitz, JS, and Benfey, PN. "3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture." Proceedings of the National Academy of Sciences of the United States of America 110, no. 18 (April 11, 2013): E1695-E1704. Full Text
  - Topp, , CN, , Iyer-Pascuzzi, AS, Anderson, JT, Lee, C-R, Zurek, PR, Symonova, O, Zheng, Y, Bucksch, A, Milyeko, Y, Galkovskyi, T, Moore, BT, Harer, J, Edelsbrunner, H, Mitchell-Olds, T, Weitz, JS, and Benfey, PN. "3-dimensional phenotyping of growing root systems and QTL mapping identifies core regions of the rice genome controlling root architecture (Submitted)." PNAS 110 (2013): E1695-1704.
  - Munch, E, Shapiro, M, and Harer, J. "Failure filtrations for fenced sensor networks." The International Journal of Robotics Research 31, no. 9 (August 2012): 1044-1056. Full Text
  - Bendich, P, Harer, J, and Harer, J. "Persistent Homology Enhanced Dimension Reduction (Submitted)." Foundations of Computational Mathematics (2012). (Academic Article)
  - Galkovskyi, T, Mileyko, Y, Bucksch, A, Moore, B, Symonova, O, Price, CA, Topp, CN, Iyer-Pascuzzi, AS, Zurek, PR, Fang, S, Harer, J, Benfey, PN, and Weitz, JS. "GiA Roots: software for the high throughput analysis of plant root system architecture." Bmc Plant Biology 12 (January 2012): 116-null. Full Text
  - Michael Jenista, . "Realizing Boolean Dynamics in Switching Networks (Submitted)." Siam Journal of Applied Dynamical Systems (2012): 12-. (Academic Article)
  - Munch, E, Shapiro, M, and Harer, J. "Failure filtrations for fenced sensor networks." International Journal of Robotics Research 31, no. 9 (2012): 1044-1056. Full Text
  - Bendich, P, Galkovskyi, T, and Harer, J. "Improving homology estimates with random walks." Inverse Problems 27, no. 12 (December 1, 2011): 124002-124002. Full Text
  - Mileyko, Y, Mukherjee, S, and Harer, J. "Probability measures on the space of persistence diagrams." Inverse Problems 27, no. 12 (December 1, 2011): 124007-124007. Full Text
  - Bendich, P, and Harer, J. "Persistent Intersection Homology." Foundations of Computational Mathematics 11, no. 3 (June 2011): 305-336. Full Text
  - Bini, G, and Harer, J. "Euler characteristics of moduli spaces of curves." Journal of the European Mathematical Society (2011): 487-512. Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, Harer, J, and Mileyko, Y. "Lipschitz Functions Have L p -Stable Persistence." Foundations of Computational Mathematics 10, no. 2 (April 2010): 127-139. Full Text
  - Iyer-Pascuzzi, AS, Symonova, O, Mileyko, Y, Hao, Y, Belcher, H, Harer, J, Weitz, JS, and Benfey, PN. "Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems." Plant Physiology 152, no. 3 (March 2010): 1148-1157. Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, and Harer, J. "Extending Persistence Using Poincaré and Lefschetz Duality." Foundations of Computational Mathematics 9, no. 1 (February 2009): 79-103. Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, and Harer, J. "Extending Persistence Using Poincaré and Lefschetz Duality." Foundations of Computational Mathematics 9, no. 1 (February 2009): 133-134. Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Persistent homology for kernels, images, and cokernels." Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (2009): 1011-1020.
  - Edelsbrunner, H, and Harer, J. "The Persistent Morse Complex Segmentation of a 3-Manifold." (2009): 36-50. Full Text
  - Fink, T, Ahnert, S, Bar On, R, and Harer, J. "Exact dynamics of Boolean networks with connectivity one (Submitted)." PRL (2009). (Academic Article)
  - Edelsbrunner, H, Harer, J, Mascarenhas, A, Pascucci, V, and Snoeyink, J. "Time-varying Reeb graphs for continuous space–time data." Computational Geometry 41, no. 3 (November 2008): 149-166. Full Text
