John Harer, Professor of Mathematics and Electrical and Computer Engineering

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.

Contact Info:

Office Location:	109 Physic Bldg, Durham, NC 27708
Office Phone:	(919) 660-2845
Email Address:
Web Page:	http://cms.math.duke.edu/harer/?q=home

Teaching (Fall 2019):

• MATH 412.01, TOPOLOGICAL DATA ANALYSIS Synopsis

  Physics 259, TuTh 01:25 PM-02:40 PM

  (also cross-listed as MATH 713.01)

Education:

Ph.D.	University of California at Berkeley	1979
BS	Haverford College	1974
B.A.	Haverford College	1974

Specialties:

Topology
Geometry
Mathematical Biology
Applied Math

Research Interests: Computational Topology, Computational Biology, Algorithms

Current projects: Biochronicity, Computational Topology, Statistical Topology, Self-Healing Networks, Network Inference, Geometric Image 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.

Areas of Interest:

Computational Biology
Computational Topology
Dynamics on Networks
Algorithms

Keywords:

Algorithms • Automatic Data Processing • Biomass • Chromosome Mapping • Crosses, Genetic • Genome, Plant • Genotype • Image Processing, Computer-Assisted • Imaging, Three-Dimensional • Inbreeding • Models, Biological • Multivariate Analysis • Oryza sativa • Phenotype • Plant Roots • Principal Component Analysis • Quantitative Trait Loci • Quantitative Trait, Heritable • Recombination, Genetic • Reproducibility of Results • Software • Workflow

Curriculum Vitae

Current Ph.D. Students   (Former Students)

• Christopher Traile  
• Hamza Ghadyali  
• Colbert Sesanker  
• Darryl Wade  

Postdocs Mentored

• Henry Adams (2014 - 2015)  
• Francis Motta (2014/12-present)  
• Justin Curry (2014/12-present)  
• Anastasia Deckard (2014/12-present)  
• Ellen Gasparovic (2013 - 2015)  
• Xin Guo (2013 - 2014)  
• Xin Guo (2013 - 2015)  
• Omer Bobrowski (2012 - 2014)  
• Joshua Vogelstein (2012 - 2014)  
• Jurgen Sladeczek (2011 - 2015)  
• Jose' Perea (2011 - 2015)  
• Kevin McGoff (2011 - 2015)  
• Nate Strawn (2011 - 2015)  
• Paul Bendich (January 01, 2011 - present)  
• Chris Topp (2009 - 2011)  
• Anjali Iyer-Pascuzzi (2007 - 2011)  
• Yuriy Mileyko (2008 - 2011)  

Recent Publications   (More Publications)

1. Tralie, CJ; Smith, A; Borggren, N; Hineman, J; Bendich, P; Zulch, P; Harer, J, Geometric cross-modal comparison of heterogeneous sensor data, Ieee Aerospace Conference Proceedings, vol. 2018-March (June, 2018), pp. 1-10, IEEE [doi]  [abs]
2. Garagić, D; Peskoe, J; Liu, F; Claffey, MS; Bendich, P; Hineman, J; Borggren, N; Harer, J; Zulch, P; Rhodes, BJ, Upstream fusion of multiple sensing modalities using machine learning and topological analysis: An initial exploration, Ieee Aerospace Conference Proceedings, vol. 2018-March (June, 2018), pp. 1-8, IEEE, ISBN 9781538620144 [doi]  [abs]
3. 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; Hogenesch, JB, Guidelines for Genome-Scale Analysis of Biological Rhythms., Journal of Biological Rhythms, vol. 32 no. 5 (October, 2017), pp. 380-393 [doi]  [abs]
4. Bendich, P; Chin, SP; Clark, J; DeSena, J; Harer, J; Munch, E; Newman, A; Porter, D; Rouse, D; Strawn, N; Watkins, A, Topological and statistical behavior classifiers for tracking applications, Ieee Transactions on Aerospace and Electronic Systems, vol. 52 no. 6 (December, 2016), pp. 2644-2661, Institute of Electrical and Electronics Engineers (IEEE) [doi]  [abs]
5. McGoff, KA; Guo, X; Deckard, A; Kelliher, CM; Leman, AR; Francey, LJ; Hogenesch, JB; Haase, SB; Harer, JL, The Local Edge Machine: inference of dynamic models of gene regulation., Genome Biology, vol. 17 no. 1 (October, 2016), pp. 214 [doi]  [abs]

Recent Grant Support

• Geometric and Topological Methods for Multi-Modal Data Analysis and Fusion, Air Force Office of Scientific Research, FA9550-18-1-0266, 2018/06-2021/06.      
• Geometric and Topological Methods for Multi-Modal Data Analysis and Fusion, Air Force Office of Scientific Research, FA9550-18-1-0266, 2018/06-2021/06.      
• An Adaptive Pipeline from Scientific Data to Models, Defense Advanced Research Projects Agency, 2017/09-2020/03.      
• An Adaptive Pipeline from Scientific Data to Models, Defense Advanced Research Projects Agency, 2017/09-2020/03.      
• BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features, National Science Foundation, IIS-1447491, 2014/09-2019/08.      
• BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features, National Science Foundation, IIS-1447491, 2014/09-2019/08.      
• Quantifying Complex Spatiotemporal Systems, Rutgers, The State University of New Jersey, 2016/08-2018/07.      
• EMSW21-RTG: Geometric, Topological, National Science Foundation, DMS-1045153, 2011/08-2018/07.      
• ATD: Online Multiscale Algorithms for Geometric Density Estimation in High-Dimensions and Persistent Homology of Data fo, National Science Foundation, DMS-1222567, 2012/09-2017/08.      
• Foundation of Information Systems, Johns Hopkins University, 108852, 2012/04-2017/03.