Curriculum Vitae

John Harer

Box 90320, Durham, NC 27708-0034
(email)
Education

Ph.D.University of California, Berkeley1979
BSHaverford College1974
B.A.Haverford College1974
Areas of Research

Computational Topology, Computational Biology, Algorithms

Areas of Interest

Computational Biology
Computational Topology
Dynamics on Networks
Algorithms

Professional Experience / Employment History

Duke University
Professor of Electrical and Computer Engineering, 2011 - present
Director, Computational Biology and Bioinformatics Program, Institute for Genome Sciences and Policy, 2008 - present
Director, Center for Computational Science, Engineering and Medicine, 2002 - 2007
Professor of Computer Science, Computer Science, 2001 - present
Secondary Appointment
Vice-Provost for Acdemic Affairs, July 01, 1999 - December 31, 2004
Department Chair, Mathematics, July 01, 1994 - June 30, 1999
Professor of Mathematics, Mathematics, 1993 - present
Washington and Lee University
Professor, Mathematics Chair, Rupert Distinguished Professor, Mathematics, 1991 - 1992
University of Michigan
Professor, Mathematics, 1989 - 1991
Associate Professor, Mathematics, 1985 - 1989
University of Maryland
Assistant Professor, Mathematics, 1983 - 1985
Columbia University
Ritt Assistant Professor, Mathematics, 1979 - 1983
Visiting Positions
Visitor, Institute Curie, July 01, 2007 - June 30, 2008
Professor, Scuola Normale Superiore, 1997 - 1998
Professor, Duke University, 1992 - 1993
Awards, Honors, and Distinctions

Henry Russell Award, University of Michigan, July, 1988
Faculty Recognition Award, University of Michigan, July, 1987
Fellowship, Sloane Foundation, July, 1987
Postdoctoral Fellowship, NSF, July, 1983
Recent Grant Support

Professional Service

A&S Council
Conflict of Interest Committee, 2013 - present  
Review Committee for Dean of Engineering, 2011 - 2012  
CBB Admissions Committee, 2008 - 2012  
CBB Advisory Comittee, 2008 - 2012  
Computational Biology and Bioinformatics PhD Program, 2008 - 2012  
Modeling Biological Systems Undergraduate Certificate, 2008 - 2011  
Thesis Committee - Jacob Frelinger - CBB, December 2010  
Thesis Committee - Ying Zheng- CS, December 2010  
Thesis Committee - Andreas Pfenning - CBB, December 2010  
Center for Systems Biology, December 2010  
Center for Systems Biology Steering Committee, December 2008  
Nescent Director Search Committee, October 2008  
Associate Director, Center for Systems Biology Steering Committee, 2006 - 2007  
University Committee
Review Committee for Brittany Fasy, October 2008  
Computational Biology Section Proposal, December 2007  
AP&T, September 1, 2005 - June 30, 2007  
Departmental Computing Support, September, 2005 - May, 2006  
Chair, Strategic Planning for Research Computing, August, 2005 - May, 2006  
Chair, Task Force for Computation and Data Analysis in the Social Sciences, January 01, 2005 - July 01, 2005  
B&B Chair Search Committee, 1999 - July 01, 2005  
Research Committee, September, 2005 - May, 2005  
Academic Space Committee, 2003 - December 31, 2004  
Global Change Steering Committee, 2000 - December 31, 2004  
Member, Academic Priorities Committee, 1999 - December 31, 2004  
Provost's Inner Staff, 1999 - December 31, 2004  
Duke Forest Advisory Committee, 1999 - December 31, 2004  
Project Advisory Committee for French Science Center, 2003 - 2004  
Materials Science Governance Committee, 2000 - 2004  
Review Committee for Dean of Pratt School of Engineering, 2002 - 2003  
IGSP Director Search, 1999 - 2003  
IGSP Leadership Committee, July 01, 1999 - July 01, 2003  
Search Committee for Dean of the Nicholas School of the Environment, 2000 - 2001  
Chair, CBCB Director Search Committee, 2000 - 2001  
Strategic Planning Oversight Committee, 1999 - 2001  
Chair, Science and Engineering Working Group, 1999 - 2001  
Dept Committee
Nolan Promotion Committee, 2014 - present  
Appointments Committee, 1993 - present  
Chair, Layton Full Professor Promotion, December 2014  
Committee to write basic linear algebra exam, 2011 - 2012  
Chair, A. Layton Tenure Committee, December 2011  
Paul Magwene Tenure Committee, December 2011  
Applied ARP, 2010-2011  
Applied ARP, 2009-2010  
Maggioni Promotion Committee, December 2009  
Renewal for Mauro Maggioni, October 2008  
Mathematical Biology Search Commitee, 2004 - 2005  
Papers Refereed
Refereed numerous papers, 1993 - present  
Department Review, Mathematics, University of Montana Bozeman, December 2014  
Chief Organizer, Workshop for Data Analytics and Cyber Security, October, 2014  
Chairman : Board of Trustees, London Institute for Mathematical Sciences, Chairman : Board of Trustees, London Institute for Mathematical Sciences. 2013, 2013 - 2014  
Consultant to RESCON, Ltd., Consultant to RESCON, Ltd.. December 22, 2013, December 2013  
Program Review Committee - MBI, Program Review Committee - MBI. December 22, 2013, December 2013  
Organizer : Workshops of the Mathematics of Cyber for NSF, Organizer : Workshops of the Mathematics of Cyber for NSF. 2013, 2013  
Member of 3 person organizing committee : Workshop on Topological Data Analysis - IMA, Member of 3 person organizing committee : Workshop on Topological Data Analysis - IMA. October, 2016, October, 2013  
Panel Member : NSF Review Panel - CDS&E program, Panel Member : NSF Review Panel - CDS&E program. December 18, 2012, December 2012  
Consultant to ARGON ST, Consultant to ARGON ST. 2011 - 2012, 2011 - 2012  
Consultant to Grassroots Technology, Consultant to Grassroots Technology. 2009 - 2011, 2009 - 2011  
NSF Reviews And Panels
Participant, NSF Workshop in Mathematics and Robotics, 2000  
Math Community Services
Review Committee for all Tulane PhD science programs, Review Committee for all Tulane PhD science programs. March, 2013, 1 March 2013  
Review Committee for all Tulane PhD science programs, December 22, 2013  
Univ Services
Committee for Vice Provost for Research, 10 December 2013  
SAMSI Scienctific Advisory Committee, 2004 - 2010  
Director, Center for Computational Science, Engineering and Medicine, 2001 - 2007  
Search Committee for A&S IT director, December 2005  
Board Member, NISS Board of Trustees, 2002 - 2005  
Reviewer for Research Day, March 30, 2005  
Vice-Provost for Academic Affairs, Provost's Office:, July 01, 1999 - February 28, 2005  
TUCASI, July 1, 1999 - January 01, 2005  
Member, SAMSII Board of Govenors, 2003 - December 31, 2004  
Chief Staff, Academic Affairs Committee - Duke Board of Trustees, July 01, 1999 - December 31, 2004  
Chair, DFELL Advisory Committee, 1999 - 2004  
Reviewer for Research Day, March, 2004  
Search Committee for Neural Analysis Faculty - BME, 2002  
Search Committee for Vice-Provost for Research, 2001  
Chair, Committee on Academic Practices and Policies, North Carolina School of Science and Math Board of Trustees, 1999 - 2001  
Strategic Planning Process Coordinator, 1999 - 2001  
Selected Recent Invited Talks

