[12][13][14] Haussler was elected a member of the National Academy of Engineering in 2018 for developments in computational learning theory and bioinformatics, including first assembly of the human genome, its analysis, and data sharing.

[9] While pursuing his doctorate in theoretical computer science at the University of Colorado, Haussler became interested in the mathematical analysis of DNA along with fellow students Gene Myers, Gary Stormo, and Manfred Warmuth.

With Blumer, Ehrenfeucht, and Warmuth he introduced the Vapnik-Chervonenkis framework to computational learning theory, solving some problems posed by Leslie Valiant.

[21][22][23][24] He is credited with pioneering the use of Hidden Markov models (HMMs), stochastic context-free grammars, and the discriminative kernel method for analyzing DNA, RNA, and protein sequences.

He was the first to apply the latter methods to the genome-wide search for gene expression biomarkers in cancer, now a major effort of his laboratory.

[38] With Cyrus Chothia and Michael Waterman, Haussler was awarded the 2015 Dan David Prize for his contributions to the field of bioinformatics.