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, brain imaging, biological networks and gene expression.

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

  • B.A., Harvard University 1974

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2021

BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features awarded by National Science Foundation (Principal Investigator). 2014 to 2018

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

GEPR: Genome-wide analysis of root traits awarded by National Science Foundation (Co-Principal Investigator). 2008 to 2012


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

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 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-.

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

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

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 15.9 (September 5, 2014): 446-. Full Text

Turner, K, Mileyko, Y, Mukherjee, S, and Harer, J. "Fréchet Means for Distributions of Persistence Diagrams." Discrete & Computational Geometry 52.1 (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 15.3 (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) 29.24 (December 2013): 3174-3180. Full Text


Bendich, P, Gasparovic, E, Harer, J, and Tralie, C. "Geometric models for musical audio data." June 1, 2016. Full Text

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." 2008.

Bendich, P, Cohen-Steiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Inferring Local Homology from Sampled Stratified Spaces." IEEE Computer Society, 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