Topological Data Analysis, NCState, November 24, 2014  
Topological Data Analysis, ICERM (Brown University), October 23, 2014  
Topological Data Analysis and Machine Learning for Behavioral Description, Air Force Research Lab - Rome NY, August 12, 2014  
Topological Data Analysis, CCR Princeton, May 8, 2014  
Topological Data Analysis, Valley Tech Systems, May 5, 2014  
Topological Data Analysis, APL - JHU, April 17, 2014  
Inferring Control from Topology & Data, AFOSR Annual Review, DC, December 17, 2013  
Topological Data Analysis, Raytheon Corporation, Woburn Mass, July, 2013  
Finding Gene Regulatory Networks and Their Parameters from Time Series Gene Expression Data, Duke - National University of Singapore, June 11, 2013  
Learning Tracks and Group Behavior, Melbourne University - Defence Sciences Institute, June, 2013  
Persistent Homology of Time-Delay Embeddings, Melbourne University - Defence Sciences Institute, June, 2013  
Topological Data Analysis, Australian National University, Canberra, Australia, June, 2013  
Topological Data Analysis, Melbourne University - Defence Sciences Institute, June, 2013  
Topological Data Analysis, Duke University - LAS Leadership Visit, May 31, 2013  
DARPA BIochronicity: Biochronicity: Time, evolution, networks, and function, Arlington, Va., May, 2013  
Topology for Tracking, APL, March 15, 2013  
Obstruction Theory and Quantum Information, Oxford University, March, 2013  
Topology and Security, London Institute for Mathematical Sciences, March, 2013  
Topological Data Analysis, Haverford College, February, 2013  
Topological Data Analysis,, UNCG, February, 2013  
Inferring Control from Topology & Data, AFOSR Annual Review, DC, December 21, 2012  
Building Regulatory Networks for Periodic Procceses, Duke Systems Biology Seminar, November, 2012  
Building Regulatory Networks _x000B_for Periodic Procceses, Duke Systems Biology Seminar, 1 November 2012  
Frechet means for persistence diagrams and vineyads, BIRS, October, 2012  
Mathematical Ideas in the Life Sciences Modeling Cellular Clocks, DIMACS (Rutgers), September, 2012  
Topological Data Analysis, Applied Communication Sciences, September, 2012  
Building Gene Regulatory Networks for Periodic Processes, Duke CBB, August, 2012  
DARPA Biochronicity: Toward Building a Unified Biological Clock and Understanding its Response to External Factors, Seattle, August, 2012  
DARPA BIochronicity: Biochronicity: Time, evolution, networks, and function, Duke University, May 08, 2012  
DARPA Biochronicity Kick-Off: Biochronicity: Time, evolution, networks, and function, San Diego, February, 2012  
DARPA Biochronicity: Algorithms and methods of discovering periodicity in biological datasets, San Diego, February, 2012  
Time Series, Time Varying Data, Geometry and Topology, Incline Village, Nevada, February, 2012  
Topological & Geometric Structure in Noisy Data, Incline Village, Nevada, February, 2012  
Inferring Control from Topology & Data, AFOSR Annual Review, November 29, 2011  
Structure in Noisy Data, Siam Conference NCState University, October 7, 2011  
Structure in Data, Duke RTG Seminar, September 8, 2011  
Modeling Gene Networks, DARPA Fun Bio Final Review, August 29, 2011  
Networks That Self-Heal: Slime Molds in Action, Duke RTG Seminar, May 19, 2011  
Structure in Data, Johns Hopkins Advanced Physics Laboratory, May 17, 2011  
Statistics on Persistence Diagrams, Ohio State Computatiional Geometry Seminar, April 09, 2011  
Structure in Data, Ohio State Colloquium, April 8, 2011  
Structure in Data, Virginia Tech Colloquium, April 1, 2011  
Community Network - Biological Inspiration, Princeton University, 17 December 2010  
Community Network -_x000B_Biological Inspiration, Princeton University, 17 December 2010  
Computational Topology Methods for Dimension Reduction, Duke Univesity, 17 December 2010  
Computational Topology _x000B_Methods for _x000B_Dimension Reduction, Duke Univesity, 17 December 2010  
Control of the Yeast Cell Cycle, Dana Point California, 17 December 2010  
FunBio - Biologically Inspiration for Networks, Princeton University, 17 December 2010  
FunBio_x000B_- Biologically Inspiration_x000B_for Networks, Princeton University, 17 December 2010  
Inferring Control from Topology and Data, AFOSR annual program review, Arlington, VA, November 29, 2010  
Self-Healing Networks, London Institute for Mathematical Sciences, June, 2010  
Network Node FunBio, DARPA FunBio Annual Review -Dana Point California, January, 2010  
Persistent Local Homology for Root Shape, Duke University Workshop on Plant Root Architecture, October 01, 2009  
Dynamics of Biological Models of Gene Regulator y Networks, Curie Institute, Paris, August 10, 2009  
Finding Cycles in Boolean Networks, London Institute of Mathematical Sciences, June 11, 2009  
Plant Root Architecture, Georgia Tech, May 27, 2009  
Dynamics on Biological Networks, Duke FunBio DARPA Meeting, April 3, 2009  
Persistence, Point Clouds and Local Homology, George Washington University, March 23, 2009  
Gene Regulatory Network Clocks., Duke University Systems Biology Seminar, March 18, 2009  
Persistence, Point Clouds and Local Homology, Rutgers - IAS Workshop, March 04, 2009  
Persistent Homology and Applications, Dept of Mathematics, UNCG, November 10, 2008  
How do Biological Networks Keep Time, CBB Retreat, Sept, 2008  
Persistence, Point Clouds and Local Homology, Ecole Normale Superior, March, 2008  
Persistent Intersection Homology, INRIA - Sophia Antipolis, June, 2008  
Persistent Homology for root shape description, DARPA TDA meeting - San Diego, December, 2007  
Topology and Biology, DARPA FunBio meeting - San Diego, December, 2007  
Topological Persistence, Rutgers University, November, 2006  
Persistence for Image Analysis, MSRI, October, 2006  
Extended Persistence with Applications, MSRI, September, 2006  
Discovering Stratified Structures in Datasets, DARPA meeting - Santa Barbara, May, 2006  
Discovering stratified structure using local homology, DARPA meeting, Duke University, December 15, 2005  
Using flattening for surface comparison, NIST site review, Geomagic, RTP, November 29, 2005  
Extended Persistence and Intersection Homology, DARPA meeting, San Raphael, California, October 30, 2005  
2004 IMA New Directions Short Course in Computational Topology, Institute for Mathematics and its Applications, July 6-16, 2004  
Extreme elevation on a 2-manifold, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004  
Time-varying Contour Trees for Continuous Space-Time Data, ACM Annual Symposium on Computational Geometry, SCG 2004, 15 December 2004  
HPRM: A Hierarchical PRM, International Conference on Robotics and Automation, 2003  
Loops in Reeb Graphs of 2-Manifolds, 19th ACM Symposium on Computational Geometry, 2003  
Morse Complexes for Piecewise Linear 3-Manifolds, 19th ACM Symposium on Computational Geometry, 2003  
Workshop on Computaional Topology, INRIA Sophia Antipolis, Oct 21-25, 2002  
Combinatorial Morse Theory and Persistence, with Applications to Distinguishing Noise from Feature, Lawrence Livermore National Labs, Feb, 2001  
Conference on Algebraic Topological Methods in Computer Science, Stanford University, 2001  
Minimal Trap Design, ICRA 2001 , Seoul, 2001  
Doctoral Theses Directed

