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Publications of John Harer    :chronological  combined  bibtex listing:

Books

  1. H. Edelsbrunner and J. Harer, Computational Topology, An Introduction (January 13, 2010), American Mathematical Society, ISBN 0-8218-4925-5 (http://www.ams.org/bookstore-getitem/item=mbk-69.)  [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. 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]
  2. Elizabeth Munch , Michael Shapiro and John Harer, Failure Filtrations for Fenced Sensor Networks, The International Journal of Robotics Research, vol. 31 no. 9 (2012)
  3. 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]
  4. with Paul Bendich, Taras Galkovskyi, Improving Homology Estimates with Random Walks, Journal of Inverse Problems, vol. 27 no. 12 (2011), pp. 16  [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)
  6. with Gilberto Bini, Euler characteristics of moduli spaces of curves, Journal of the European Mathematical Society, vol. 13 no. 2 (2011), pp. 487-512  [abs]
  7. with Paul Bendich, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (2011), pp. 305-336  [abs]
  8. 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]
  9. 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]
  10. 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]
  11. 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
  12. 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]
  13. 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]
  14. 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.
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. with P. Agarwal and A. Collins, HPRM: A Hierarchical PRM, Proc. Intl. Conf. Robotics and Automation (2003)  [abs]
  23. 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]
  24. 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]
  25. P. Agarwal, A. Collins and J. Harer, Minimal Trap Design, Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA), (2001)  [abs]
  26. H. Edelsbrunner, J. Harer and A. Zomorodian, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proc. 17th Sympos. Comput. Geom. 2001, 70-79.  [abs]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. Harer, John, How to construct all fibered knots and links, Topology, vol. 21, no. 3, pp. 263--280, 1982 [MR83e:57007]
  41. 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]
  42. Harer, John, On handlebody structures for hypersurfaces in C3 and CP3, Math. Ann., vol. 238, no. 1, pp. 51--58, 1978 [MR80d:57020]

Papers Submitted

  1. 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 (2012)
  2. 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 (2012)  [abs]
  3. 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 (2012)  [abs]
  4. Paul Bendich , Jacob Harer and John Harer, Persistent Homology Enhanced Dimension Reduction, Foundations of Computational Mathematics (2012)
  5. with Michael Jenista, Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2012), pp. 12  [abs]
  6. with Elizabeth Munch, Michael Shapiro, Failure Filtrations for Fenced Sensor Networks, The International Journal of Robotics Research (2011), pp. 14  [abs]
  7. T. Fink, S. Ahnert, R. Bar-On, J. Harer, Exact dynamics of Boolean networks with connectivity one, PRL (2009)  [abs]
  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)  [abs]

Preprints

  1. Katherine Turner, Yuriy Mileyko, Sayan Mukherjee and John Hare, Fréchet Means for Distributions of Persistence diagrams, arXiv:1206.2790 [math.ST] (2012)  [abs]
  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

Other

  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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