Ayres, M. P., M. J. Lombardero. 2018. Forest pests and their management in the Anthropocene. Canadian Journal of Forest Research 48:292-301.
Valtonen, A., A. Hirka, L. Szocs, M. P. Ayres, H. Roininen, and G. Csoka. 2017. Long-term species loss and homogenization of moth communities in Central Europe. Journal of Animal Ecology 86:730-738. doi: 10.1111/1365-2656.12687
Lovett, Gary M., Marissa Weiss, Andrew M. Liebhold, Thomas P. Holmes, Brian Leung, Kathy-Fallon Lambert, David A. Orwig, Faith T. Campbell, Jonathan Rosenthal,Deborah G. McCullough, Radka Wildova, Matthew P. Ayres, Charles D. Canham, David R. Foster, Shannon L. LaDeau, Troy Weldy. 2016. Nonnative forest insects and pathogens in the United States: impacts and policy options. Ecological Applications 26: 1437-1455, doi: 10.1890/15-1176.1
Valtonen, Anu, Reima Leinonen, Juha Pöyry, Heikki Roininen, Jukka Tuomela, and Matthew P. Ayres. 2014. Is climate warming more consequential towards poles? The phenology of Lepidoptera in Finland. Global Change Biology 20:16-27
Lombardero, Maria J., Matthew P. Ayres, Flora E. Krivak-Tetley, and Katrin N.E. Fitza. 2016. Population biology of the European woodwasp, Sirex noctilio, in Galicia, Spain. Bulletin of Entomological Research 106: 569-580.
Culler, Lauren E., Matthew P. Ayres, and Ross A. Virginia. 2015. In a warmer Arctic, mosquitoes avoid increased mortality from predators by growing faster. Proceedings of the Royal Society B 282: 20151549.
Symes, Laurel. B. , Nancy Serrell, and M. P. Ayres. 2015. A practical guide for mentoring scientific inquiry. Bulletin of the Ecological Society of America 96(2): 352-367.
Weed, Aaron S., M.P. Ayres, and Jeffrey A. Hicke. 2013. Consequences of climate change for biotic disturbances in North American forests. Ecological Monographs 83:441–470.
Martinson, S. J., T. Ylioja, B. T. Sullivan, R. F. Billings, and M. P. Ayres. 2013. Alternate attractors in the population dynamics of a tree-killing bark beetle. Population Ecology 55:95-106.
Valtonen, A., F. Molleman, C.A. Chapman, J.R. Carey, M.P. Ayres, and H. Roininen. 2013. Tropical phenology: bi-annual rhythms and interannual variation in an Afrotropical butterfly assemblage. Ecography, in press.
Marini, L., M. P. Ayres, A. Battisti, and M. Faccoli. 2012. Climate affects severity and altitudinal distribution of outbreaks in an eruptive bark beetle. Climatic Change 115:327-341.
Shi, Peijan, Bo Wang, MP Ayres, Feng Gea, Ling Zhong, and Bai-Lian Li. 2012. Influence of temperature on the northern distribution limits of Scirpophaga incertulas Walker (Lepidoptera: Pyralidae) in China. Journal of Thermal Biology 37:130-137.
Garnas, JR., DR Houston, MP Ayres, and C. Evans. 2011. Disease ontogeny overshadows effects of climate and species interactions on population dynamics in a nonnative forest disease complex. Ecography 34: 1-10.
Stange, E. E., M. P. Ayres, and J. A. Bess. 2011. Concordant population dynamics of Lepidoptera herbivores in a forest ecosystem. Ecography 34: 772-779
Garnas, JR., MP Ayres, AM Liebhold, and C Evans. 2011. Subcontinental impacts of an invasive tree disease on forest structure and dynamics. Journal of Ecology 99: 532-541.
Stange, E. E., M. P. Ayres, and J. A. Bess. 2011. Concordant population dynamics of Lepidoptera herbivores in a forest ecosystem. Ecography 34: 772-779
Valtonen, A, MP Ayres, H Roininen, J Pöyry and R Leinonen. 2011. Environmental controls on the phenology of moths - predicting plasticity and constraint under climate change. Oecologia 165: 237-248.
Seppälä, R., A. Buck, and P. Katila. (eds.). 2009. Adaptation of Forests and People to Climate Change: A Global Assessment Report. International Union of Forest Research Organizations, Helsinki. IUFRO World Series Volume 22. 224 p.
Lombardero, M.J., P. Vázquez-Mejuto, and M.P. Ayres. 2008. Role of plant enemies in the forestry of indigenous versus nonindigenous pines. Ecological Applications 18: 1171-1181.
Martinson, S.J., R.W. Hofstetter, and M.P.Ayres. 2007. Why does longleaf pine have low susceptibility to southern pine beetle? Canadian Journal of Forest Research 37: 1966–1977.
Friedenberg, N.A., J.A. Powell and M.P. Ayres. 2007 Synchrony's double edge: transient dynamics and the Allee effect in stage-structured populations. Ecology Letters 10: 564–573.
Tran , J.K., T. Ylioja, R. Billings, J. Régnière, and M.P. Ayres. 2007. Impact of minimum winter temperatures on the population dynamics of Dendroctonus frontalis (Coleoptera: Scolytinae) Ecological Applications 17: 882-899.
Reynolds, L.V., M.P. Ayres, T.G. Siccama, and R.T. Holmes. 2007. Climatic effects on caterpillar fluctuations in northern hardwood forests. Canadian Journal of Forest Research 37: 481-491
Hofstetter, R.W., J.T. Cronin, K.D. Klepzig, J.C. Moser, and M.P. Ayres. 2006. Antagonisms, mutualisms and commensalisms affect outbreak dynamics of the southern pine beetle. Oecologia 147: 679-691.
Lombardero, M.J., M. P. Ayres, R. W. Hofstetter, J.C. Moser, and K.D. Klepzig. 2003. Strong indirect interactions of Tarsonemus mites (Acarina, Tarsonemidae) and Dendroctonus frontalis (Coleoptera:Scolytidae).Oikos 102: 243-252.
Lombardero, M.J., M.P. Ayres, P.L. Lorio, Jr., and J.J. Ruel. 2000. Environmental effects on constitutive and inducible resin defenses of loblolly pine.Ecology Letters 3:329-339.
Ayres, M.P., Wilkens, R.T., Ruel, J.J., M.J. Lombardero, and E. Vallery. 2000. Nitrogen budgets of phloem-feeding bark beetles with and without symbiotic fungi (Coleoptera: Scolytidae).Ecology 81:2198-2210.
Ruel, J. J., and M.P. Ayres. 1999. Jensen's inequality predicts effects of environmental variation. Trends in Ecology and Evolution 14:361-366.
Ayres, M. P., T. P. Clausen, S. F. MacLean, Jr., A. M. Redman, and P. B. Reichardt. 1997. Diversity of structure and anti-herbivore activity in condensed tannins.Ecology 78: 1696-1712.
Ayres, M.P., and J.M. Scriber. 1994. Local adaptation to regional climates in Papilio canadensis (Lepidoptera:Papilionidae).Ecological Monographs 64: 465-482.
Schamel, D., and M. P. Ayres. 1992. The "minds-on" approach: student creativity and personal involvement in the undergraduate science laboratory. Journal of College Science Teaching 21:226-229.
Ayres, M.P. and S.F. MacLean, Jr. 1987. Development of birch leaves and the growth energetics of Epirrita autumnata (Geometridae).Ecology 68:558-568.