Anne Collins, Configuration Spaces in Robotic Manipulation and Motion Planning, (2002)  
Chris Odden, (1997)  
Joel Foisy, (1996)  

Publications

Books

  1. Edelsbrunner, H; Harer, J, Computational Topology - an Introduction. (2010), American Mathematical Society, ISBN 978-0-8218-4925-5 (http://www.ams.org/bookstore-getitem/item=mbk-69.)
  2. Penner, R. C. and Harer, J. L., Combinatorics of train tracks, pp. xii+216, 1992, Princeton University Press, Princeton, NJ

Papers Published

  1. Motta, FC; McGoff, K; Moseley, RC; Cho, C-Y; Kelliher, CM; Smith, LM; Ortiz, MS; Leman, AR; Campione, SA; Devos, N; Chaorattanakawee, S; Uthaimongkol, N; Kuntawunginn, W; Thongpiam, C; Thamnurak, C; Arsanok, M; Wojnarski, M; Vanchayangkul, P; Boonyalai, N; Smith, PL; Spring, MD; Jongsakul, K; Chuang, I; Harer, J; Haase, SB, The parasite intraerythrocytic cycle and human circadian cycle are coupled during malaria infection., Proceedings of the National Academy of Sciences of the United States of America, vol. 120 no. 24 (June, 2023), pp. e2216522120
  2. Motta, FC; McGoff, KA; Deckard, A; Wolfe, CR; Bonsignori, M; Moody, MA; Cavanaugh, K; Denny, TN; Harer, J; Haase, SB, Assessment of Simulated Surveillance Testing and Quarantine in a SARS-CoV-2-Vaccinated Population of Students on a University Campus., JAMA Health Forum, vol. 2 no. 10 (October, 2021), pp. e213035
  3. Smith, AD; Bendich, P; Harer, J, PERSISTENT OBSTRUCTION THEORY FOR A MODEL CATEGORY OF MEASURES WITH APPLICATIONS TO DATA MERGING, Transactions of the American Mathematical Society Series B, vol. 8 no. 1 (February, 2021), pp. 1-38
  4. Denny, TN; Andrews, L; Bonsignori, M; Cavanaugh, K; Datto, MB; Deckard, A; DeMarco, CT; DeNaeyer, N; Epling, CA; Gurley, T; Haase, SB; Hallberg, C; Harer, J; Kneifel, CL; Lee, MJ; Louzao, R; Moody, MA; Moore, Z; Polage, CR; Puglin, J; Spotts, PH; Vaughn, JA; Wolfe, CR, Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus - Duke University, Durham, North Carolina, August 2-October 11, 2020., MMWR Morb Mortal Wkly Rep, vol. 69 no. 46 (November, 2020), pp. 1743-1747
  5. Smith, LM; Motta, FC; Chopra, G; Moch, JK; Nerem, RR; Cummins, B; Roche, KE; Kelliher, CM; Leman, AR; Harer, J; Gedeon, T; Waters, NC; Haase, SB, An intrinsic oscillator drives the blood stage cycle of the malaria parasite Plasmodium falciparum., Science (New York, N.Y.), vol. 368 no. 6492 (May, 2020), pp. 754-759
  6. Tralie, CJ; Bendich, P; Harer, J, Multi-Scale Geometric Summaries for Similarity-Based Sensor Fusion, IEEE Aerospace Conference Proceedings, vol. 2019-March (March, 2019), ISBN 9781538668542
  7. Garagić, D; Peskoe, J; Liu, F; Claffey, MS; Bendich, P; Hineman, J; Borggren, N; Harer, J; Zulch, P; Rhodes, BJ, Upstream fusion of multiple sensing modalities using machine learning and topological analysis: An initial exploration, IEEE Aerospace Conference Proceedings, vol. 2018-March (June, 2018), pp. 1-8, IEEE, ISBN 9781538620144
  8. Tralie, CJ; Smith, A; Borggren, N; Hineman, J; Bendich, P; Zulch, P; Harer, J, Geometric Cross-Modal Comparison of Heterogeneous Sensor Data, Proceedings of the 39th IEEE Aerospace Conference, vol. 2018-March (March, 2018), pp. 1-10, IEEE, ISBN 9781538620144
  9. Bendich, P; Gasparovic, E; Harer, J; Tralie, CJ, Scaffoldings and Spines: Organizing High-Dimensional Data Using Cover Trees, Local Principal Component Analysis, and Persistent Homology, vol. 13 (January, 2018), pp. 93-114
  10. Hughes, ME; Abruzzi, KC; Allada, R; Anafi, R; Arpat, AB; Asher, G; Baldi, P; de Bekker, C; Bell-Pedersen, D; Blau, J; Brown, S; Ceriani, MF; Chen, Z; Chiu, JC; Cox, J; Crowell, AM; DeBruyne, JP; Dijk, D-J; DiTacchio, L; Doyle, FJ; Duffield, GE; Dunlap, JC; Eckel-Mahan, K; Esser, KA; FitzGerald, GA; Forger, DB; Francey, LJ; Fu, Y-H; Gachon, F; Gatfield, D; de Goede, P; Golden, SS; Green, C; Harer, J; Harmer, S; Haspel, J; Hastings, MH; Herzel, H; Herzog, ED; Hoffmann, C; Hong, C; Hughey, JJ; Hurley, JM; de la Iglesia, HO; Johnson, C; Kay, SA; Koike, N; Kornacker, K; Kramer, A; Lamia, K; Leise, T; Lewis, SA; Li, J; Li, X; Liu, AC; Loros, JJ; Martino, TA; Menet, JS; Merrow, M; Millar, AJ; Mockler, T; Naef, F; Nagoshi, E; Nitabach, MN; Olmedo, M; Nusinow, DA; Ptáček, LJ; Rand, D; Reddy, AB; Robles, MS; Roenneberg, T; Rosbash, M; Ruben, MD; Rund, SSC; Sancar, A; Sassone-Corsi, P; Sehgal, A; Sherrill-Mix, S; Skene, DJ; Storch, K-F; Takahashi, JS; Ueda, HR; Wang, H; Weitz, C; Westermark, PO; Wijnen, H; Xu, Y; Wu, G; Yoo, S-H; Young, M; Zhang, EE; Zielinski, T; Hogenesch, JB, Guidelines for Genome-Scale Analysis of Biological Rhythms., Journal of biological rhythms, vol. 32 no. 5 (October, 2017), pp. 380-393
