John Harer, Professor of Mathematics and Computer Science

Contact Info:

Office Location:	109 Physics
Office Phone:	(919) 660-2845
Email Address:
Web Page:	http://cms.math.duke.edu/harer/?q=home

Teaching (Fall 2013):

• MATH 412.01, TOPOLOGY WITH APPLICATIONS Synopsis

  Physics 235, TuTh 10:05 AM-11:20 AM

  (also cross-listed as COMPSCI 434.01)

Education:

PhD	University of California, Berkeley	1979
BS	Haverford College	1974

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)

• Michael Casey  
• Elizabeth A Munch  
• Anastasia Deckhard  

Postdocs Mentored

• Omer Bobrowski (2012/11-present)  
• Joshua Vogelstein (2012/11-present)  
• Jurgen Sladeczek (2011 - present)  
• Jose Peres (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. Katherine Turner, Yuriy Mileyko, Sayan Mukherjee and John Hare, Fréchet Means for Distributions of Persistence diagrams, arXiv:1206.2790 [math.ST] (Preprint, 2012)  [abs]
2. T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C. Topp, A. Iyer-Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey and J. Weitz, GiA Roots: software for the high throughput analysis of plant root system architecture, BMC Plant Biology, vol. 12 no. 116 (2012)  [abs]
3. 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, Nature Biotechnology (Submitted, 2012)
4. Anastasia Deckard, Ron C. Anafi, John B. Hogenesch, Steven B. Haase, John Harer, Design and Analysis of Large-Scale Biological Rhythm Studies: A Comparison of Algorithms for Detecting Periodic Signals in Biological Data, PLOS Computational Biology (Submitted, 2012)  [abs]
5. Anastasia Deckard, Jurgen Sladeczek, David A. Orlando, Steven B. Haase and John Harer, Biochronicity Website: Sharing the results of running periodicity detection algorithms on biological data (Submitted, 2012)  [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.      
• 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.