  - Edelsbrunner, H, Harer, J, and Patel, AK. "Reeb spaces of piecewise linear mappings." Proceedings of the Twenty Fourth Annual Symposium on Computational Geometry Scg '08 (2008). Full Text
  - "Alpha-beta witness complexes." Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4619 LNCS (December 1, 2007): 386-397.
  - Bendich, P, Cohen-Steiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Inferring Local Homology from Sampled Stratified Spaces." 48th Annual Ieee Symposium on Foundations of Computer Science (Focs'07) (October 2007). Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, and Harer, J. "Stability of Persistence Diagrams." Discrete & Computational Geometry 37, no. 1 (January 2007): 103-120. Full Text
  - Agarwal, PK, Edelsbrunner, H, Harer, J, and Wang, Y. "Extreme Elevation on a 2-Manifold." Discrete & Computational Geometry 36, no. 4 (December 2006): 553-572. Full Text
  - Cohen-Steiner, D, Edelsbrunner, H, and Harer, J. "Stability of persistence diagrams." Proceedings of the Twenty First Annual Symposium on Computational Geometry Scg '05 (2005). Full Text
  - "Extreme elevation on a 2-manifold." Proceedings of the Annual Symposium on Computational Geometry (September 29, 2004): 357-365.
  - "Time-varying Reeb graphs for continuous space-time data." Proceedings of the Annual Symposium on Computational Geometry (September 29, 2004): 366-372.
  - Cole-McLaughlin, K, Edelsbrunner, H, Harer, J, Natarajan, V, and Pascucci, V. "Loops in Reeb Graphs of 2-Manifolds." Discrete & Computational Geometry 32, no. 2 (July 2004). Full Text
  - "HPRM: A hierarchical PRM." Proceedings Ieee International Conference on Robotics and Automation 3 (December 9, 2003): 4433-4438.
  - "Morse-Smale complexes for piecewise linear 3-manifolds." Proceedings of the Annual Symposium on Computational Geometry (July 28, 2003): 361-370.
  - Pascucci, V. "Loops in Reeb graphs of 2-manifolds." Proceedings of the Annual Symposium on Computational Geometry (July 28, 2003): 344-350.
  - Edelsbrunner, H, Harer, J, and Zomorodian, A. "Hierarchical Morse--Smale Complexes for Piecewise Linear 2-Manifolds." Discrete and Computational Geometry 30, no. 1 (May 21, 2003): 87-107. Full Text
  - "A geometric parametrization for the virtual euler characteristics of the moduli spaces of real and complex algebraic curves." Transactions of the American Mathematical Society 353, no. 11 (December 1, 2001): 4405-4427.
  - "Hierarchical Morse complexes for piecewise linear 2-manifolds." Proceedings of the Annual Symposium on Computational Geometry (January 1, 2001): 70-79.
  - Harer, J. "The third homology group of the moduli space of curves." Duke Mathematical Journal 63, no. 1 (June 1991): 25-55. Full Text
  - Harer, JL. "Stability of the homology of the moduli spaces of Riemann surfaces with spin structure." Mathematische Annalen 287, no. 1 (March 1990): 323-334. Full Text
  - "The Euler characteristic of the moduli space of curves." Inventiones Mathematicae 85, no. 3 (October 1, 1986): 457-485. Full Text
  - HARER, J, KAS, A, and KIRBY, R. "HANDLEBODY STRUCTURES FOR COMPLEX-SURFACES." MEMOIRS OF THE AMERICAN MATHEMATICAL SOCIETY 62, no. 350 (July 1986): 1-102. Link to Item
  - Harer, JL. "The virtual cohomological dimension of the mapping class group of an orientable surface." Inventiones Mathematicae 84, no. 1 (February 1986): 157-176. Full Text
  - HARER, J. "The virtual cohomological dimension of the mapping class group of an orientable surface." Invent. Math. 84 (1986): 157-176. Full Text
  - Harer, J, and Zagier, D. "The Euler characteristic of the moduli space of curves." Inventiones Mathematicae 85, no. 3 (1986): 457-485. Full Text
  - Harer, J. "The second homology group of the mapping class group of an orientable surface." Inventiones Mathematicae 72, no. 2 (June 1983): 221-239. Full Text
