[7] Berger did her undergraduate studies at Brandeis University, and earned her doctorate from MIT in 1990 under the supervision of Silvio Micali.

[2][9][10] Her former doctoral students include Serafim Batzoglou,[3] Lior Pachter,[4] Mona Singh,[5] Manolis Kellis, and Phil Bradley.

Berger has served as vice president of the International Society for Computational Biology (ISCB)[11] and chair of the steering committee for RECOMB.

[19] She was included in the 2019 class of fellows of the American Mathematical Society "for contributions to computational biology, bioinformatics, algorithms and for mentoring".

[22] She was elected as a Fellow of the Society for Industrial and Applied Mathematics, in the 2022 Class of SIAM Fellows, "for pioneering work in computational molecular biology, including comparative and compressive genomics, network inference, genomic privacy, and protein structure prediction".