introduction to lectures

Joseph M. Mahaffy
Publications

Recent Publications
(After 2000)

Aileen Nguyen, Joseph Mahaffy, and Naveen K. Vaidya. Modeling transmission dynamics of lyme disease: Multiple vectors, seasonality, and vector mobility, Infectious Disease Modelling, doi.org/10.1016/j.idm.2019.03.001 (2019) (PDF)
Gabriel P. Langlois, Morgan Craig, Antony R. Humphries, Michael C. Mackey, Joseph M. Mahaffy, Jacques Bélair, Thibault Moulin, Sean R. Sinclair, and Liangliang Wang. Normal and pathological dynamics of platelets in humans, J. Theor. Biol., DOI 10.1007/s00285-017-1125-6 (2017) (PDF)
J. M. Mahaffy and T. C. Busken, Regions of Stability for a Linear Differential Equation with Two Rationally Dependent Delays, DCDS A, 35, 4955-4986 (2015) (PDF) - Supplement
D. Lyons, J. Mahaffy, S. Wang, A. Palacios and V. In. Geometry of Basins of Attraction and Heteroclinic Connections in Coupled Bistable Systems, International Journal of Bifurcation and Chaos, 24, 1430029 (2014) (PDF)
Jerry S. Chen, Abygail M. Gumbayan, Robert W. Zeller, and Joseph M. Mahaffy, An expanded Notch-Delta model exhibiting long-range patterning and incorporating microRNA regulation, PLoS Computational Biology,10, e1003655 (2014) (PDF)
Beltran Rodriguez-Brito, LinLin Li, Linda Wegley, Mike Furlan, Florent Angly, Mya Breitbart, John Buchanan, Christelle Desnues, Elizabeth Dinsdale, Robert Edwards, Ben Felts, Dana Willner, Matthew Haynes, Hong Liu, David Lipson, Joseph Mahaffy, Anna Belen Martin-Cuadrado, Alex Mira, Jim Nulton, Lejla Pašic, Steve Rayhawk, Jennifer Rodriguez-Mueller, Francisco Rodriguez-Valera, Peter Salamon, Shailaja Srinagesh, Tron Frede Thingstad, Tuong Tran, Rebecca Vega Thurber, Merry Youle, Forest Rohwer, Viral and microbial community dynamics in four aquatic environments, ISME Journal, 4, 739-751 (2010)
Daniel Lyons, Joseph M. Mahaffy, Antonio Palacios, Visarath In, Patrick Longhini, Andy Kho, Basins of attraction in a ring of overdamped bistable systems with delayed coupling, Physics Letters A , 374 , 2709–2722 (2010) (PDF)
M. Breitbart, M. Haynes, S. Kelley, F. Angly, R. A. Edwards, B. Felts, J.M. Mahaffy, J. Mueller, J. Nulton, S. Rayhawk, B. Rodriguez-Brito, P. Salamon, F. Rohwer, Viral Diversity and Dynamics in an Infant's Gut, Research in Microbiology , 159 , 367-373 (2008) (PDF)
J. M. Mahaffy and L. Edelstein-Keshet, Modeling cyclic waves of circulating T cells in autoimmune diabetes, SIAM J. Appl. Math ., 67 , 915-937 (2007) (PDF)
F. Angly, B. Felts, M. Breitbart, P. Salamon, R. Edwards, C. Carlson, A. Chan, M. Haynes, S. Kelley, H. Liu, J. Mahaffy, J. Mueller, J. Nulton, R. Olson, R. Parsons, S. Rayhawk, C. Suttle, F. Rohwer, The Marine Viromes of Four Oceanic Regions, PLoS Biology, 4 , e368 (2006) (PDF)
F. Angly, B. Rodriguez-Brito, D. Bangor, P. McNairnie, M. Breitbart, P. Salamon, B. Felts, J. Nulton, J. Mahaffy, and F. Rohwer, (2005), PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information, BMC Bioinformatics, 6 , 41. (PDF)
A. Ponnuswamy, J. Nulton, J. Mahaffy, P. Salamon, T. Frey and A. R. C. Baljon, (2005) Modeling tubular shapes of mitochondrial membranes, Physical Biology, 2 , 73-79. (PDF)
M. Breitbart, B. Felts, S. Kelley, J. M. Mahaffy, J. Nulton, P. Salamon, and F. Rohwer (2004) Diversity and population structure of a nearshore marine sediment viral community. Proceedings of the Royal Society B. (PDF)
M. Breitbart, I. Hewson, B. Felts, J. M. Mahaffy, J. Nulton, , P. Salamon, and F. Rohwer (2003) Metagenomic analysis of an uncultured viral community from human feces. J. Bacteriol. 185, 6220-6223. (PDF)
A. V. Grigorian, R. B. Lustig, E. C. Guzman, J. M. Mahaffy, and J. W. Zyskind (2002) Escherichia coli cells with increased levels of DnaA require recombinant repair for viability. J. Bacteriol. 185, 630-644. (PDF)
M. Breitbart, P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall, D. Mead, F. Azam, and F. Rohwer (2002) Genomic analysis of uncultured marine viral communities. PNAS 99, 14250-14255. (PDF)
J. Bélair and J. M. Mahaffy (2001) Variable maturation velocity and parameter sensitivity in a model of haematopoiesis. IMA Journal of Mathematics Applied in Medicine and Biology 18, 193-211. (PDF)
M. Santillán, J. M. Mahaffy, J. Bélair and M. C. Mackey (2000) Regulation of platelet production: The normal response to perturbation and cyclical platelet disease. J. Theor. Biol. 206, 585-603. (PDF)

