- Buchheister, A., T. J. Miller, E. D. Houde, D. H. Secor, R. J. Latour. 2016. Spatiotemporal dynamics of Atlantic menhaden (Brevoortia tyrannus) recruitment along the Northwest Atlantic Ocean. ICES Journal of Marine Science 73(4):1147-1159.
- Schaffler, J. J., T. J. Miller, C. M. Jones. 2014. Spatial and temporal variation in otolith chemistry of juvenile Atlantic menhaden in the Chesapeake Bay. Transactions of the American Fisheries Society 143:1061-1071.
- Peer, A. C. and T. J. Miller. 2014. Climate change, migration phenology and fisheries management interact with unexpected consequences. North American Journal of Fisheries Management 34:94-110.
- Frisk, M. G., A. Jordaan and T. J. Miller. 2014. Moving beyond the current paradigm in marine population connectivity: Are adults the missing link? Fish and Fisheries. 15:242-254.
- Peer, A. C., G. M. Selckmann and T. J. Miller. 2012. A standardized method and analytical approach for predicting reproductive stage in teleosts using ovary color and female characteristics. Transactions of the American Fisheries Society. 141:1036-1044
- Williams, E. P., A. C. Peer, T. J. Miller, D. H. Secor and A. R. Place. 2012. A phylogeny of the temperate sea basses (Moronidae) characterized by a unique translocation of the ND6 gene. J. Fish Biol. 80:110-130. DOI:10.1111/j.1095-8649.2011.03158.x
- Miller, T. J., O. Fiksen and A. Gallego. 2009. Growth. p24-27 In North, E. W., A. Gallego and P. Petitigas. Manual of Recommended Best Practices for Modelling Physical-Biological Interactions During Fish Early Life. ICES Cooperative Research Report 295: 25-27.
- Hinckley, S., B. A. Megrey and T. J. Miller. 2009. Recruitment prediction. P 78-83 In North, E. W., A. Gallego and P. Petitigas. Manual of Recommended Best Practices for Modelling Physical-Biological Interactions During Fish Early Life. ICES Cooperative Research Report 295: 77-82.
- Miller, T. J. (2007). Contribution of individual-based coupled physical biological models to understanding recruitment in marine fish populations. Marine Ecology Progress Series 347:127-138
- Fulford, R. S., J. A. Rice, T. J. Miller, F. P. Binkowski, J. M. Detmers and B. Belonger. 2006. Foraging selectivity by larval yellow perch (Perca flavescens): Implications for understanding recruitment in small and large lakes. Can. J. Fish. Aquat. Sci 63:28-42
- Fulford, R. S., J. A. Rice, T. J. Miller and F. P. Binkowski. 2006. Elucidating patterns of size-dependent predation on larval yellow perch (Perca flavescens) in Lake Michigan: an experimental and modeling approach. Can. J. Fish. Aquat. Sci 63:11-27.
- Yellow Perch Task Group (2004). Yellow Perch Research and Management in Lake Michigan: Evaluating Progress in a Cooperative Effort, 19972001. Fisheries. Nov 2004. 11- 19
- Miller, T. J. 2002. Assemblages, communities, and species interactions. Chapter 8 In L. A. Fuiman and R. G. Werner (Eds.). Concepts in Fishery Science: The Unique Contributions of Early Life Stages. Blackwell Sciences.
- Heyer, C. J., T. J. Miller, F. P. Binkowski, E. M. Calderone and J. A. Rice. 2001. Understanding maternal effects as a recruitment mechanism in Lake Michigan yellow perch (Perca flavescens). Can. J. Fish. Aquat. Sci. 58:1477-1487.
- Quinlan, J. A., B. O. Blanton, T. J. Miller and F. E. Werner. 2000. From spawning grounds to the estuary: Using linked individual-based and hydrodynamic models to interpret patterns and processes in the oceanic phase of Atlantic menhaden Brevoortia tyrannus life history. Fisheries Oceanography 8 (suppl. 2):224-246
- Miller, T. J., T. Herra and W. C. Leggett 1999. The relationship between larval size and otolith size at hatch in Atlantic cod, Gadus morhua. Fish Bull U.S. 97(2):294-305.
- Bertram, D. F., T. J. Miller and W. C. Leggett. 1997. Individual variation in growth and development during the early life stages of winter flounder. Fish Bull. 95:1-10.
