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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:  http://cms.math.duke.edu/harer/?q=home

Teaching (Spring 2015):

  • BIOLOGY 218.01, BIOLOGICAL CLOCKS Synopsis
    Bio Sci 155, TuTh 10:05 AM-11:20 AM
    (also cross-listed as MATH 190.01)
Education:

PhDUniversity of California, Berkeley1979
BSHaverford College1974
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

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

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

  • Henry Adams (2014/12-present)  
  • Francis Motta (2014/12-present)  
  • Justin Curry (2014/12-present)  
  • Anastasia Deckard (2014/12-present)  
  • Ellen Gasparovic (2013/12-present)  
  • Xin Guo (2013 - 2014)  
  • Omer Bobrowski (2012/11-present)  
  • Joshua Vogelstein (2012 - 2014)  
  • 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, Fr├ęchet Means for Distributions of Persistence diagrams, Discrete and Computational Geometry, vol. 52 (July, 2014), pp. 44-70 [arXiv:1206.2790], [doi]  [abs]
  2. Jose Perea and J. Harer, Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis, Foundations of Computational Mathematics (May, 2014), ISSN 1615-3375 (http://arxiv.org/abs/1307.6188.)  [abs]
  3. S. Bristow, A. Leman, L. Simmons Kovacs, A. Deckard, J. Harer, S. B. Haase, Checkpoints Couple Transcription Network Oscillator Dynamics to Cell-Cycle Progression, Genome Biology, vol. 15:446 (2014) [doi]  [abs]
  4. J. Perea, A. Deckard, S. Haase and J. Harer, Sliding Windows and 1-Persistence Scoring; Discovering Periodicity in Gene Expression Time Series Data, BMC Bioinformatics (Submitted, 2014)  [abs]
  5. K.A. McGoff, X. Guo, A. Deckard, A.R. Leman, C.M. Kelliher, S.B. Haase, and J.L. Harer, The Local Edge Machine: Inference of dynamic models of gene regulation, Nature Methods (Submitted, 2014)  [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.      

 

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

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