  11. Bendich, P; Chin, SP; Clark, J; DeSena, J; Harer, J; Munch, E; Newman, A; Porter, D; Rouse, D; Strawn, N; Watkins, A, Topological and statistical behavior classifiers for tracking applications, IEEE Transactions on Aerospace and Electronic Systems, vol. 52 no. 6 (December, 2016), pp. 2644-2661, Institute of Electrical and Electronics Engineers (IEEE)
  12. McGoff, KA; Guo, X; Deckard, A; Kelliher, CM; Leman, AR; Francey, LJ; Hogenesch, JB; Haase, SB; Harer, JL, The Local Edge Machine: inference of dynamic models of gene regulation., Genome biology, vol. 17 no. 1 (October, 2016), pp. 214
  13. Bendich, P; Gasparovic, E; Harer, J; Tralie, C, Geometric Models for Musical Audio Data, Proceedings of the 32st International Symposium on Computational Geometry (SOCG) (June, 2016)
  14. Bendich, P; Gasparovic, E; Harer, J; Tralie, C, Geometric models for musical audio data, Leibniz International Proceedings in Informatics Lipics, vol. 51 (June, 2016), pp. 65.1-65.5, ISBN 9783959770095
  15. Bendich, P; Gasparovic, E; Harer, J; Izmailov, R; Ness, L, Multi-scale local shape analysis and feature selection in machine learning applications, Proceedings of the International Joint Conference on Neural Networks, vol. 2015-September (September, 2015), IEEE, ISBN 9781479919604
  16. Perea, JA; Deckard, A; Haase, SB; Harer, J, SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data., BMC bioinformatics, vol. 16 (August, 2015), pp. 257
  17. Perea, JA; Harer, J, Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis, Foundations of Computational Mathematics, vol. 15 no. 3 (June, 2015), pp. 799-838, Springer Nature
  18. Munch, E; Turner, K; Bendich, P; Mukherjee, S; Mattingly, J; Harer, J, Probabilistic Fréchet means for time varying persistence diagrams, Electronic Journal of Statistics, vol. 9 no. 1 (January, 2015), pp. 1173-1204, Institute of Mathematical Statistics
  19. Rouse, D; Watkins, A; Porter, D; Harer, J; Bendich, P; Strawn, N; Munch, E; Desena, J; Clarke, J; Gilbert, J; Chin, S; Newman, A, Feature-aided multiple hypothesis tracking using topological and statistical behavior classifiers, Proceedings of SPIE the International Society for Optical Engineering, vol. 9474 (January, 2015), SPIE, ISSN 10.1117/12.2179555, ISBN 9781628415902
  20. Farr, RS; Harer, JL; Fink, TMA, Easily repairable networks: reconnecting nodes after damage., Physical review letters, vol. 113 no. 13 (September, 2014), pp. 138701, ISSN 0031-9007
  21. Bristow, SL; Leman, AR; Simmons Kovacs, LA; Deckard, A; Harer, J; Haase, SB, Checkpoints couple transcription network oscillator dynamics to cell-cycle progression., Genome biology, vol. 15 no. 9 (September, 2014), pp. 446
  22. Turner, K; Mileyko, Y; Mukherjee, S; Harer, J, Fréchet Means for Distributions of Persistence Diagrams, Discrete and Computational Geometry, vol. 52 no. 1 (January, 2014), pp. 44-70, Springer Nature, ISSN 0179-5376
  23. Elizabeth Munch, Paul Bendich, Katharine Turner, Sayan Mukherjee, Jonathan Mattingly, John Harer, Probabilistic Fréchet Means and Statistics on Vineyards (2014) (http://arxiv.org/abs/1307.6530.)
  24. Turner, K; Mileyko, Y; Mukherjee, S; Harer, J, Fréchet Means for Distributions of Persistence Diagrams, Discrete & Computational Geometry (2014)
  25. Topp, CN; Iyer-Pascuzzi, AS; Anderson, JT; Lee, C-R; Zurek, PR; Symonova, O; Zheng, Y; Bucksch, A; Mileyko, Y; Galkovskyi, T; Moore, BT; Harer, J; Edelsbrunner, H; Mitchell-Olds, T; Weitz, JS; Benfey, PN, 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture., Proceedings of the National Academy of Sciences of the United States of America, vol. 110 no. 18 (April, 2013), pp. E1695-E1704
