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Publications of John Harer    :chronological  alphabetical  combined  bibtex listing:


  1. H. Edelsbrunner and J. Harer, Computational Topology, An Introduction (January 13, 2010), American Mathematical Society, ISBN 0-8218-4925-5 (  [abs]
  2. Penner, R. C. and Harer, J. L., Combinatorics of train tracks, pp. xii+216, 1992, Princeton University Press, Princeton, NJ [MR94b:57018]

Papers Published

  1. Katharine Turner, Yuriy Mileyko, Sayan Mukherjee, John Harer, Fréchet 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 (  [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. Elizabeth Munch, Paul Bendich, Katharine Turner, Sayan Mukherjee, Jonathan Mattingly, John Harer, Probabilistic Fréchet Means and Statistics on Vineyards (2014) (  [abs]
  5. 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) (  [abs]
  6. 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 (2013)  [abs]
  7. 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]
  8. Elizabeth Munch , Michael Shapiro and John Harer, Failure Filtrations for Fenced Sensor Networks, The International Journal of Robotics Research, vol. 31 no. 9 (2012)
  9. Yuriy Mileyko, Sayan Mukherjee and John Harer, Probability measures on the space of persistence diagrams, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 25  [abs] [author's comments]
  10. Paul Bendich, Taras Galkovskyi and John Harer, Improving Homology Estimates with Random Walks, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 16  [abs]
  11. 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)
  12. Gilberto Bini and John Harer, Euler characteristics of moduli spaces of curves, Journal of the European Mathematical Society, vol. 13 no. 2 (2011), pp. 487-512  [abs]
  13. Paul Bendich and John Harer, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (2011), pp. 305-336  [abs]
  14. Anjali Iyer-Pascuzzi, Joshua S. Weitz, Olga Symonova,Yuriy Mileyko, Yueling Hao, Heather Belcher, John Harer, and Philip N. Benfey, Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems, Plant Physiology, vol. 152 (2010), pp. 1148-1157  [abs]
  15. D. Cohen-Steiner, H. Edelsbrunner, J. Harer and Y. Mileyko., Lipschitz functions have L_p-stable persistence., Foundations of Computional Mathematics, vol. 10 no. 2 (2010), pp. 127-139 [available here]  [abs]
  16. D. Cohen-Steiner, H. Edelsbrunner and J. Harer., Extending persistence using Poincare and Lefschetz duality, Found. Comput. Math., vol. p (2009), pp. 79-103, Erratum 133-134.  [abs]
  17. H. Edelsbrunner and J. Harer, The persistent Morse complex segmentation of a 3-manifold., in 3D Physiological Human Workshop, 2009, Lecture Notes Comp. Sci., edited by N. Magnenat-Thalmann, vol. 5903 (2009), pp. 36-50, Springer-Verlag, Berlin
  18. D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov., Persistent homology for kernels, images, and cokernels., Proc. Sympos. Discret Alg. (2009) [available here]  [abs]
  19. P. Bendich, D. Cohen-Steiner, H. Edelsbrunner, J. Harer and D. Morozov., Inferring local homology from sampled stratified spaces., Proc. 48th Ann. Sympos. Found. Comput. Sci. (2008), pp. 536-546 [available here]  [abs]
  20. H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci and J. Snoeyink, Time-varying Reeb graphs for continuous space-time data., Comput. Geom. Theory Appl., vol. 41 (2008), pp. 149-166.
  21. D. Cohen-Steiner, H. Edelsbrunner and J. Harer., Stability of persistence diagrams., Discrete Comput. Geom., vol. 37 (2007), pp. 103-120  [abs] [author's comments]
  22. H. Edelsbrunner and J. Harer, Persistent homology --- a survey., In Twenty Years After, eds. J. E. Goodman, J. Pach and R. Pollack, AMS. (2007) [pdf]  [abs]
  23. D. Attali, H. Edelsbrunner, J. Harer, Y. Milokov, Alpha-beta witness complexes, Proc. 10th Workshop Algor. Data Struct., 2007, Springer LNCS 4619, 386-397. (2007)  [abs]
  24. with H. Edelsbrunner, V. Natarajan, V. Pascucci., Local and Global Comparison of Continuous Functions, Proc. IEEE Conf. Visualization, 2004, 275-280. (2004), pp. 275-280  [abs]
  25. with P. K. Agarwal, H. Edelsbrunner, and Y. Wang, Extreme elevation on a 2-manifold., Proc. 20th Ann. Sympos. Comput. Geom. (2004), pp. 357-365  [abs]
  26. with H. Edelsbrunner, A. Mascarenhas and V. Pascucci, Time-varying Reeb graphs for continuous space-time data., Proc. 20th Ann. Sympos. Comput. Geom. (2004), pp. 366-372.  [abs]
  27. with K. Cole-McLaughlin, H. Edelsbrunner, V. Natarajan and V. Pascucci, Loops in Reeb graphs of 2-manifolds., Discrete Comput. Geom., vol. 32 (2004), pp. 231-244.  [abs]
  28. with P. Agarwal and A. Collins, HPRM: A Hierarchical PRM, Proc. Intl. Conf. Robotics and Automation (2003)  [abs]
  29. with H. Edelsbrunner, V. Natarajan and V. Pascucci., Morse-Smale complexes for piecewise linear 3-manifolds., Proc. 19th Ann. Sympos. Comput. Geom. (2003), pp. 361-370.  [abs]
  30. 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  [abs]
  31. P. Agarwal, A. Collins and J. Harer, Minimal Trap Design, Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA), (2001)  [abs]
  32. H. Edelsbrunner, J. Harer and A. Zomorodian, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proc. 17th Sympos. Comput. Geom. 2001, 70-79.  [abs]
  33. Goulden, I. P. and Harer, J. L. and Jackson, D. M., A geometric parametrization for the virtual Euler characteristics of the moduli spaces of real and complex algebraic curves, Trans. Amer. Math. Soc., vol. 353, no. 11, pp. 4405--4427 (electronic), 2001 [MR1851176]
  34. 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 [MR94h:14008]
  35. Harer, John, The third homology group of the moduli space of curves, Duke Math. J., vol. 63, no. 1, pp. 25--55, 1991 [MR92d:57012]
  36. Harer, John L., Stability of the homology of the moduli spaces of Riemann surfaces with spin structure, Math. Ann., vol. 287, no. 2, pp. 323--334, 1990 [MR91e:57002]
  37. Harer, John L., The cohomology of the moduli space of curves, Theory of moduli (Montecatini Terme, 1985), pp. 138--221, 1988, Springer, Berlin [MR90a:32026]
  38. 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 [MR88e:57030]
  39. Harer, J. and Zagier, D., The Euler characteristic of the moduli space of curves, Invent. Math., vol. 85, no. 3, pp. 457--485, 1986 [MR87i:32031]
  40. Harer, John L., The virtual cohomological dimension of the mapping class group of an orientable surface, Invent. Math., vol. 84, no. 1, pp. 157--176, 1986 [MR87c:32030]
  41. 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 [MR87f:57009]
  42. 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 [MR87a:57003]
  43. 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 [MR86c:57010]
  44. Harer, John, The second homology group of the mapping class group of an orientable surface, Invent. Math., vol. 72, no. 2, pp. 221--239, 1983 [MR84g:57006]
  45. Harer, John, Representing elements of pi1(M3) by fibred knots, Math. Proc. Cambridge Philos. Soc., vol. 92, no. 1, pp. 133--138, 1982 [MR83j:57005]
  46. Harer, John, How to construct all fibered knots and links, Topology, vol. 21, no. 3, pp. 263--280, 1982 [MR83e:57007]
  47. Casson, Andrew J. and Harer, John L., Some homology lens spaces which bound rational homology balls, Pacific J. Math., vol. 96, no. 1, pp. 23--36, 1981 [MR83h:57013]
  48. Harer, John, On handlebody structures for hypersurfaces in C3 and CP3, Math. Ann., vol. 238, no. 1, pp. 51--58, 1978 [MR80d:57020]

