Molt conegut pels seus estudis d'ascomicets, especialment Pyrenomycets (avui Sordariomycetes). Va fer recol·leccions d'espècimens, i amb la seva esposa, van preparar 200.000 mostres que enviaven a subscriptors, en sèries, entre 1878 i 1894. Amb els seus col·legues William A. Kellerman i Benjamin Matlack Everhart, van fundar l'any 1885, el Journal of Mycology, (avui Mycologia). Va descriure 4.000 espècies de fongs, i la seva col·lecció de 110.000 espècimens s'allotja en l'herbari del New York Botanical Gardens. Ellis és anomenat en 100 tàxons de fongs.
Cooke, M.C.; Ellis, J.B. (1876). Some New Jersey fungi. Grevillea 4 (32): 178-180 [Nº 2297-2318]
Cooke, M.C.; Ellis, J.B. (1876). New Jersey fungi [cont.]. In M.C. Cooke [ed.], Grevillea 5 (33): 30-35, pl. 75 [ens 2319-2362]. Edinburgh; Williams & Norgate
Cooke, M.C.; Ellis, J.B. (1876). New Jersey fungi [cont.]. Grevillea 5 (34): 49-55 [Nº 2363-2423]
Cooke, M.C.; Ellis, J.B. (1877). New Jersey fungi [cont.]. Grevillea 5 (35): 89-95
Cooke, M.C.; Ellis, J.B. (1877). New Jersey fungi [cont.]. In M.C. Cooke [ed.], Grevillea 6 (37): 1-18. Edinburgh; Williams & Norgate
Cooke, M.C.; Ellis, J.B. (1878). New Jersey fungi [cont.]. Grevillea 6 (39): 81-96, pls 99-100.
Cooke, M.C.; Ellis, J.B. (1878). New Jersey fungi [cont.]. Grevillea 7 (41): 4-10
Cooke, M.C.; Ellis, J.B. (1878). New Jersey fungi [cont.]. Grevillea 7 (42): 37-42
Cooke, M.C.; Ellis, J.B. (1879). New Jersey fungi [cont.]. Grevillea 8 (45): 11-16
Ellis, J.B. (1881). New species of North American fungi. Bulletin of the Torrey Botanical Club 8: 64-[65]
Ellis, J.B. (1882). New Fungi. Am. Naturalist 16 (10): 810-[811]
Ellis, J.B. (1882). New North American fungi. Bull. of the Torrey Botanical Club 9: 18-[?]
Ellis, J.B. (1882). New North American fungi [cont.]. Bull. of the Torrey Botanical Club 9: 73-[74]
Ellis, J.B. (1882). New North American fungi [concl.]. Bull. of the Torrey Botanical Club 9: 133-[?]
Ellis, J.B. (1882). North American Fungi. Sèries 1. Century IX (Nº 801-900). Newfield, New Jersey; Ellis
Ellis, J.B. (1882). North American Fungi. Sèries 1. Century VII (ens 701-800). Newfield, New Jersey; Ellis
Ellis, J.B. (1883). New species of North American fungi. Am. Midland Naturalist 17 (febrer): [194]-[196]
Ellis, J.B. (1883). New North American fungi. Bull. of the Torrey Botanical Club 10: 52-[?]
Ellis, J.B. (1893). Descriptions of some new species of fungi. J. of Mycology 7: 274-278
Ellis, J.B.; Bartholomew, I. (1896). New Kansas fungi. Erythea 4 (2): 23-29
Ellis, J.B.; Bartholomew, I. (1896). New species of Kansas fungi. I. Erythea 4: 79-83
Ellis, J.B.; Bartholomew, I. (1897). New species of Kansas fungi. II. Erythea 5: 47-51
Ellis, J.B.; Bartholomew, I. (1902). New species of fungi from various localities. J. of Mycology 8: 173-178
Ellis, J.B.; Dearness, J. (1893). New species of Canadian fungi. Canadian Record of Science Mont-real 5 (Jan.): 267-272
Ellis, J.B.; Dearness, J. (1897). New species of Canadian fungi. Proc. of the Canadian Inst. N. S. 1: 89-93
Ellis, J.B.; Everhart, B.M. (1883). New species of fungi [cont.]. Bull. of the Torrey Botanical Club 10: 97-[?]
