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John Harer, Professor of Mathematics and Electrical and Computer Engineering

John Harer

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.

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

Teaching (Spring 2017):

  • MATH 412.01, TOPOLOGY WITH APPLICATIONS Synopsis
    Gross Hall 318, TuTh 11:45 AM-01:00 PM
Education:

Ph.D.University of California at Berkeley1979
BSHaverford College1974
B.A.Harvard University1974
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 G. 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. 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: biology for the post-genomic era, vol. 17 no. 1 (October, Submitted, 2016), pp. 214  [abs]
  2. Bendich, P; Gasparovic, E; Harer, J; Tralie, C, Geometric models for musical audio data, LIPIcs, vol. 51 (June, 2016), pp. 65.1-65.5, ISBN 9783959770095 [doi]  [abs]
  3. Bendich, P; Gasparovic, E; Harer, J; Izmailov, R; Ness, L, Multi-scale local shape analysis and feature selection in machine learning applications, Proceedings of the International Joint Conference on Neural Networks, vol. 2015-September (September, Accepted, 2015) [doi]  [abs]
  4. Perea, JA; Deckard, A; Haase, SB; Harer, J, SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data., BMC Bioinformatics, vol. 16 (August, 2015), pp. 257 [doi]  [abs]
  5. Rouse, D; Watkins, A; Porter, D; Harer, J; Bendich, P; Strawn, N; Munch, E; Desena, J; Clarke, J; Gilbert, J; Chin, S; Newman, A, Feature-aided multiple hypothesis tracking using topological and statistical behavior classifiers, Proceedings of SPIE - The International Society for Optical Engineering, vol. 9474 (January, 2015), ISSN 10.1117/12.2179555, ISBN 9781628415902 [doi]  [abs]
Recent Grant Support

  • BIGDATA: F: DKA: CSD: Topological Data Analysis and Machine-Learning with Community-Accepted Features, National Science Foundation, IIS-1447491, 2014/09-2018/08.      
  • Quantifying Complex Spatiotemporal Systems, Rutgers, The State University of New Jersey, 2016/08-2017/07.      
  • Foundation of Information Systems, Johns Hopkins University, 108852, 2012/04-2017/03.      
  • Biochronicity: Time, Evolution, Networks, and Function, Defense Advanced Research Projects Agency, D12AP00025-0002, 2012/03-2016/03.      
  • Biochronicity: Time, Evolution Networks, Defense Advanced Research Projects Agency, D12AP00001, 2011/12-2015/12.      
  • Inferring Network Controls, Air Force Office of Scientific Research, FA9550-10-1-0436, 2010/09-2015/08.      

 

dept@math.duke.edu
ph: 919.660.2800
fax: 919.660.2821

Mathematics Department
Duke University, Box 90320
Durham, NC 27708-0320