Pemberton, R.W., Collins, T.M., and Koptur, S. 2008. An asian orchid, Eulophia graminea (Orchidaceae: Cymbidieae), naturalizes in Florida. Lankesteriana 8:5-14.

Buendia, P., Collins, T.M. & Narasimhan, G. 2008. The role of internal node sequences and the molecular clock in the analysis of serially-sampled data. International Journal of Bioinformatics Research and Applications 4:107-121.

Almodovar, S., del Colon, M.C., Malodnado, I.M., Villafane, R., Abreu, S., Melendez, I., Dominguez, C., Cuevas, W., Collins, T.M. & Lorenzo, E. 2007. HIV-1 infection of monocytes is directly related to the success of HAART. Virology 369:35-46.

Freeman, B., Nico, L.G., Osentoski, M., Jelks, H.L. & Collins, T.M. 2007. Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories. Zootaxa 1484:1-38. open access link

Rawlings T.A., Hayes, K.A., Cowie, R.H. & Collins, T.M. 2007. The identity, distribution, and impacts of non-native apple snails in the continental United States. BMC Evolutionary Biology 7:97 (14 pages). open access link

Buendia, P., Collins T. M. & Narasimhan, G. 2006. Reconstructing ancestor-descendant lineages from serially-sampled data: A comparison study. Lecture Notes in Computer Science 3992: 807-814.

Collins, T.M., Fedrigo, O. and Naylor, G.J.P. 2005. Choosing the best genes for the job: The case for stationary genes in genome-scale phylogenetics. Systematic Biology 54: 493-500.

Rawlings, T. A., Collins, T. M., and R. Bieler. 2003. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. PNAS 100:15700-15705.

Collins T.M., Trexler J., Nico L., and T. A. Rawlings. 2002. Genetic diversity in a morphologically conservative invasive taxon: Multiple introductions of swamp eels to the southeastern United States. Conservation Biology 16: 1024-1035.

Rawlings, T. A., Collins T. M., and R. Bieler 2001. A major mitochondrial gene rearrangement among closely related species. Molecular Biology and Evolution v. 18, n. 8 p. 1604-1609.

Lee, D. W. and Collins, T. M. 2001. Phylogenetic and ontogenetic influences on the distribution of red pigments in leaves of tropical plants. International Journal of Plant Sciences 162:5:1141-1153.

Medina, M., Collins, T.M., and P.J. Walsh. 2001. MtDNA Ribosomal Gene Phylogeny of Sea Hares in the Genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): Implications for Comparative Neurobiology. Systematic Biology 50: 676-688.

Lorenzo, E., Collins T. M., Fisher, E., Herrera R. J., 2001 The Use of tat and env Sequences from Human Immunodeficiency Virus 1 in Phylogenetic Epidemiological Studies. Electrophoresis 22:3 438-444.

Cunningham, C. W., and Collins, T. M. 1998. Beyond area relationships: Extinction and recolonization in molecular marine biogeography. p. 297-321 in Molecular Approaches to Ecology and Evolution Birkhauser, DeSalle R. and Schierwater, B. eds. Verlag, Basel, Switzerland.

Collins, T. M., Frazer, K. S., Palmer, A. R. ,Vermeij, G. J. and W. M. Brown. 1996. Evolutionary history of Northern Hemisphere Nucella: Molecules, morphology, ecology, and fossils. Evolution v.50, n. 4, p. 2287-2304.

Collins, L. S. and Collins, T. M. 1996 Evolution of Life. MacMillan Encyclopedia of Earth Sciences p. 552-555

Brawn, J. D., Collins, T. M., Medina, M. and E. Bermingham. 1996. Associations between physical isolation and geographic variation within three species of Neotropical birds. Molecular Ecology v.5, n. 1, p. 33-46.

Collins, T. M. 1996. in Molecular comparisons of transisthmian species pairs: Rates and patterns of evolution. in: Environmental and Biological Change in Neogene and Quaternary Tropical America. Jackson, J .B. C., Coates, A. G., and A. Budd eds.

Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L., and W. M. Brown. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature v. 376 163-165.

Naylor, G. J. P., Collins, T. M., and W. M. Brown. 1995. Hydrophobicity and Phylogeny. Nature v.373, p. 565-566.

Collins, T. M., Kraus, F., and G. Estabrook. 1994. Compositional effects and weighting of nucleotide sequences for phylogenetic analysis. Systematic Biology. v. 43, n. 3, p. 449-459.

Cunningham, C. W., and Collins, T. M. 1994. Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates. p. 406-433. in: Molecular Ecology and Evolution: Approaches and applications. B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle eds. Birkhauser Verlag, Basel, Switzerland.

Collins, T. M., Wimberger, P., and G. J. P. Naylor. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology v. 43, n.4, p. 482-496.

Vermeij, G. J. and Collins, T. M. 1988. Nerita fortidentata, a new gastropod from the Neogene of Panama, with comments on the fossil record of Nerita in Tropical America. Nautilus 102 (3) p.102-105.