[6] Warnow did both her undergraduate and graduate studies in mathematics at the University of California, Berkeley, earning a bachelor's degree in 1984 and a PhD[2] in 1991 under the supervision of Eugene Lawler.

In 2014, Warnow joined the faculty of the University of Illinois at Urbana–Champaign (UIUC), where she is the Grainger Distinguished Chair in Engineering and Associate Head of the Department of Computer Science.

[5][7] In 1995, research by Warnow, Donald Ringe, and Ann Taylor at the University of Pennsylvania based on perfect phylogeny computations provided a comprehensive theory for the timing of the early subdivisions in the Indo-European languages.

[10] Their software is based less strongly on firm mathematical principles than some previous co-estimation methods (such as BAli-Phy[11]), but is significantly faster, allowing the fast construction of highly accurate trees and alignments for thousands of species.

[5] In 2015, she was named a Fellow of Association for Computing Machinery (ACM) "For contributions to mathematical theory, algorithms, and software for large-scale molecular phylogenetics and historical linguistics".