John Harer, Professor of Mathematics and Computer Science

Contact Info:

Office Location:	207 Physics
Office Phone:	(919) 660-2845
Email Address:
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:

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)

• Elizabeth A. Munch  
• Anastasia Deckhard  

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.