# 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

##### Computational Mathematics

##### Signals, Images & Data

##### Topology

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.

### Selected Grants

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

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

## Pages

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

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, and Hughey, JJ et al. "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 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-.
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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

## Pages

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