At Wesleyan University, Trinkaus majored in biology. In his memoirs, he recalled feeling that his high school had not prepared him well for the work required by college students, and that his freshman year in 1936 started off on a bad note, during which he failed his first math exam and got a D on an English assignment. During that first year in college, Trinkaus found a job making charts for biology classes for Professor Hubert B. Goodrich, who later became his research mentor at Wesleyan. His undergraduate research began with a study on the effect of ultraviolet light on the skin pigmentation of Carassius auratus, the common goldfish. Trinkaus remembered his first try at scientific research as a good learning experience, as he learned how to handle biological specimens carefully, how to observe and record any changes in the treatments at regular time intervals, and how to read the literature on his research topic to acquire the appropriate scientific context and background. This work led to Trinkaus’s first publication in the Biological Bulletin, titled “The differential effect of radiations on Mendelian phenotypes of the goldfish,” in 1939. The next research project assigned to Trinkaus was also related to the developmental physiology of the pigmentation patterns in fish; this time, on the guppy, or Poecilia reticulate. This research was the basis for Trinkaus’s undergraduate honours project, in which he described the genetics of a new variety of this species of fish. Trinkaus graduated from Wesleyan in 1940 with high distinction and published his work on P. reticulate in Genetics in 1944.
- Atz, James W. "Fundulus heteroclitus in the laboratory: a history." American zoologist 26, no. 1 (1986): 111-120.
- Betchaku, Teiichi, and J. P. Trinkaus. “Programmed endocytosis during epiboly of Fundulus heteroclitus.” American zoologist 26, no. 1 (1986): 193-199.
- Davis, Edward M., and J. P. Trinkaus. "Significance of cell-to-cell contacts for the directional movement of neural crest cells within a hydrated collagen lattice." Journal of embryology and experimental morphology 63, no. 1 (1981): 29-51.
- DuPont, Ellen M. "John Philip Trinkaus (1918-2003)." Embryo Project Encyclopedia (2012).
- Goodrich, H. B., and J. P. Trinkaus. "The differential effect of radiations on mendelian phenotypes of the goldfish, Carassius auratus." The Biological Bulletin 77, no. 2 (1939): 192-199.
- Goodrich, H. B., and J. P. Trinkaus. "The differential effect of radiations on mendelian phenotypes of the goldfish, Carassius auratus." The Biological Bulletin 77, no. 2 (1939): 192-199.
- Goodrich, H. B., N. D. Josephson, J. P. Trinkaus, and Jeanne M. Slate. "The cellular expression and genetics of two new genes in Lebistes reticulatus." Genetics 29, no. 6 (1944): 584-592.
- Keller, Ray, Wallis H. Clark, and Frederick Griffin (Eds.) Gastrulation: Movements, Patterns, and Molecules. New York: Plenum Press, 1991.
- Kimmel, Charles B., and James A. Weston. "An overview of Trink's scientific accomplishments." Developmental Dynamics 228, no. 4 (2003): 586-587.
- Saunders, John W. "Trink, the man." Developmental Dynamics 228, no. 4 (2003): 588-590
- Schoenwolf, Gary C. "Trink: His life, his philosophy." Developmental Dynamics 228, no. 4 (2003): 591-593.
- Tickle, Cheryll A., and J. P. Trinkaus. "Change in surface extensibility of Fundulus deep cells during early development." Journal of cell science 13, no. 3 (1973): 721-726.
- Tickle, Cheryll A, and J. P. Trinkaus. "Observations on nudging cells in culture." Nature 261, no. 5559 (1976): 413-413.
- Trinkaus, J. Philip. "Factors concerned in the response of melanoblasts to estrogen in the Brown Leghorn fowl." Journal of Experimental Zoology 109, no. 1 (1948): 135-169.
- Trinkaus, John Philip. "The surface gel layer of Fundulus eggs in relation to epiboly." Proceedings of the National Academy of Sciences of the United States of America 35, no. 4 (1949): 218.
- Trinkaus, John Philip. "A study of the mechanism of epiboly in the egg of Fundulus heteroclitus." Journal of Experimental Zoology 118, no. 2 (1951): 269-319.
- Trinkaus, John Philip. "The differentiation of tissue cells." American Naturalist (1956): 273-289.
- Trinkaus, John Philip. “Procurement, maintenance and use of Fundulus eggs,” Methods in Developmental Biology. F.H. Wells and N.K. Wessells (Eds.) Crowell, New York: 1967, 113-122.
- Trinkaus, J. P. "The cellular basis of Fundulus epiboly. Adhesivity of blastula and gastrula cells in culture." Developmental biology 7 (1963): 513-532.
- Trinkaus, J. P. "Surface activity and locomotion of Fundulus deep cells during blastula and gastrula stages." Developmental biology 30, no. 1 (1973): 68-103.
- Trinkaus, J. P. "Mechanism of Fundulus epiboly—a current view." America n Zoologist 24, no. 3 (1984): 673-688.
- Trinkaus, John Philip. Cells into organs: the forces that shape the embryo. (2nd Ed.) New Jersey: Prentice-Hall, Inc., 1984.
- Trinkaus, John Philip. “Directional cell movement during early development of the teleost Blennius Pholis. I. Formation of epithelial cell clusters and their pattern and mechanism of movement.” Journal of Experimental Zoology 245 (1988a): 157-186.
- Trinkaus, John Philip. “Directional cell movement during early development of the teleost Blennius Pholis. II. Transformation of the cells of epithelial clusters into dendritic melanocytes, their dissociation from each other, and their migration to and invasion of the pectoral fin buds.” Journal of Experimental Zoology 248 (1988b): 55-72.
- Trinkaus, John Philip. Embryologist: My Eight Decades in Developmental Biology. J&S Publishing Company, 2003