John Harer
 Professor of Mathematics
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
Geometric and Topological Methods for MultiModal Data Analysis and Fusion awarded by Air Force Office of Scientific Research (Principal Investigator). 2018 to 2021
BIGDATA: F: DKA: CSD: Topological Data Analysis and MachineLearning with CommunityAccepted Features awarded by National Science Foundation (Principal Investigator). 2014 to 2019
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
EMSW21RTG: Geometric, Topological awarded by National Science Foundation (Principal Investigator). 2011 to 2018
ATD: Online Multiscale Algorithms for Geometric Density Estimation in HighDimensions and Persistent Homology of Data fo awarded by National Science Foundation (CoPrincipal Investigator). 2012 to 2017
Foundation of Information Systems awarded by Johns Hopkins University (Principal Investigator). 2012 to 2017
Analysis of High Dimensional Complex SpatioTemporal 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 (CoPrincipal Investigator). 2011 to 2013
Pages
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 CrossModal Comparison of Heterogeneous Sensor Data." Proceedings of the 39th Ieee Aerospace Conference (March 2018). Open Access Copy
Hughes, ME, Abruzzi, KC, Allada, R, Anafi, R, Arpat, AB, Asher, G, Baldi, P, de Bekker, C, BellPedersen, D, Blau, J, Brown, S, Ceriani, MF, Chen, Z, Chiu, JC, Cox, J, Crowell, AM, DeBruyne, JP, Dijk, DJ, DiTacchio, L, Doyle, FJ, Duffield, GE, Dunlap, JC, EckelMahan, K, Esser, KA, FitzGerald, GA, Forger, DB, Francey, LJ, Fu, YH, 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, SassoneCorsi, P, Sehgal, A, SherrillMix, S, Skene, DJ, Storch, KF, Takahashi, JS, Ueda, HR, Wang, H, Weitz, C, Westermark, PO, Wijnen, H, Xu, Y, Wu, G, Yoo, SH, Young, M, Zhang, EE, Zielinski, T, and Hogenesch, JB. "Guidelines for GenomeScale Analysis of Biological Rhythms." Journal of Biological Rhythms 32.5 (October 2017): 380393. 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): 26442661. 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. "Multiscale local shape analysis and feature selection in machine learning applications." Proceedings of the International Joint Conference on Neural Networks 2015September (September 28, 2015). Full Text Open Access Copy
Perea, JA, Deckard, A, Haase, SB, and Harer, J. "SW1PerS: Sliding windows and 1persistence scoring; discovering periodicity in gene expression time series data." BMC bioinformatics 16 (August 16, 2015): 257. Full Text
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 cellcycle progression." Genome Biology 15.9 (September 5, 2014): 446null. 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): 4470. Full Text
Pages
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. "Featureaided 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.
Bendich, P, CohenSteiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Inferring Local Homology from Sampled Stratified Spaces." IEEE Computer Society, 2007. Full Text
Bendich, P, CohenSteiner, D, Edelsbrunner, H, Harer, J, and Morozov, D. "Inferring local homology from sampled stratified spaces." 2007. Full Text
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Former Graduate Students

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