  26. 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) (http://www.pnas.org/content/early/2013/04/10/1304354110.abstract.)
  27. Topp; CN; Iyer-Pascuzzi, AS; Anderson, JT; Lee, C-R; Zurek, PR; Symonova, O; Zheng, Y; Bucksch, A; Milyeko, Y; Galkovskyi, T; Moore, BT; Harer, J; Edelsbrunner, H; Mitchell-Olds, T; Weitz, JS; Benfey, PN, 3-dimensional phenotyping of growing root systems and QTL mapping identifies core regions of the rice genome controlling root architecture, PNAS, vol. 110 (2013), pp. E1695-1704
  28. Munch, E; Shapiro, M; Harer, J, Failure filtrations for fenced sensor networks, International Journal of Robotics Research, vol. 31 no. 9 (August, 2012), pp. 1044-1056, SAGE Publications
  29. Galkovskyi, T; Mileyko, Y; Bucksch, A; Moore, B; Symonova, O; Price, CA; Topp, CN; Iyer-Pascuzzi, AS; Zurek, PR; Fang, S; Harer, J; Benfey, PN; Weitz, JS, GiA Roots: software for the high throughput analysis of plant root system architecture., BMC plant biology, vol. 12 no. 116 (July, 2012), pp. 116
  30. Bendich, P; Harer, J; Harer, J, Persistent Homology Enhanced Dimension Reduction, Foundations of Computational Mathematics (2012)
  31. Deckard, A; Anafi, RC; Hogenesch, JB; Haase, SB; Harer, J, Design and Analysis of Large-Scale Biological Rhythm Studies: A Comparison of Algorithms for Detecting Periodic Signals in Biological Data, PLOS Computational Biology, vol. 29 no. 24 (2012), pp. 3174-3180
  32. Michael Jenista, Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2012), pp. 12
  33. Bendich, P; Galkovskyi, T; Harer, J, Improving homology estimates with random walks, Inverse Problems, vol. 27 no. 12 (December, 2011), pp. 124002-124002, IOP Publishing, ISSN 0266-5611
  34. Mileyko, Y; Mukherjee, S; Harer, J, Probability measures on the space of persistence diagrams, Inverse Problems, vol. 27 no. 12 (December, 2011), pp. 124007-124007, IOP Publishing, ISSN 0266-5611
  35. Bendich, P; Harer, J, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (June, 2011), pp. 305-336, Springer Nature, ISSN 1615-3375
  36. 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, John Harer and Philip N. Benfey, Quantitative Genetic Analysis of Root System Architecture in Rice Plant and Animal Genomes, XX Genome Conference (2011)
  37. Bini, G; Harer, J, Euler characteristics of moduli spaces of curves, Journal of the European Mathematical Society, vol. 13 no. 2 (December, 2010), pp. 487-512, European Mathematical Society - EMS - Publishing House GmbH
  38. Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Mileyko, Y, Lipschitz functions have Lp-stable persistence, Foundations of Computational Mathematics, vol. 10 no. 2 (April, 2010), pp. 127-139, Springer Nature, ISSN 1615-3375
  39. Iyer-Pascuzzi, AS; Symonova, O; Mileyko, Y; Hao, Y; Belcher, H; Harer, J; Weitz, JS; Benfey, PN, Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems., Plant physiology, vol. 152 no. 3 (March, 2010), pp. 1148-1157
  40. Edelsbrunner, H; Harer, J, The persistent Morse complex segmentation of a 3-manifold, in 3D Physiological Human Workshop, 2009, Lecture Notes Comp. Sci., edited by N. Magnenat-Thalmann, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5903 LNCS (December, 2009), pp. 36-50, Springer Berlin Heidelberg, ISSN 0302-9743
  41. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Extending persistence using poincaré and lefschetz duality (Foundations of Computational Mathematics DOI 10.1007/s10208-008-9027-z), Foundations of Computational Mathematics, vol. 9 no. 1 (February, 2009), pp. 133-134, Springer Nature, ISSN 1615-3375
  42. Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Morozov, D, Persistent homology for kernels, images, and cokernels, Proceedings of the Annual ACM SIAM Symposium on Discrete Algorithms (January, 2009), pp. 1011-1020
  43. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Extending persistence using poincaré and lefschetz duality, Foundations of Computational Mathematics, vol. 9 no. 1 (January, 2009), pp. 79-103, Springer Nature, ISSN 1615-3375
  44. Fink, T; Ahnert, S; Bar On, R; Harer, J, Exact dynamics of Boolean networks with connectivity one, PRL (2009)
