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John Harer, Professor of Mathematics and Computer Science

John Harer
Contact Info:
Office Location:  207 Physics
Office Phone:  (919) 660-2845
Email Address: send me a message
Web Page:  http://cms.math.duke.edu/harer/?q=home

Teaching (Fall 2012):

  • MATH 323S.01, GEOMETRY Synopsis
    Physics 205, TuTh 01:25 PM-02:40 PM
  • CBB 510S.01, COMP BIO SEMINAR Synopsis
    TBA, M 10:20 AM-11:10 AM
  • MATH 573S.01, MODELING BIO SYSTEMS Synopsis
    TBA, TuTh 11:45 AM-01:00 PM
Office Hours:

Tuesday, Thursday, 9:45-10:45
Education:

PhDUniversity of California, Berkeley1979
BSHaverford College1974
Specialties:

Topology
Geometry
Applied Math
Research Interests: Computational Topology, Computational Biology, Algorithms

Current projects: Systems Biology, 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, plant root architecture, biological networks and gene expression.

Areas of Interest:

Computational Biology
Computational Topology
Dynamics on Networks
Algorithms

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

Postdocs Mentored

  • Jose Peres (2011-2014)  
  • Kevin McGoff (2011/12-present)  
  • Nate Strawn (2011/12-present)  
  • Paul Bendich (January 01, 2011 - present)  
  • Chris Topp (2009 - present)  
  • Anjali Iyer-Pascuzzi (2007 - present)  
  • Yuriy Mileyko (2008 - 2011)  
Recent Publications   (More Publications)

  1. with Taras Galkovskyi, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles A Price, Christopher Topp, Anjali Iyer-Pascuzzi, Paul Zurek, Suqin Fang, Philip N Benfey, and Joshua S Weitz, GiA Roots: Software for the High Throughput Analysis of Plant Root System Images, BMC Plant Biology (Submitted, 2011)  [abs]
  2. with Yuriy Mileyko, Sayan Mukherjee, Probability measures on the space of persistence diagrams, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 25  [abs] [author's comments]
  3. with Paul Bendich, Taras Galkovskyi, Improving Homology Estimates with Random Walks, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 16  [abs]
  4. with Elizabeth Munch, Michael Shapiro, Failure Filtrations for Fenced Sensor Networks, The International Journal of Robotics Research (Submitted, 2011), pp. 14  [abs]
  5. with Anjali S. Iyer-Pascuzzi, Christopher N. Topp, Jill T. Anderson, Cheng-Ruei Lee, Olga Symonova, Yuriy Mileyko, Taras Galkovsky, Ying Zheng, Randy Clark, Leon Kochian, Herbert Edelsbrunner, Joshua S. Weitz, Thomas Mitchell-Olds and Philip N. Benfey, Quantitative Genetic Analysis of Root System Architecture in Rice Plant and Animal Genomes, XX Genome Conference (2011)
Recent Grant Support

  • 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, Defense Advanced Research Projects Agency, 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.      
  • 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.      
  • Predictive Biology: Adaptability, Robustness and the Fundamental Laws of Biology, Princeton University, 00001744, 2009/09-2011/09.      
  • Duke on Network Security, Air Force Office of Scientific Research, FA9550-10-1-0465, 2010/09-2011/08.      
  • Microstates to Macrodynamics: A New Mathematics of Biology, Princeton University, 00001107-9, 2005/09-2010/10.      
  • Doctoral Program in Management and Analysis of Large Data Acquired from Sensors, Department of Education, P200A070505, 2007/08-2010/08.      
  • Bioinformatics and Computational Biology Training Program, National Institutes of Health, 5T32-GM071340-05S1, 2009/08-2010/08.      

 

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

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