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Zhou, C., M. Fujiwara, W. Grant (2016). Finding regulation among seemingly unregulated populations: a practical framework for analyzing multivariate population time series for their interactions. Environmental and Ecological Statistics 23(2): 181-204.

Fujiwara, M., C. Zhou, C., Acres, F. Matinez-Andrade. (2016). Interaction between Penaeid Shrimp and Fish Populations in the Gulf of Mexico: Importance of Shrimp as Forage Species. Plos One 11(11). (DOI:10.1371/journal.pone.0166479)

Fujiwara, M. (2016) Incorporating demographic diversity into food web models: Effects on community structure and dynamics. Ecological Modelling, 322: 10-18.

Bani-Yaghoub, M., Y. Guangming, M. Fujiwara, D.E. Amundsen. (2015) Understanding the interplay between density dependent birth function and maturation time delay using a reaction-diffusion population model. Ecological Complexity, 21: 14-26. (DOI:10.1016/j.ecocom.2014.10.007)

Fujiwara. M., J.E. Cohen (2014) Mean and variance of population density and temporal Taylor’s law in stochastic stage-structured density-dependent models of exploited fish populations. Theoretical Ecology (DOI:10.1007/s12080-014-0242-8)

Baker, R., M. Fujiwara, T.J. Minello (2014) Juvenile growth and mortality effects on white shrimp Litopenaeus setiferus population dynamics in the northern Gulf of Mexico. Fisheries Research . 155:74-82 (DOI:10.1016/j.fishres.2014.02.026)

Fujiwara, M., Mohr, M.S., Greenberg, A. (2013) The effects of disease-induced juvenile mortality on the transient and asymptotic population dynamics of Chinook salmon (Oncorhynchus tshawytscha) PLOS One 9(1): e85464. (DOI:10.1371/journal.pone.0085464)

Zhou, C., Fujiwara, M., Grant, W.E. (2013) Dynamics of a predator–prey interaction with seasonal reproductionand continuous predation. Ecological Modelling 268: 25-36 (DOI:10.1016/j.ecolmodel.2013.07.028)

Fujiwara, M., Zhou, C. (2013) Population dynamics of stage-structured sequential hermaphrodites. Canadian Journal of Fisheries and Aquatic Sciences 70: 1296-1305 (DOI:10.1139/cjfas-2012-0520)

Anderson, K.E., Fujiwara, M., Rothstein, S.I. (2012) Demography and dispersal of juvenile and adult Brown-headed cowbirds (Molothrus ater) in the eastern Sierra Nevada, California, estimated using multistate models. The Auk 129 (2):307-318 (DOI:10.1525/auk.2012.11164)

Gil-Weir, K.C., Grant, W.E., Slack, R.D., Wang, H., and Fujiwara, M. (2012) Demography and population trends of Whooping Cranes. Journal of Field Ornithology 83(1): 1–10 (DOI:10.1111/j.1557-9263.2011.00349.x)

Fujiwara, M. (2012) Demographic diversity and sustainable fisheries. PLOS One 7(5): e34556 (DOI:10.1371/journal.pone.0034556)

Fujiwara, M., Pfeiffer, G., Boggess, M., Day, S., Walton, J. (2011) Coexistence of competing stage-structured populations. Scientific Reports 1, 107 (DOI:10.1038/srep00107)

Kendall, B.E., Fox, G.A., Fujiwara, M., Nogeire, T. (2011) Demographic Heterogeneity, Cohort Selection and Population Growth. Ecology 92(10): 1985-1993 (DOI:10.1890/11-0079.1)

Fujiwara, M., Mohr, M.S., Greenberg, A., Foott, J.S., Bartholomew, J.L. (2011) Effects of Ceratomyxosis on Population Dynamics of Klamath Fall-Run Chinook Salmon. Transactions of American Fisheries Society 140:1380–1391 (DOI:10.1080/00028487.2011.621811)

Fujiwara, M. Mohr M.S.(2009) Identifying multiple environmental signals from population time-series: Application to salmon spawner counts. Oikos 118: 1712-172 (PDF)

Wiedenmann, J., Fujiwara, M., Mangel, M. (2009) Transient population dynamics and viable stage or age distributions for effective conservation and recovery. Biological Conservation 142: 2990-2996 (DOI:10.1016/j.biocon.2009.07.031)

Fujiwara, M. (2009) Environmental Stochasticity. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester. (DOI:10.1002/9780470015902.a0021220)

Fujiwara, M. (2008) Identifying interactions among salmon populations from observed dynamics. Ecology 89: 4-11 (PDF)

Fujiwara, M. (2008) Effects of an autocorrelated stochastic environment and fisheries on the age at maturity of Chinook Salmon (Oncorhynchus tshawytscha). Theoretical Ecology (DOI:10.1007/s12080-007-0008-7)

Fujiwara, M. (2007) Extinction-effective population index for population comparisons. Ecology 88: 2345-2353 (PDF)

Fujiwara M., Anderson K.E., Neubert M.G., Caswell H (2006) On the estimation of dispersal kernels from individual mark-recapture data. Environmental and Ecological Statistics 13: 183-197 (DOI:10.1007/s10651-005-0007-z)

Kraus, S.D., M.W. Brown, H. Caswell, C.W. Clark, M. Fujiwara, P.K. Hamilton, R.D. Kenney, A.R. Knowlton, S. Landry, C.A. Mayo, W.A. McLellan, M.J. Moore, D.P. Nowacek, D.A. Pabst, A.J. Read, R.M. Rolland (2005) North Atlantic Right Whales in Crisis. Science 309: 561-562 (DOI:10.1126/science.1111200)

Fujiwara, M., Kendall, B, Nisbet, R., and Bennett, W. (2005) Analysis of size trajectory data using an energetic-based growth model. Ecology 86 (6): 1441-1451 (PDF)

Harding, K., Fujiwara, M., Harkonen, T., and Axberg, Y. (2005) Mass-dependent energetics and survival in harbour seal pups. Functional Ecology 19: 129-135 (DOI:10.1111/j.0269-8463.2005.00945.x)

Caswell, H. and Fujiwara, M. (2004) Beyond survival estimation: mark-recapture, matrix population models, and population dynamics. Animal Biodiversity and Conservation 27.1: 471-488 (PDF)

Fujiwara, M., Kendall, B.E., and Nisbet, R.M. (2004) Growth autocorrelation and animal size variation. Ecology Letters 7(2): 104-113 (PDF)

Fujiwara, M. and Caswell, H. (2002) A general approach to temporary emigration in mark-recapture analysis. Ecology 83(12): 3266-3275 (PDF)

Fujiwara, M. and Caswell, H. (2002) Estimating population projection matrices from multi-stage mark-recapture data. Ecology 83(12): 3257-3265 (PDF)

Fujiwara, M. and Caswell, H. (2001) Demography of the endangered North Atlantic right whale. Nature 414: 537-541 (DOI:10.1038/35107054)

Neubert, M.G. and Fujiwara, M. (2000) Book Reviews: Introduction to Chaos: Physics and mathematics of Chaotic phenomena, by Hiroyuki Nagashima and Yoshikazu Baba. Translated by Mikio Nakahara. Institute of Physics Publishing, Bristol, UK. SIAM Review 42: 756-758

Caswell, H., Fujiwara, M., and Brault, S. (1999) Declining survival probability threatens the North Atlantic right whale. Proceedings of the National Academy of Sciences USA 96: 3308-3313 (DOI:10.1073/pnas.96.6.3308)