  45. Edelsbrunner, H; Harer, J; Patel, AK, Reeb spaces of piecewise linear mappings, Proceedings of the Annual Symposium on Computational Geometry (December, 2008), pp. 242-250, ACM Press
  46. Edelsbrunner, H; Harer, J; Mascarenhas, A; Pascucci, V; Snoeyink, J, Time-varying Reeb graphs for continuous space-time data, Computational Geometry Theory and Applications, vol. 41 no. 3 (November, 2008), pp. 149-166, Elsevier BV, ISSN 0925-7721
  47. Edelsbrunner, H; Harer, J, Persistent homology - a survey, edited by Goodman, JE; Pach, J; Pollack, R, SURVEYS ON DISCRETE AND COMPUTATIONAL GEOMETRY: TWENTY YEARS LATER, vol. 453 (January, 2008), pp. 257-+, AMER MATHEMATICAL SOC, ISBN 978-0-8218-4239-3
  48. Bendice, P; Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Morozov, D, Inferring local homology from sampled stratified spaces, Proceedings Annual IEEE Symposium on Foundations of Computer Science Focs (December, 2007), pp. 536-546, IEEE, ISSN 0272-5428
  49. Czumaj, A; Sohler, C, Testing Expansion in Bounded-Degree Graphs, 48th Annual IEEE Symposium on Foundations of Computer Science (FOCS'07), vol. 2 (October, 2007), pp. 570-578, IEEE, ISBN 9780769530109
  50. Bendich, P; Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Morozov, D, Inferring Local Homology from Sampled Stratified Spaces, 48th Annual IEEE Symposium on Foundations of Computer Science (FOCS'07), vol. 19 (October, 2007), pp. 536-546, IEEE, ISBN 9780769530109
  51. Attali, D; Edelsbrunner, H; Harer, J; Mileyko, Y, Alpha-beta witness complexes, Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, vol. 4619 LNCS (January, 2007), pp. 386-397, ISSN 0302-9743
  52. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Stability of persistence diagrams, Discrete and Computational Geometry, vol. 37 no. 1 (January, 2007), pp. 103-120, Springer Nature, ISSN 0179-5376
  53. Agarwal, PK; Edelsbrunner, H; Harer, J; Wang, Y, Extreme elevation on a 2-manifold, Discrete and Computational Geometry, vol. 36 no. 4 (January, 2006), pp. 553-572, Springer Nature, ISSN 0179-5376
  54. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Stability of persistence diagrams, Proceedings of the Annual Symposium on Computational Geometry (December, 2005), pp. 263-271, ACM Press
  55. with Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Local and global comparison of continuous functions, IEEE Visualization 2004 Proceedings Vis 2004 (December, 2004), pp. 275-280, IEEE Comput. Soc
  56. with Edelsbrunner, H; Harer, J; Mascarenhas, A; Pascucci, V, Time-varying Reeb graphs for continuous space-time data, Proceedings of the Annual Symposium on Computational Geometry (January, 2004), pp. 366-372
  57. with Agarwal, PK; Edelsbrunner, H; Harer, J; Wang, Y, Extreme elevation on a 2-manifold, Proceedings of the Annual Symposium on Computational Geometry (January, 2004), pp. 357-365
  58. with Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Loops in Reeb graphs of 2-manifolds, Discrete and Computational Geometry, vol. 32 no. 2 (January, 2004), pp. 231-244, Springer Nature
  59. with Collins, AD; Agarwal, PK; Harer, JL, HPRM: A hierarchical PRM, Proceedings IEEE International Conference on Robotics and Automation, vol. 3 (December, 2003), pp. 4433-4438
  60. with Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Morse-Smale complexes for piecewise linear 3-manifolds, Proceedings of the Annual Symposium on Computational Geometry (January, 2003), pp. 361-370
  61. Edelsbrunner, H; Harer, J; Zomorodian, A, Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds, Discrete and Computational Geometry, vol. 30 no. 1 (January, 2003), pp. 87-107, Springer Nature, ISSN 0179-5376
  62. Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Loops in Reeb graphs of 2-manifolds, Proceedings of the Annual Symposium on Computational Geometry (January, 2003), pp. 344-350
  63. with H. Edelsbrunner., Jacobi sets of multiple Morse functions., Foundations of Computational Mathematics, Minneapolis, eds. F. Cucker, R. DeVore, P. Olver and E. Sueli, Cambridge Univ. Press, England, (2002), pp. 37-57