- Dower, J. F., T. J. Miller and W. C. Leggett. 1997. The role of microscale turbulence in the feeding ecology of larval fish. Adv. Mar. Biol. 31:169-220.
- Miller, T. J. 1996. The use of field studies to investigate selective processes in fish early life history. Chapter 7 In R. C. Chambers and E. Trippel (eds). The Role of Early Life History Studies in Understanding Fish Biology. Chapman and Hall, New York, NY
- Landry, F. P., T. J. Miller, and W. C. Leggett. 1995. The influence of small-scale turbulence on the ingestion rate of fathead minnow (Pimphales promelas) larvae. Can. J. Fish. Aquat. Sci. 52:1714-1719.
- Miller, T. J., T. Herra and W. C. Leggett. 1995. Characteristics of eggs and their subsequent newly-hatched larvae of Atlantic cod (Gadus morhua). Can. J. Fish. Aquat. Sci. 52:1083-1093.
- Chambers, R.C and T. J. Miller. 1995. Statistical analysis of reconstructed life histories from otoliths: Special properties of longitudinal data. pp 155 -175 In D. Secor, J. Dean and S. E. Campana (eds.). Recent Developments in Otolith Research. University of South Carolina Press, Columbia, S.C.
- MacKenzie, B. R., T. J. Miller, W. C. Leggett and S. Cyr. 1994 The influence of small-scale turbulence on the ingestion rate of larval fish. Limnology and Oceanography. 39:1790-1799.
- Miller, T. J., L. B. Crowder and J. A. Rice. 1993. Ontogenetic changes in behavioural and histological measures of visual acuity in three species of fish. Env. Biol. Fish. 37:1-8.
- Pepin, P. and T. J. Miller 1993. Potential use and abuse of general empirical models of early life history processes in fish. Can. J. Fish. Aquat. Sci. 50:1343-1345.
- Rice, J. A., T. J. Miller, K. A. Rose, L. B. Crowder, E. A. Marschall, A. Trebitz, and D. L. DeAngelis. 1993. Growth rate variation and larval survival: Inferences from an individual-based size-dependent predation model. Can. J. Fish. Aquat. Sci. 50:133-142.
- Miller T. J., L. B. Crowder, J. A. Rice and F. P. Binkowski. 1992. Body size and the ontogeny of the functional response in fishes. Can. J. Fish. Aquat. Sci. 49:805-812.
- Crowder, L. B., J. A. Rice, T. J. Miller and E. A. Marschall. 1992. Empirical and theoretical approaches to size-based interactions and recruitment variability in fishes. p 237-255. In: D. L. DeAngelis, and L. J. Gross (Eds.) Individual-Based Approaches in Ecology Chapman Hall. London. 544 pp.
- Miller, T. J., L. B. Crowder and F. P. Binkowski. 1990. The effect of changes in the zooplankton assemblage on growth in bloater and its implications for recruitment success. Trans. Am. Fish. Soc. 119:483-491.
- Miller, T. J., L. B. Crowder, J. A. Rice and E. A. Marschall. 1988. Larval size and recruitment mechanisms in fishes: Toward a conceptual framework. Can. J. Fish. Aquat. Sci. 45:1678-1670.
- Michael J. Wilberg, M. J. , T. F. Ihde, D. H. Secor, and T. J. Miller. 2009. FishSmart: A stakeholder-centered approach to improve fisheries conservation and management. ICES CM/O:15
- Wilberg, M. J., T. F. Ihde, T. J. Miller and D. H. Secor. 2008. Enhancing sustainability in marine recreational fisheries: a stakeholder-driven process for evaluating angling practices and management options for king mackerel in the U.S. ICES CM 2008/K:17
- Kendall, M. S. and T. J. Miller. 2008. The influence of thematic and spatial resolution on maps of a coral reef ecosystem. Marine Geodesy 31:75-102.
- Wilberg, M. J and T. J. Miller. 2007. Problems with inferences of fish population dynamics based on maximum catch. Science 316:1285.
- Miller, T. J. 2006. Patterns of total removals. Pages 189-212 In Fisheries ecosystem planning for the Chesapeake Bay. American Fisheries Society, Trends in Fisheries Science and Management 3, Bethesda, Maryland.
- Miller, T. J., E. D. Houde, and E. A. Watkins. 1996. Chesapeake Bay Fisheries: Prospects for Multispecies Management and Sustainability. Chesapeake Research Consortium Literature Synthesis. Ref [UMCEES]CBL 96-141
- Hewitt, D. A., D. M. Lambert, J. M. Hoenig, R. N. Lipcius, D. B. Bunnell and T. J. Miller (2007). Direct and indirect estimates of natural mortality for blue crab. Trans. Am. Fish. Soc 136:1030-1040.
