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Publications of John Harer    :chronological  combined  bibtex listing:

Books

  1. Penner, R. C. and Harer, J. L., Combinatorics of train tracks, pp. xii+216, 1992, Princeton University Press, Princeton, NJ [MR94b:57018]
  2. 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.)  [abs]

Papers Published

  1. 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
  2. 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]
  3. 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 [23580618], [doi]  [abs]
  4. 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 [MR1851176], [doi]  [abs]
  5. 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 [doi]  [abs]
  6. 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 [doi]  [abs]
  7. 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 [doi]  [abs]
  8. 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 [doi]  [abs]
  9. 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 [doi]  [abs]
  10. 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 [doi]  [abs]
  11. 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)  [abs]
  12. 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 [doi]
  13. Fink, T; Ahnert, S; Bar On, R; Harer, J, Exact dynamics of Boolean networks with connectivity one, PRL (2009)  [abs]
  14. 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 [doi]  [abs]
  15. 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 [doi]
  16. 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 [doi]  [abs]
  17. 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 [doi]  [abs]
  18. 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 [1109.6535v1], [doi]  [abs]
  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 [doi]  [abs]
  20. 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 [arXiv:1206.2790], [doi]  [abs]
  21. Turner, K; Mileyko, Y; Mukherjee, S; Harer, J, Fréchet Means for Distributions of Persistence Diagrams, Discrete & Computational Geometry (2014) [1206.2790v2]  [abs]
  22. 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 [doi]  [abs]
  23. 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)
  24. 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 [doi]  [abs]
  25. 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]
  26. 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]
  27. 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 [doi]  [abs]
  28. 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]
  29. 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
  30. 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 [doi]  [abs]
  31. 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 [doi]  [abs]
  32. 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 [MR83e:57007], [doi]
  33. 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  [abs]
  34. 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 [20107024], [doi]  [abs]
  35. 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 [doi]  [abs]
  36. 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 [doi]  [abs]
  37. 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 [available here], [doi]  [abs]
  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 (FOCS'07) (October, 2007), pp. 536-546, IEEE, ISBN 9780769530109 [doi]
  39. 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]
  40. 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 [available here], [doi]  [abs]
  41. 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 [doi]  [abs]
  42. 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 [doi]  [abs]
  43. 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 [doi]  [abs]
  44. 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 [doi]  [abs]
  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 (January, 2003), pp. 361-370 [doi]  [abs]
  46. 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 [doi]  [abs]
  47. 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 [doi]  [abs]
  48. 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) [doi]  [abs]
  49. 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 [MR80d:57020], [doi]
  50. 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 [pdf]  [abs]
  51. Bendich, P; Harer, J; Harer, J, Persistent Homology Enhanced Dimension Reduction, Foundations of Computational Mathematics (2012)
  52. 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 [available here], [doi]  [abs]
  53. 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 [doi]  [abs]
  54. 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 [doi]  [abs]
  55. 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]
  56. 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 [1307.6530v3], [doi]  [abs]
  57. 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 [doi]  [abs] [author's comments]
  58. 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)
  59. Michael Jenista, , Realizing Boolean Dynamics in Switching Networks, Siam Journal of Applied Dynamical Systems (2012), pp. 12  [abs]
  60. 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 [doi]  [abs]
  61. 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]
  62. 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 [doi]  [abs]
  63. 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 [1307.6188v2], [doi]  [abs]
  64. 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 [MR83h:57013], [doi]  [abs]
  65. 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 [doi]  [abs] [author's comments]
  66. 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 [doi]  [abs]
  67. 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]
  68. 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 [MR91e:57002], [doi]
  69. 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]
  70. Czumaj, A; Sohler, C, Testing Expansion in Bounded-Degree Graphs, 48th Annual IEEE Symposium on Foundations of Computer Science (FOCS'07) (October, 2007), pp. 536-546, IEEE, ISBN 9780769530109 [doi]
  71. 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]
  72. 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 [doi]  [abs]
  73. 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]
  74. 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 [doi]  [abs]
  75. 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 [doi]  [abs]
  76. 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 [doi]  [abs]
  77. 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]
  78. 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 [MR84g:57006], [doi]
  79. 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 [doi]
  80. 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]
  81. 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 [MR87c:32030], [doi]
  82. 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 [doi]  [abs]
  83. 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 [doi]  [abs]
  84. 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) [doi]  [abs]
  85. 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 [doi]  [abs]

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)  [abs]

Papers Submitted

  1. P. Bendich, Jacob Harer and John Harer, A Persistent Homology Based Geodesic Distance Estimator, Journal of Machine Learning Research (2014)  [author's comments]
  2. J. Perea, A. Deckard, S. Haase and J. Harer, Applications of SWiPerS to the discovery of periodic genes (2013)
  3. 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]
  4. P. Bendich and J. Harer, Elevation for singular spaces using persistent intersection homology (2009)
  5. 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]
  6. 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]
  7. 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]
  8. 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]

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)  [abs] [author's comments]

 

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