Selected Publications
(Before 2000)

J. M. Mahaffy (1999) Age-structured modeling of hematopoiesis, Technical Report, Centre recherches mathématiques, Université de Montréal, CRM-2609 . (PDF)
J. M. Mahaffy, Samuel W. Polk, and Roland K. W. Roeder (1999) An age-structured model for erythropoiesis following a phlebotomy, Technical Report, Centre recherches mathématiques, Université de Montréal, CRM-2598. (PDF)
J. M. Mahaffy and E. S. Savev (1999) Stability analysis for mathematical models of the lac operon, Quart. Appl. Math. 57, 37-53. (PDF)
J. M. Mahaffy, J. Bélair and M. C. Mackey (1998) Hematopoietic model with moving boundary condition and state dependent delay: Applications in erythropoiesis, J. Theor. Biol. 190, 135-146. (PDF)
J. M. Mahaffy (1996) Modeling erythropoiesis: Relating age-structure and delays, in Differential Equations and Applications to Biology and to Industry, eds. M. Martelli, K. Cooke, E. Cumberbatch, B. Tang, and H. Thieme, World Scientific, Singapore, 327-336.
J. Bélair, M. C. Mackey and J. M. Mahaffy (1995) Age-structured and two delay models for erythropoiesis, Math. Biosci., 128, 317-346. (PDF)
J. M. Mahaffy, P. J. Zak and K. M. Joiner (1993) A three parameter stability analysis for a linear differential equation with two delays, Technical Report, Department of Mathematical Sciences, San Diego State University, San Diego, CA. (PDF)
J. M. Mahaffy, P. J. Zak and K. M. Joiner (1995) A geometric analysis of stability regions for a linear differential equation with two delays, Int. J. Bifur. Chaos, 5, 779-796. (PDF)
J. M. Mahaffy (1993) Variation in concentrations of RNAs and proteins involved in gene expression of Escherichia coli}, J. Theor. Biol., 162, 153-186. (PDF)
J. M. Mahaffy, D. A. Jorgensen and R. L. Vanderheyden (1992) Stability results for a model of repression with external control, Quart. Appl. Math., 50, 415-435. (PDF)
J. M. Mahaffy, D. A. Jorgensen and R. L. Vanderheyden (1992) Oscillations in a model of repression with external control, J. Math. Biol. 30, 669-691. (PDF)
J. M. Mahaffy and J. W. Zyskind (1991) A comparison of two models for initiation of replication in Escherichia coli, Proceedings of the Second International Conference on Mathematical Population Dynamics (eds. O. Arino, D. E. Axelrod, and M. Kimmel), Marcel Dekker, 747-766.
J. M. Mahaffy and J. W. Zyskind (1989) A model for the initiation of replication in Escherichia coli, J. Theor. Biol.140, 453-477. (PDF)
S. N. Busenberg and J. M. Mahaffy (1989), A compartmental reaction-diffusion cell cycle model, Comp. Math. Appl.. 18, 883-892. (PDF)
S. N. Busenberg and J. M. Mahaffy (1988), The effects of dimension and size for a compartmental model of repression, SIAM J. Appl. Math.. 48, 882-903. (PDF)
J. M. Mahaffy (1988), Genetic control models with diffusion and delays, Math. Bios. 90, 519-533. (PDF)
J. M. Mahaffy (1985), Stability of periodic solutions for a model of genetic repression with delays, J. Math. Biol. 22, 137-144. (PDF)
S. N. Busenberg and J. M. Mahaffy (1985), Interaction of spatial diffusion and delays in models of genetic control by repression, J. Math. Biol. 22, 313-333. (PDF)
C. V. Pao and J. M. Mahaffy (1985), A three-compartment reaction system with the effect of diffusion and time delay, ed. J. H. Lightbourne III and S. M. Rankin III in Physical Mathematics and Nonlinear Partial Differential Equations, 111-114. (PDF)
C. V. Pao and J. M. Mahaffy (1985), Qualitative analysis of a coupled reaction-diffusion model in biology with time delays, J. Math. Anal. Appl. 109, 355-371. (PDF)
J. M. Mahaffy and C. V. Pao (1984), Models of genetic control by repression with time delays and spatial effects, J. Math. Biol. 20, 39-58. (PDF)
J. M. Mahaffy (1984), Cellular control models with linked positive and negative feedback and delays. I. The models, J. theor. Biol. 106, 89-102. (PDF)
J. M. Mahaffy (1984), Cellular control models with linked positive and negative feedback and delays. II. Linear analysis and local stability, J. theor. Biol. 106, 103-112. (PDF)
J. M. Mahaffy (1982), A test for stability of linear differential delay equations, Quart. Appl. Math. 40, 72-105. (PDF)
J. M. Mahaffy (1980), Periodic Solutions for Certain Protein Synthesis Models, J. Math. Anal. Appl.. 74, 193-202. (PDF)
H. T. Banks and J. M. Mahaffy (1978), Stability of cyclic gene models for systems involving repression, J. theor. Biol. 74, 323-324. (PDF)
H. T. Banks and J. M. Mahaffy (1978), Global asymptotic stability of certain models for protein synthesis and repression, Quart. Appl. Math. 36, 209-221. (PDF)