- Brylawski, B. J. and T. J. Miller. (2006). Temperature dependent growth of the blue crab (Callinectes sapidus), a molt process approach. Can. J. Fish. Aquat. Sci.63:1298-1308.
- Bunnell, D. B. and T. J. Miller (2005). An individual-based modeling approach to per-recruit models: blue crabs (Callinectes sapidus) in the Chesapeake Bay. Can. J. Fish. Aquat. Sci. 62:1560-15720.
- Jensen, O. P., M. C. Christman and T. J. Miller. (2006). Landscape-based geostatistics: A case study of the distribution of blue crab in Chesapeake Bay. Environmetrics 17:605-621
- Jensen, O. P. and T. J. Miller. (2005). Geostatistical analysis of blue crab (Callinectes sapidus) abundance and winter distribution patterns in Chesapeake Bay. Transactions of the American Fisheries Society 134:1582-1598.
- Jensen, O. P., R. Seppelt and T. J. Miller (2005). Winter distribution of blue crab (Callinectes sapidus) in Chesapeake Bay: application of a two-stage generalized additive model (GAM) . Mar Ecol Progr Ser. 299:229-255
- Fogarty, M. J. and T. J. Miller (2004). Impact of a Change in Reporting Systems in the Maryland Blue Crab Fishery. Fish. Res. 54: 737-738. In press.
- Brylawski, B. and T. J. Miller. 2003. The bioenergetic modeling of the blue crab (Callinectes sapidus) using the computer-based Wisconsin model. Bull. Mar. Sci.72:491-504.
- Miller, T. J. 2003. Incorporating space into models of blue crab populations. Bull. Mar. Sci. 72:567-588.
- Miller, T. J. and S. G. Smith 2003. Modeling Crab Growth and Population Dynamics: Insights from the Blue Crab Conference. Bull. Mar. Sci. 72:537-541.
- Miller, T. J. 2001. Matrix-based modeling of blue crab population dynamics with applications to the Chesapeake Bay. Estuaries 24(4):535-544.
- Frisk, M. G. and T. J. Miller. 2009. Maturation, of little skate, Leucoraja erinacea, and winter skate, L. ocellata in the western Atlantic from Cape Hatteras to Georges Bank.. Marine and Coastal Fisheries: Dynamics, Management and Ecosystem Sciences 1: 1-11.
- Frisk, M. G., T. J. Miller, S. J. D. Martell and K. K. Sosebee. 2008. New hypothesis helps explain elasmobranch “outburst” on Georges Bank in the 1980’s. Ecological Applications 18:234-245.
- Frisk, M. G. and T. J. Miller. (2006). Age and growth of winter skate and little skate. Can. J. Fish. Aquat. Sci. 63:1078-1091
- Alvarado Bremer, J. R., M. G. Frisk, T. J. Miller, Jennifer Turner, J. Viñas and K. Kwil (2004). Genetic identification of the cryptic juveniles of little skate and winter skate. J. Fish Biol.
- Frisk, M. G., N. K. Dulvy and T. J. Miller (2005). Life history and vulnerability to exploitation of elasmobranchs: Inferences from elasticity, perturbation and phylogenetic analyses. Journal of the Northwest Atlantic Fisheries Organization.35:27-45.
- Miller, T. J., M. G. Frisk and M. J. Fogarty. (2003). Comment on Mollet and Caillet: Confronting Models with Data. Mar.Frshwtr. Res.54:000-000.
- Frisk, M. G., T. J. Miller and M. J. Fogarty. 2002. The population dynamics of little skate Leucoraja erinacea, winter skate Leucoraja ocellata, and barndoor skate Dipturus laevis: predicting exploitation limits using matrix analyses. ICES Journal of Marine Science. 59:576-586.
- Frisk, M. G., T. J. Miller and M. J. Fogarty 2001. Estimation and analysis of biological parameters in elasmobranch fishes: a comparative life history study. Can. J. Fish. Aquat. Sci. 58: 969-981
- Brewster-Geisz, K. K., and T. J. Miller. 2000. Management of sandbar shark (Carcharhinus plumbeus): implications from a stage-based model. Fish Bull. U.S. 98(2):236-249.