  - HARER, JL. "The second homology group of the mapping class group of an orientable surface." Invent.Math. 72 (1983): 221-239. Full Text
  - Harer, J. "Representing elements of π1 M3 by fibred knots." Mathematical Proceedings of the Cambridge Philosophical Society 92, no. 01 (July 1982): 133-133. Full Text
  - HARER, J. "How to construct all fibered knots and links." Topology 21 (1982): 263-280. Full Text
  - Harer, J. "How to construct all fibered knots and links." Topology 21, no. 3 (1982): 263-280. Full Text
  - Casson, A, and Harer, J. "Some homology lens spaces which bound rational homology balls." Pacific Journal of Mathematics 96, no. 1 (September 1, 1981): 23-36. Full Text
  - Harer, J. "On handlebody structures for hypersurfaces in ?3 and ?P 3." Mathematische Annalen 238, no. 1 (February 1978): 51-58. Full Text
  - Agarwal, PK, Collins, AD, and Harer, JL. "Minimal trap design(Accepted)." Proceedings 2001 Icra. Ieee International Conference on Robotics and Automation (Cat. No.01ch37164) . Full Text
  - Bern, M, Eppstein, D, Agarwal, PK, Amenta, N, Chew, P, Dey, T, Dobkin, DP, Edelsbrunner, H, Grimm, C, Guibas, LJ, Harer, J, Hass, J, Hicks, A, Johnson, CK, Lerman, G, Letscher, D, Plassmann, P, Sedgwick, E, Snoeyink, J, Weeks, J, Yap, C, and Zorin, D. "Emerging Challenges in Computational Topology." Link to Item
  - Edelsbrunner, H, Harer, J, Natarajan, V, and Pascucci, V. "Local and global comparison of continuous functions(Accepted)." Ieee Visualization 2004 . Full Text
  - Turner, K, Mileyko, Y, Mukherjee, S, and Harer, J. "Fréchet Means for Distributions of Persistence diagrams." Open Access Copy Link to Item
- Conference Papers
  - Garagic, D, Peskoe, J, Liu, F, Claffey, MS, Bendich, P, Hineman, J, Borggren, N, Harer, J, Zulch, P, and Rhodes, BJ. "Upstream fusion of multiple sensing modalities using machine learning and topological analysis: An initial exploration." 2018 IEEE Aerospace Conference. March 3, 2018 - March 10, 2018.: IEEE, March 2018. Full Text
  - "Geometric models for musical audio data." June 1, 2016. Full Text Open Access Copy
  - Rouse, D, Watkins, A, Porter, D, Harer, J, Bendich, P, Strawn, N, Munch, E, DeSena, J, Clarke, J, Gilbert, J, Chin, P, and Newman, A. "Feature-aided multiple hypothesis tracking using topological and statistical behavior classifiers." SPIE Defense + Security.: SPIE, May 21, 2015. Full Text
  - Edelsbrunner, H, and Harer, J. "Persistent homology - a survey." Joint Summer Research Conference of the AMS/IMS/SIAM. Snowbird, UT. June 18, 2006 - June 22, 2006.: AMER MATHEMATICAL SOC, January 1, 2008. Link to Item
  - Czumaj, A, and Sohler, C. "Testing Expansion in Bounded-Degree Graphs." 48th Annual IEEE Symposium on Foundations of Computer Science (FOCS'07). October 21, 2007 - October 23, 2007.: IEEE, October 2007. Full Text
  - Bendich, P, Cohen-Steiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Inferring local homology from sampled stratified spaces." 2007. Full Text Link to Item
Teaching & Mentoring
Recent Courses
- MATH 412: Topological Data Analysis 2018
- MATH 494: Research Independent Study 2018
- MATH 713: Topological Data Analysis 2018
- MATH 493: Research Independent Study 2017
- MATH 611: Algebraic Topology I 2017
Scholarly, Clinical, & Service Activities
Presentations & Appearances
Outreach & Engaged Scholarship
- Bass Connections Faculty Team Member. Data+. June 2016 - July 2016 2016
Service to the Profession
Service to Duke

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Books

Academic Articles

Conference Papers

Recent Courses

Presentations & Appearances

Outreach & Engaged Scholarship

Service to the Profession

Service to Duke