Publications of John Harer

Books

  1. Edelsbrunner, H; Harer, J, Computational Topology - an Introduction. (January 13, 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. 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
  2. Bendich, P; Gasparovic, E; Harer, J; Tralie, C, Geometric models for musical audio data, LIPIcs, vol. 51 (June, 2016), pp. 65.1-65.5, ISBN 9783959770095
  3. 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
  4. 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
  5. 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), ISSN 10.1117/12.2179555, ISBN 9781628415902
  6. 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
  7. 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: biology for the post-genomic era, vol. 15 no. 9 (September, 2014), pp. 446
  8. Turner, K; Mileyko, Y; Mukherjee, S; Harer, J, Fréchet Means for Distributions of Persistence Diagrams, Discrete & Computational Geometry, vol. 52 no. 1 (July, 2014), pp. 44-70, ISSN 0179-5376
  9. 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.)
  10. Perea, JA; Harer, J, Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis, Foundations of Computational Mathematics, vol. 15 no. 3 (May, 2014), pp. 799-838, ISSN 1615-3375 (http://arxiv.org/abs/1307.6188.)
  11. Perea, J; Harer, J, Sliding Windows and Persistence: An Application of Topological Methods to Signal Analysis (July, 2013)
  12. 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 USA, vol. 110 no. 18 (April, 2013), pp. E1695-E1704
  13. 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.)
  14. 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
  15. 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
  16. Turner, K; Mileyko, Y; Mukherjee, S; Harer, J, Fréchet Means for Distributions of Persistence diagrams (June, 2012)
  17. Munch, E; Shapiro, M; Harer, J, Failure filtrations for fenced sensor networks, International Journal of Robotics Research, vol. 31 no. 9 (2012), pp. 1044-1056, ISSN 0278-3649
  18. 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 (2013), pp. 3174-3180
  19. Munch, E; Shapiro, M; Harer, J, Failure Filtrations for Fenced Sensor Networks (September, 2011)
  20. 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)
  21. Bendich, P; Harer, J, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (2011), pp. 305-336, ISSN 1615-3375
  22. Bendich, P; Galkovskyi, T; Harer, J, Improving homology estimates with random walks, Inverse Problems, vol. 27 no. 12 (2011), pp. 16, ISSN 0266-5611
  23. Mileyko, Y; Mukherjee, S; Harer, J, Probability measures on the space of persistence diagrams, Inverse Problems, vol. 27 no. 12 (2011), pp. 25, ISSN 0266-5611
  24. Bini, G; Harer, J, Euler characteristics of moduli spaces of curves, Journal of the European Mathematical Society, vol. 13 no. 2 (2011), pp. 487-512, ISSN 1435-9855
  25. 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 (2010), pp. 1148-1157
  26. Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Mileyko, Y, Lipschitz functions have Lp-stable persistence, Foundations of Computational Mathematics, vol. 10 no. 2 (2010), pp. 127-139, ISSN 1615-3375
  27. 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 (2009), pp. 1011-1020
  28. 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, vol. 5903 LNCS (2009), pp. 36-50, Springer-Verlag, Berlin, ISSN 0302-9743
  29. 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 (2009), pp. 133-134, ISSN 1615-3375
  30. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Extending persistence using poincaré and lefschetz duality, Foundations of Computational Mathematics, vol. 9 no. 1 (2009), pp. 79-103, ISSN 1615-3375
  31. Edelsbrunner, H; Harer, J; Patel, AK, Reeb spaces of piecewise linear mappings, Proceedings of the Annual Symposium on Computational Geometry (2008), pp. 242-250
  32. Edelsbrunner, H; Harer, J; Mascarenhas, A; Pascucci, V; Snoeyink, J, Time-varying Reeb graphs for continuous space-time data, Computational Geometry, vol. 41 no. 3 (2008), pp. 149-166, ISSN 0925-7721
  33. Edelsbrunner, H; Harer, J, Persistent homology - a survey, Contemporary Mathematics, vol. 453 (2007), pp. 257-282, ISBN 978-0-8218-4239-3
  34. Attali, D; Edelsbrunner, H; Harer, J; Mileyko, Y, Alpha-beta witness complexes, Lecture notes in computer science, vol. 4619 LNCS (2007), pp. 386-397, ISSN 0302-9743
  35. Bendice, P; Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Morozov, D, Inferring local homology from sampled stratified spaces, Annual Symposium on Foundations of Computer Science (2007), pp. 536-546, ISSN 0272-5428
  36. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Stability of persistence diagrams, Discrete & Computational Geometry, vol. 37 no. 1 (2007), pp. 103-120, ISSN 0179-5376
  37. Bendich, P; Cohen-Steiner, D; Edelsbrunner, H; Harer, J; Morozov, D, Inferring Local Homology from Sampled Stratified Spaces., FOCS (2007), pp. 536-546, IEEE Computer Society, ISBN 978-0-7695-3010-9
  38. 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, PROCEEDINGS (2007), pp. 536-546, ISBN 978-0-7695-3010-9
  39. Agarwal, PK; Edelsbrunner, H; Harer, J; Wang, Y, Extreme elevation on a 2-manifold, Discrete & Computational Geometry, vol. 36 no. 4 (2006), pp. 553-572, ISSN 0179-5376
