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Lisa Ballesteros's research is in the area of cross-language information retrieval—systems that allow a person to query in one language (e.g., English) and retrieve relevant documents in other languages (e.g., Spanish). She has also worked with colleagues in the field on applying artificial intelligence techniques to exploratory data analysis and causal induction. In addition, she has done basic research in molecular and cellular biology.

Ballesteros is particularly interested in developing techniques for text analysis and in exploring the ways in which these techniques can be used for other data types. Other areas of interest include the following: data mining (automatically identifying significant relationships from large amounts of information); data fusion (combining different types of information); extraction (identifying pre-specified types of information); and summarization (abstraction of the most important parts of text).

She teaches courses in computer systems and assembly language, intelligent information retrieval, problem solving and structured programming, and computer architecture. She is the author of many scholarly articles and several book chapters.