What are the main challenges of computational molecular biology once the genome projects are completed? Integrative Approaches to Molecular Biology focuses on molecular biology beyond sequences: from gene regulation to differentiation, a higher-level integration that will be a major theme in biology following conclusion of the genome program. It charts the course of the emerging discipline of integrative molecular biology from macromolecular sequences to a biological (and theoretical) perspective, showing that novel integrative methodologies and paradigms are emerging at the confluence of such disciplines as computer science, logic, linguistics, and mathematics. Following an introductory chapter by Richard Lewontin that offers a critique of the evolutionary process as one of engineering design, the first part of the book, on computational biology, addresses issues concerning protein and DNA sequences within genome projects and a federated infrastructure for databases. The second part brings together experimental, evolutionary, computational, and theoretical approaches dealing with regulation of gene expression, metabolic pathways, and cell differentiation. The book concludes with a chapter on problems and perspectives on artificial intelligence.