  64. Goulden, IP; Harer, JL; Jackson, DM, A geometric parametrization for the virtual euler characteristics of the moduli spaces of real and complex algebraic curves, Transactions of the American Mathematical Society, vol. 353 no. 11 (January, 2001), pp. 4405-4427, ISSN 0002-9947
  65. Edelsbrunner, H; Harer, J; Zomorodian, A, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proceedings of the Annual Symposium on Computational Geometry (January, 2001), pp. 70-79
  66. Agarwal, PK; Collins, AD; Harer, JL, Minimal trap design, Proceedings IEEE International Conference on Robotics and Automation, vol. 3 (January, 2001), pp. 2243-2248, IEEE
  67. Bern, M; Eppstein, D; Agarwal, PK; Amenta, N; Chew, P; Dey, T; Dobkin, DP; Edelsbrunner, H; Grimm, C; Guibas, LJ; Harer, J; Hass, J; Hicks, A; Johnson, CK; Lerman, G; Letscher, D; Plassmann, P; Sedgwick, E; Snoeyink, J; Weeks, J; Yap, C; Zorin, D, Emerging Challenges in Computational Topology, vol. cs.CG/9909001 (September, 1999)
  68. Harer, J, The third homology group of the moduli space of curves, Duke Mathematical Journal, vol. 63 no. 1 (January, 1991), pp. 25-55, Duke University Press
  69. Harer, JL, Stability of the homology of the moduli spaces of Riemann surfaces with spin structure, Mathematische Annalen, vol. 287 no. 1 (March, 1990), pp. 323-334, Springer Nature, ISSN 0025-5831
  70. Harer, J; Zagier, D, The Euler characteristic of the moduli space of curves, Inventiones Mathematicae, vol. 85 no. 3 (October, 1986), pp. 457-485, ISSN 1435-9855
  71. Harer, JL, The virtual cohomological dimension of the mapping class group of an orientable surface, Inventiones Mathematicae, vol. 84 no. 1 (February, 1986), pp. 157-176, Springer Nature, ISSN 0020-9910
  72. HARER, J; KAS, A; KIRBY, R, HANDLEBODY STRUCTURES FOR COMPLEX-SURFACES, MEMOIRS OF THE AMERICAN MATHEMATICAL SOCIETY, vol. 62 no. 350 (1986), pp. 1-102
  73. Harer, J, The second homology group of the mapping class group of an orientable surface, Inventiones Mathematicae, vol. 72 no. 2 (June, 1983), pp. 221-239, Springer Nature, ISSN 0020-9910
  74. Harer, J, How to construct all fibered knots and links, Topology, vol. 21 no. 3 (January, 1982), pp. 263-280, Elsevier BV, ISSN 0040-9383
  75. Harer, J, On Almost-Everywhere Convergent Eigenfunction Expansions of the Laplace-Beltrami Operator, Mathematical Proceedings of the Cambridge Philosophical Society, vol. 92 no. 1 (January, 1982), pp. 133-138, Cambridge University Press (CUP)
  76. Casson, AJ; Harer, JL, Some homology lens spaces which bound rational homology balls, Pacific Journal of Mathematics, vol. 96 no. 1 (January, 1981), pp. 23-36, Mathematical Sciences Publishers
  77. Harer, J, On handlebody structures for hypersurfaces in ℂ3 and ℂP3, Mathematische Annalen, vol. 238 no. 1 (February, 1978), pp. 51-58, Springer Nature, ISSN 0025-5831
  78. Harer, John L., The rational Picard group of the moduli space of Riemann surfaces with spin structure, Mapping class groups and moduli spaces of Riemann surfaces (Gottingen, 1991/Seattle, WA, 1991), pp. 107--136, 1993, Amer. Math. Soc., Providence, RI
  79. Harer, John, The third homology group of the moduli space of curves, Duke Math. J., vol. 63, no. 1, pp. 25--55, 1991
  80. Harer, John L., The cohomology of the moduli space of curves, Theory of moduli (Montecatini Terme, 1985), pp. 138--221, 1988, Springer, Berlin
  81. Harer, John and Kas, Arnold and Kirby, Robion, Handlebody decompositions of complex surfaces, Mem. Amer. Math. Soc., vol. 62, no. 350, pp. iv+102, 1986
  82. Harer, John L., Stability of the homology of the mapping class groups of orientable surfaces, Ann. of Math. (2), vol. 121, no. 2, pp. 215--249, 1985
  83. Geometry and topology, Proceedings of the special year held at the University of Maryland, College Park, Md., 1983/84, edited by Alexander, J. and Harer, J., pp. vi+292, 1985, Springer-Verlag, Berlin
  84. Harer, John, The homology of the mapping class group and its connection to surface bundles over surfaces, Four-manifold theory (Durham, N.H., 1982), pp. 311--314, 1984, Amer. Math. Soc., Providence, RI
  85. Harer, John, Representing elements of pi1(M3) by fibred knots, Math. Proc. Cambridge Philos. Soc., vol. 92, no. 1, pp. 133--138, 1982

