Department of Mathematics
 Search | Help | Login | pdf version | printable version

Math @ Duke





.......................

.......................


Publications of John Harer    :chronological  alphabetical  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. 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 [doi]  [abs]
  2. David Rouse ; Adam Watkins ; David Porter ; John Harer ; Paul Bendich ; Nate Strawn ; Elizabeth Munch ; Jonathan DeSena ; Jesse Clarke ; Jeffrey Gilbert ; Peter Chin ; Andrew Newman, Feature-aided multiple hypothesis tracking using topological and statistical behavior classifiers, Proc. SPIE 9474, Signal Processing, Sensor/Information Fusion, and Target Recognition XXIV, 94740L (2015), ISSN 10.1117/12.2179555
  3. Farr, RS; Harer, JL; Fink, TM, Easily repairable networks: reconnecting nodes after damage., Physical Review Letters, vol. 113 no. 13 (September, 2014), pp. 138701, ISSN 0031-9007 [doi]  [abs]
  4. 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 [arXiv:1206.2790], [doi]  [abs]
  5. 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]
  6. 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.)  [abs]
  7. 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.) [doi]  [abs]
  8. Topp, CN; Iyer-Pascuzzi, AS; Anderson, JT; Lee, CR; 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 [23580618], [doi]  [abs]
  9. 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.)  [abs]
  10. 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
  11. 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 [22834569], [doi]  [abs]
  12. 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 [1109.6535v1], [doi]  [abs]
  13. 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 [doi]  [abs]
  14. 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)
  15. Bendich, P; Harer, J, Persistent Intersection Homology, Foundations of Computational Mathematics, vol. 11 no. 3 (2011), pp. 305-336, ISSN 1615-3375 [doi]  [abs]
  16. Bendich, P; Galkovskyi, T; Harer, J, Improving homology estimates with random walks, Inverse Problems, vol. 27 no. 12 (2011), pp. 16, ISSN 0266-5611 [doi]  [abs]
  17. 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 [doi]  [abs] [author's comments]
  18. 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 [doi]  [abs]
  19. 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 [20107024], [doi]  [abs]
  20. 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 [available here], [doi]  [abs]
  21. 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 [available here]  [abs]
  22. 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 [doi]  [abs]
  23. 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 [doi]
  24. 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 [doi]  [abs]
  25. Edelsbrunner, H; Harer, J; Patel, AK, Reeb spaces of piecewise linear mappings, Proceedings of the Annual Symposium on Computational Geometry (2008), pp. 242-250 [doi]  [abs]
  26. 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 [doi]  [abs]
  27. 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]
  28. 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  [abs]
  29. 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 [available here], [doi]  [abs]
  30. 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 [doi]  [abs] [author's comments]
  31. 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 [doi]  [abs]
  32. Cohen-Steiner, D; Edelsbrunner, H; Harer, J, Stability of persistence diagrams, Proceedings of the Annual Symposium on Computational Geometry (2005), pp. 263-271 [doi]  [abs]
  33. 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  [abs]
  34. 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  [abs]
  35. 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  [abs]
  36. 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  [abs]
  37. 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  [abs]
  38. 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 [doi]  [abs]
  39. 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  [abs]
  40. 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  [abs]
  41. 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]
  42. 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 [MR1851176]  [abs]
  43. 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  [abs]
  44. Agarwal, PK; Collins, AD; Harer, JL, Minimal trap design, Proceedings - IEEE International Conference on Robotics and Automation, vol. 3 (2001), pp. 2243-2248  [abs]
  45. 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 [MR91e:57002], [doi]
  46. Harer, JL, The virtual cohomological dimension of the mapping class group of an orientable surface, Inventiones mathematicae, vol. 84 no. 1 (1986), pp. 157-176, ISSN 0020-9910 [MR87c:32030], [doi]
  47. 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 [MR87i:32031], [doi]
  48. 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 [MR84g:57006], [doi]
  49. Harer, J, How to construct all fibered knots and links, Topology, vol. 21 no. 3 (1982), pp. 263-280, ISSN 0040-9383 [MR83e:57007], [doi]
  50. Harer, J, On handlebody structures for hypersurfaces in ℂ3 and ℂP3, Mathematische Annalen, vol. 238 no. 1 (1978), pp. 51-58, ISSN 0025-5831 [MR80d:57020], [doi]
  51. 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]
  52. 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]
  53. 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]
  54. 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]
  55. 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]
  56. 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]
  57. 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]
  58. 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]
  59. 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]

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. K. Mcgoff, X. Guo, A. Deckard, C. Kelliher, A. Leman, S. Haase, J. Harer, The Local Edge Machine: Inference of Dynamic Models of Gene Regulation, Genome Biology (2015)
  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)  [abs]
  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)  [abs]
  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)  [abs]
  5. P. Bendich, Jacob Harer and John Harer, A Persistent Homology Based Geodesic Distance Estimator, Journal of Machine Learning Research (2014)  [author's comments]
  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)  [abs]
  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  [abs]
  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)  [abs]

Preprints

  1. Fink, T; Ahnert, S; Bar On, R; Harer, J, Exact dynamics of Boolean networks with connectivity one, PRL (2009)  [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]

 

dept@math.duke.edu
ph: 919.660.2800
fax: 919.660.2821

Mathematics Department
Duke University, Box 90320
Durham, NC 27708-0320