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In 1499 he predicted that a deluge would cover the world on 20 February 1524. In 1507, at the instigation of Duke Ulrich I he received the newly established chair of mathematics and astronomy at the University of Tübingen, where he excelled in rich teaching and publication activities and finally was elected rector in 1522. By the time of his appointment he already enjoyed a virtual monopoly in ephemeris-making in collaboration with Jacob Pflaum, continuing the calculations of Regiomontanus through 1531, and then through 1551, the latter being published posthumously in 1531.
His treatise on the construction and the use of the astrolabe, entitled Elucidatio fabricae ususque astrolabii, was published in several editions and served astronomers and surveyors for a long time as a standard work.
Philipp Melanchthon and Sebastian Münster rank among his most famous students. When a plague epidemic forced the division and relocation of his university to the surrounding countryside in 1530, Stöffler went to Blaubeuren and died there on 16 February 1531 of the plague. He was buried in the choir of the collegiate church (Stiftskirche) in Tübingen.
1499: An Almanac (Almanach nova plurimis annis venturis inserentia) published in collaboration with the astronomer Jakob Pflaum of Ulm, which was designated as a continuation of the ephemeris of Regiomontanus. It had a large circulation, underwent 13 editions until 1551 and exerted a strong effect on Renaissance astronomy.
1512 - 1514: Commentary on Ptolemy's Geography. Unpublished manuscript with comments on books 1 and 2 of the Geography, preserved at University of Tübingen; the remaining commentaries were lost in a fire in 1534.
1513: A book on the construction and use of the astrolabe (Elucidatio fabricae ususque astrolabii), published in 16 editions up until 1620, and, in 2007, for the first time in English.
1514: Astronomical tables (Tabulae astronomicae).
1518: A proposal for a calendar revision (Calendarium romanum magnum) which formed a foundation for the Gregorian calendar.
1534 (posthumously published): Commentary on the Sphaera of pseudo-Proclus (Ioannis Stoefleri Iustingensis mathematici eruditissimi, faciléque omnium principis, in Procli Diadochi, authoris grauissimi Sphæram mundi, omnibus numeris longè absolutissimus commentarius) 
^"Ten Notable Apocalypses That (Obviously) Didn't Happen". Smithsonian magazine. November 12, 2009. Retrieved . In 1499, the German mathematician and astronomer Johannes Stöffler predicted that a vast flood would engulf the world on 20 February 1524. (His calculations foretold 20 planetary conjunctions during this year--16 of which would take place in a "watery sign," a.k.a. Pisces.)
^Alessandro Gunella and John Lamprey, Stoeffler's Elucidatio (The translation of Elucidatio fabricae ususque astrolabii into English). Published by John Lamprey, 2007. ISBN1-4243-3502-7, ISBN978-1-4243-3502-2