Papers Accepted

  1. P. Bendich, E. Gasparovic, J. Harer, R. Izmailov, and L. Ness, Multi-Scale Local Shape Analysis and Feature Selection in Machine Learning Applications, AISTATS (2014)  [abs]
  2. 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)  [abs]

Papers Submitted

  1. 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)  [abs]
  2. 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)  [abs]
  3. 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)  [abs]
  4. P. Bendich, Jacob Harer and John Harer, A Persistent Homology Based Geodesic Distance Estimator, Journal of Machine Learning Research (2014)  [author's comments]
  5. J. Perea, A. Deckard, S. Haase and J. Harer, Applications of SWiPerS to the discovery of periodic genes (2013)
  6. 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)  [abs]
  7. Paul Bendich , Jacob Harer and John Harer, Persistent Homology Enhanced Dimension Reduction, Foundations of Computational Mathematics (2012)
  8. Michael Jenista and John Harer, Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2012), pp. 12  [abs]
  9. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2009)
  10. 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)  [abs]


  1. T. Fink, S. Ahnert, R. Bar-On, J. Harer, Exact dynamics of Boolean networks with connectivity one (2009)
  2. John Harer, Algorithms for Enumerating Triangulations and Other Maps in Surfaces, 1998 , preprint 1998
  3. John Harer, An Alternative Approach to Trap Design for Vibratory Bowl Feeders, 1998 , preprint 1998
  4. John Harer, The Euler Characteristic of the Deligne-Mumford Compactification of the Moduli Space of Curves, 1996 , preprint 1996


  1. with H. Edelsbrunner, Persistent Morse Complex Segmentation of a 3-Manifold, Raindrop Geomagic Technical Report, vol. 066 (2004)  [abs] [author's comments]
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