Ellis, J.B.; Everhart, B.M. (1884). New North American Fungi [cont.]. Bull. of the Torrey Botanical Club 11: 73-[75]
Ellis, J.B.; Everhart, B.M. (1885). Enumeration of the North American Cercosporae. J. of Mycology 1 (2): 17-24
Ellis, J.B.; Everhart, B.M. (1885). Enumeration of the North American Cercosporae [cont.] J. of Mycology 1: 33-40
Ellis, J.B.; Everhart, B.M. (1885). New fungi. J. of Mycology 1: 42-44
Ellis, J.B.; Everhart, B.M. (1885). Enumeration of the North American Cercosporae. With descriptions of the species [cont.]. J. of Mycology 1: 49-56
Ellis, J.B.; Everhart, B.M. (1885). Enumeration of the North American Cercosporae [concl.] J. of Mycology 1 (5): 61-67
Ellis, J.B.; Everhart, B.M. (1885). On Ramularia obovata, Fuck. J. of Mycology 1 (5): 69-70
Ellis, J.B.; Everhart, B.M. (1885). North American species of Ramularia. J. of Mycology 1 (6): 73-83
Ellis, J.B.; Everhart, B.M. (1885). New species of fungi. J. of Mycology 1 (7): 88-93
Ellis, J.B.; Everhart, B.M. (1885). North American species of Cylindrosporium. J. of Mycology 1 (10): 126-128
Ellis, J.B.; Everhart, B.M. (1885). New fungi. J. of Mycology 1 (12): 148-154
Ellis, J.B.; Everhart, B.M. (1885). New fungi [concl.] J. of Mycology 1 (12): 148-154
Ellis, J.B.; Everhart, B.M. (1886). New fungi. Hedwigia 25: 108-110
Ellis, J.B.; Everhart, B.M. (1886). Supplementary enumeration of the Cercosporae. J. of Mycology 2 (1): 1-2
Ellis, J.B.; Everhart, B.M. (1886). New species of fungi from various localities. J. of Mycology 2 (4): 37-42
Ellis, J.B.; Everhart, B.M. (1886). New species of fungi from various localities. J. of Mycology 2: 87-89
Ellis, J.B.; Everhart, B.M. (1886). New species of fungi from various localities. J. of Mycology 2 (9): 99-104
Ellis, J.B.; Everhart, B.M. (1887). Additions to Cercospora, Gloeosporium and Cylindrosporium. J. of Mycology 3 (2): 13-22
Ellis, J.B.; Everhart, B.M. (1887). New species of fungi. J. of Mycology 3 (4): 41-45
Ellis, J.B.; Everhart, B.M. (1887). New species of Ustilagineae and Uredineae. J. of Mycology 3 (2): 55-57
Ellis, J.B.; Everhart, B.M. (1887). Additions to Hypocreaceae. J. of Mycology 3: 113-116
Ellis, J.B.; Everhart, B.M. (1887). New species of fungi from various localities. J. of Mycology 3: 127-130
Ellis, J.B.; Everhart, B.M. (1895). New species of fungi from various localities. Proc. of the Academy of Natural Sciences of Philadelphia 47: 413-441
Ellis, J.B.; Everhart, B.M. (1896). New species of tropical fungi. Bull. of the Laboratory of Natural History of Iowa State University 4: 67-72
Ellis, J.B.; Everhart, B.M. (1897). New species of fungi from various localities. Am. Midland Naturalist 31: 339-343, 426-440
Ellis, J.B.; Everhart, B.M. (1897). New species of fungi from various localities. Bull. of the Torrey Botanical Club 24: 125-137
Ellis, J.B.; Everhart, B.M. (1897). New species of North American fungi from various localities. Bull. of the Torrey Botanical Club 24: 277-292
Ellis, J.B.; Everhart, B.M. (1897). New species of fungi from various localities. Bull. of the Torrey Botanical Club 24 (10): 457-477
