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This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Unlike other books that are steeped in mathematical jargon and language, this book gives explanations in intuitive terms; and in cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are presented that can be used in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal in forming the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, and systems biology.