  40. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Stability of persistence diagrams, Proceedings of the Annual Symposium on Computational Geometry (2005), pp. 263-271
  41. 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 (2004), pp. 366-372
  42. with Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Local and global comparison of continuous functions, IEEE Visualization 2004 - Proceedings, VIS 2004 (2004), pp. 275-280
  43. with Agarwal, PK; Edelsbrunner, H; Harer, J; Wang, Y, Extreme elevation on a 2-manifold, Proceedings of the Annual Symposium on Computational Geometry (2004), pp. 357-365
  44. with Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V, Loops in Reeb graphs of 2-manifolds, Discrete and Computanional Geometry, vol. 32 no. 2 (2004), pp. 231-244
  45. 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 (2003), pp. 361-370
  46. Edelsbrunner, H; Harer, J; Zomorodian, A, Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds, Discrete & Computational Geometry, vol. 30 no. 1 (2003), pp. 87-107, ISSN 0179-5376
  47. 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 (2003), pp. 344-350
  48. with Collins, AD; Agarwal, PK; Harer, JL, HPRM: A hierarchical PRM, Proceedings - IEEE International Conference on Robotics and Automation, vol. 3 (2003), pp. 4433-4438
  49. 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
  50. 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 (2001), pp. 4405-4427, ISSN 0002-9947
  51. Edelsbrunner, H; Harer, J; Zomorodian, A, Hierarchical Morse complexes for piecewise linear 2-manifolds, Proceedings of the Annual Symposium on Computational Geometry (2001), pp. 70-79
  52. Agarwal, PK; Collins, AD; Harer, JL, Minimal trap design, Proceedings - IEEE International Conference on Robotics and Automation, vol. 3 (2001), pp. 2243-2248
  53. HARER, J, THE 3RD HOMOLOGY GROUP OF THE MODULI SPACE OF CURVES, Duke Mathematical Journal, vol. 63 no. 1 (June, 1991), pp. 25-55
  54. Harer, JL, Stability of the homology of the moduli spaces of Riemann surfaces with spin structure, Mathematische Annalen, vol. 287 no. 1 (1990), pp. 323-334, ISSN 0025-5831
  55. HARER, J; KAS, A; KIRBY, R, HANDLEBODY STRUCTURES FOR COMPLEX-SURFACES, Memoirs of the American Mathematical Society, vol. 62 no. 350 (July, 1986), pp. 1-102
  56. HARER, J, The virtual cohomological dimension of the mapping class group of an orientable surface, Invent. Math., vol. 84 no. 1 (1986), pp. 157-176, ISSN 0020-9910
  57. Harer, J; Zagier, D, The Euler characteristic of the moduli space of curves, Inventiones mathematicae, vol. 85 no. 3 (1986), pp. 457-485, ISSN 0020-9910
  58. Harer, J, The second homology group of the mapping class group of an orientable surface, Inventiones mathematicae, vol. 72 no. 2 (1983), pp. 221-239, ISSN 0020-9910
  59. HARER, JL, The second homology group of the mapping class group of an orientable surface, Invent.Math., vol. 72 (1983), pp. 221-239
  60. HARER, J, How to construct all fibered knots and links, Topology, vol. 21 no. 3 (1982), pp. 263-280, ISSN 0040-9383
  61. HARER, J, REPRESENTING ELEMENTS OF PI-1M3 BY FIBERED KNOTS, Cambridge Philosophical Society: Mathematical Proceedings, vol. 92 no. JUL (1982), pp. 133-138
  62. Casson, A; Harer, J, Some homology lens spaces which bound rational homology balls, Pacific Journal of Mathematics, vol. 96 no. 1 (September, 1981), pp. 23-36
  63. Harer, J, On handlebody structures for hypersurfaces in ℂ3 and ℂP3, Mathematische Annalen, vol. 238 no. 1 (1978), pp. 51-58, ISSN 0025-5831
  64. 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
  65. Harer, John, The third homology group of the moduli space of curves, Duke Math. J., vol. 63, no. 1, pp. 25--55, 1991
  66. Harer, John L., The cohomology of the moduli space of curves, Theory of moduli (Montecatini Terme, 1985), pp. 138--221, 1988, Springer, Berlin
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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. 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)
  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)

Papers Submitted

  1. 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: biology for the post-genomic era, vol. 17 no. 1 (October, 2016), pp. 214
  2. 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)
  3. 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)
  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. P. Bendich, Jacob Harer and John Harer, A Persistent Homology Based Geodesic Distance Estimator, Journal of Machine Learning Research (2014)
  6. J. Perea, A. Deckard, S. Haase and J. Harer, Applications of SWiPerS to the discovery of periodic genes (2013)
  7. 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)
  8. Bendich, P; Harer, J; Harer, J, Persistent Homology Enhanced Dimension Reduction, Foundations of Computational Mathematics (2012)
  9. Michael Jenista, , Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2012), pp. 12
  10. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2009)
  11. 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)

Preprints

  1. Fink, T; Ahnert, S; Bar On, R; Harer, J, Exact dynamics of Boolean networks with connectivity one, PRL (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

Other

  1. with H. Edelsbrunner, Persistent Morse Complex Segmentation of a 3-Manifold, Raindrop Geomagic Technical Report, vol. 066 (2004)