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Math @ Duke



John Harer, Professor of Mathematics and Computer Science

John Harer
Contact Info:
Office Location:  109 Physics
Office Phone:  (919) 660-2845
Email Address: send me a message
Web Page:

Teaching (Fall 2014):

    Physics 227, TuTh 10:05 AM-11:20 AM
Teaching (Spring 2015):

    Bio Sci 155, TuTh 10:05 AM-11:20 AM
    (also cross-listed as MATH 190.01)

PhDUniversity of California, Berkeley1979
BSHaverford College1974

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

Curriculum Vitae
Current Ph.D. Students   (Former Students)

  • Hamza Ghadyali  
  • Colbert Sesanker  
  • Darryl Wade  
  • Anastasia Deckhard  
Postdocs Mentored

  • Ellen Gasparovic (2013/12-present)  
  • Omer Bobrowski (2012/11-present)  
  • Joshua Vogelstein (2012/11-present)  
  • Jurgen Sladeczek (2011 - present)  
  • Jose' Perea (2011/12-present)  
  • Kevin McGoff (2011/12-present)  
  • Nate Strawn (2011/12-present)  
  • Paul Bendich (January 01, 2011 - present)  
  • Chris Topp (2009 - 2011)  
  • Anjali Iyer-Pascuzzi (2007 - 2011)  
  • Yuriy Mileyko (2008 - 2011)  
Recent Publications   (More Publications)

  1. Katharine Turner, Yuriy Mileyko, Sayan Mukherjee, John Harer, Fréchet Means for Distributions of Persistence diagrams, arXiv:1206.2790 (2013) (  [abs]
  2. Elizabeth Munch, Paul Bendich, Katharine Turner, Sayan Mukherjee, Jonathan Mattingly, John Harer, Probabilistic Fréchet Means and Statistics on Vineyards (2013) (  [abs]
  3. Jose Perea and J. Harer, Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis, arXiv:1307.6188 (2013) (  [abs]
  4. J. Perea, A. Deckard, S. Haase and J. Harer, Applications of SWiPerS to the discovery of periodic genes (Submitted, 2013)
  5. Christopher N Topp, Anjali S Iyer-Pascuzzi, Jill T Anderson, Cheng-Ruei Lee, Paul R Zurek, Olga Symonova, Ying Zheng, Alexander Bucksch, Yuriy Milyeko, Taras Galkovskyi, Brad Moore, John Harer, Herbert Edelsbrunner, Thomas Mitchell Olds, Joshua S Weitz, Philip N Benfey, 3-dimensional phenotyping of growing root systems combined with QTL mapping identifies core regions of the rice genome controlling root architecture, PNAS (2013) (  [abs]
Recent Grant Support

  • Foundations of Information Systems, Johns Hopkins University Applied Physics Laboratory, 108852, 2012/04-2017/03.      
  • ATD: Online Multiscale Algorithms for Geometric Density Estimation in High-Dimensions and Persistent Homology of Data for Improved Threat, National Science Foundation, DMS-1222567, 2012/09-2016/08.      
  • EMSW21-RTG: Geometric, Topological and Statistical Methods for Analyzing Massive Datasets, National Science Foundation, DMS-1045153, 2011/08-2016/07.      
  • Bioinformatics and Computational Biology Training Program, National Institutes of Health, 5T32-GM071340-05, 2005/07-2016/06.      
  • 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 from Topology Using the CHomP Database, Air Force Office of Scientific Research, FA9550-10-1-0436, 2010/09-2015/09.      
  • Designing Networks that are Capable of Self-Healing and Adapting, Defense Threat Reduction Agency, 2010/11-2013/11.      
  • Knowledge Enhanced Exapixel Photography, Defense Advanced Research Projects Agency, N66001-11-1-4002-P00005, 2012/10-2013/09.      
  • OASIS: Operationally Aware Sensing thru Information Scaling, Johns Hopkins University Applied Physics Laboratory, 110279, 2012/10-2013/09.      
  • A Multidimensional Imaging Platform to Analyze Crop Root System Dynamics in Response to Changing Environments, Department of Agriculture, 2011-67012-30773, 2011/09-2013/08.      
  • GEPR: Genome-wide analysis of root traits, National Science Foundation, NSF-DBI-0820624, 2008/09-2012/08.      
  • Conference: Foundational Mathematics for Understanding Security, Air Force Office of Scientific Research, AFOSR-FA9550-10-1-0436, 2012/07-2012/07.      
  • Duke Center for Systems Biology, NIH, 2007/07-2012/06.      
  • Data Acquisition, Processing and Modeling of Morphogenesis in 4D, NSF, 0714796, 2006/07-2012/06.      
  • Biochronicity: Time, Network, Evolution and Function, Defense Advanced Research Projects Agency, D12AP00001, 2011/11-2012/04. 
ph: 919.660.2800
fax: 919.660.2821

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