Papers Accepted

  1. E. Munch, P. Bendich, K. Turner, S. Mukherjee, J. Mattingly and J. Harer, Probabilistic Frechet Means and Statistics on Vineyards, Foundations of Computational Math (2014)

Papers Submitted

  1. 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 (2014)
  2. P. Bendich, Jacob Harer and John Harer, A Persistent Homology Based Geodesic Distance Estimator, Journal of Machine Learning Research (2014)
  3. 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 (2014)
  4. P. Bendich, S. Chin, J. Clarke, J. deSena, J. Harer, E. Munch, A. Newman, D. Porter, D. Rouse, N. Strawn, and A. Watkins, Topological and Statistical Behavior Classifiers for Tracking Applications, IEEE Trans. on Aerospace and Electronic Systems (2014)
  5. Sara Bristow, Laura A. Simmons Kovacs, Anastasia Deckard, John Harer, Steven B. Haase, Checkpoint Pathways Couple the CDK-Independent Transcriptional Oscillations to Cell Cycle Progression (2013)
  6. J. Perea, A. Deckard, S. Haase and J. Harer, Applications of SWiPerS to the discovery of periodic genes (2013)
  7. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2009)
  8. Mehak Aziz, Siobhan M. Brady, David Orlando, Appu Kuruvilla, Scott Spillias, José R. Dinneny, Terri A. Long, John Harer, Uwe Ohler, Philip N. Benfey, Gene Expression Clustering Analysis: How to Choose the Best Parameters and Clustering Algorithm (2008)

Papers In Preparation

  1. PAUL BENDICH, ELLEN GASPAROVIC, JOHN HARER, AND CHRISTOPHER TRALIE, MULTI-SCALE DATA MODELING VIA COVER TREES, LOCAL PRINCIPAL COMPONENT ANALYSIS, AND PERSISTENT HOMOLOGY (2015)
  2. K. McGoff, A. Deckard, X. Guo, S.Haase and J. Harer, Local Edge Machine: A Mathematical Methodology for Constructing Gene Regulatory Networks from Time Series Expression Data (2013)
  3. Paul Bendich, Nate Strawn, Peter Chin and J. Harer, Persistent Homology and Machine Learning: Capturing Vehicle Behavior for Improved Tracking (2013)
  4. Jose Perea, John Harer, Persistent Homology with Twisted Coefficients and Persistent Obstruction Theory (2013)
  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 (2013)
  6. with Yuriy Mileyko, Central Sets via Persistent Homology (2012)

Preprints

  1. John Harer, Algorithms for Enumerating Triangulations and Other Maps in Surfaces, 1998 , preprint 1998
  2. John Harer, An Alternative Approach to Trap Design for Vibratory Bowl Feeders, 1998 , preprint 1998
  3. John Harer, The Euler Characteristic of the Deligne-Mumford Compactification of the Moduli Space of Curves, 1996 , preprint 1996

Other

  1. with H. Edelsbrunner, Persistent Morse Complex Segmentation of a 3-Manifold, Raindrop Geomagic Technical Report, vol. 066 (2004)
Last modified: 2025/06/22