John Harer

John Harer
  • Professor of Mathematics
External address: 109 Physic Bldg, Durham, NC 27708
Internal office address: Box 90320, Durham, NC 27708-0034
Phone: (919) 660-2845

Research Areas and Keywords

Biological Modeling
Gene Regulatory Networks, Network Inference
Computational Mathematics
Topological Data Analysis, Geometric Data Analysis, Network Dynamics, Network Inference
Signals, Images & Data
Topological Data Analysis, Geometric Data Analysis
Topological Data Analysis

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.

Education & Training
  • Ph.D., University of California at Berkeley 1979

  • B.A., Haverford College 1974

Selected Grants

Geometric and Topological Methods for Multi-Modal Data Analysis and Fusion awarded by Air Force Office of Scientific Research (Principal Investigator). 2018 to 2021

An Adaptive Pipeline from Scientific Data to Models awarded by Defense Advanced Research Projects Agency (Principal Investigator). 2017 to 2020

BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features awarded by National Science Foundation (Principal Investigator). 2014 to 2019

Quantifying Complex Spatiotemporal Systems awarded by Rutgers, The State University of New Jersey (Principal Investigator). 2016 to 2018

EMSW21-RTG: Geometric, Topological awarded by National Science Foundation (Principal Investigator). 2011 to 2018

ATD: Online Multiscale Algorithms for Geometric Density Estimation in High-Dimensions and Persistent Homology of Data fo awarded by National Science Foundation (Co-Principal Investigator). 2012 to 2017

Foundation of Information Systems awarded by Johns Hopkins University (Principal Investigator). 2012 to 2017

Analysis of High Dimensional Complex Spatio-Temporal Data awarded by Defense Advanced Research Projects Agency (Principal Investigator). 2015 to 2016

Inferring Network Controls awarded by Air Force Office of Scientific Research (Principal Investigator). 2010 to 2015

A Multidimensional Imaging Platform to Analyze Crop Root System Dynamics in Response to Changing Environments awarded by Department of Agriculture (Co-Principal Investigator). 2011 to 2013


Edelsbrunner, H, and Harer, J. Computational Topology - an Introduction. American Mathematical Society, 2010.

Tralie, CJ, Smith, A, Borggren, N, Hineman, J, Bendich, P, Zulch, P, and Harer, J. "Geometric cross-modal comparison of heterogeneous sensor data." Ieee Aerospace Conference Proceedings 2018-March (June 25, 2018): 1-10. 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 32.5 (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 52.6 (December 1, 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 17.1 (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).

Bendich, P, Gasparovic, E, Harer, J, Izmailov, R, and Ness, L. "Multi-scale local shape analysis and feature selection in machine learning applications." Proceedings of the International Joint Conference on Neural Networks 2015-September (September 28, 2015). Full Text Open Access Copy

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

Perea, JA, and Harer, J. "Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis." Foundations of Computational Mathematics 15.3 (June 27, 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 (January 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 113.13 (September 26, 2014): 138701-. Full Text


Garagić, 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." June 25, 2018. Full Text

Bendich, P, Gasparovic, E, Harer, J, and Tralie, C. "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, S, and Newman, A. "Feature-aided multiple hypothesis tracking using topological and statistical behavior classifiers." January 1, 2015. Full Text

Edelsbrunner, H, and Harer, J. "Persistent homology - a survey." Joint Summer Research Conference of the AMS/IMS/SIAM. June 18, 2006 - June 22, 2006. Snowbird, UT.: AMER MATHEMATICAL SOC, January 1, 2008.

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

Former Graduate Students

  • Anne Collins (01/2002 - 01/2006): Configuration Spaces in Robotic Manipulation and Motion Planning