In addition to his teaching, Bessey published more than 150 papers and reviews. He wrote extensively on subjects such as plant diseases and fungi. He had an interest in native Grasses and primitive plants. Two of his papers, "Evolution and Classification" (1893) and "Phylogenetic Taxonomy of Flowering Plants" (1915), were Semín works. At the request of a publisher and the urging of Gray, Bessey wrote the textbook Botany for High Schools and Colleges (1880), which introduced new areas of study. His second book, The Essentials of Botany (1884), was less technical and became the most widel used botany text in the United States. Bessey was also the botanical editor for two leading Journals, American Naturalist (1880-1897) and Science (1897-1915).
In June 1884, Bessey left Iowa to accept a position as professor of botany and dean of the industrial college (which included the school of agriculture) at the University of Nebraska. When Bessey arrived, there was no program in botany, but he built a solid program that included laboratories with Microscopes and field trips. While at Nebraska, he built a Herbarium and a library housing botanical literature. Bessey served as dean of the industrial college from 1884 to 1888 and from 1895 to 1909. From 1888 to 1891, he held the dual post of acting Chancellor and dean of the college of literature, science, and the ArtNo. In 1899 and 1907, he again served as acting Chancellor. 
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