This book constitutes the proceedings of the 28th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2024, held in Cambridge, MA, USA, during April 29–May 2, 2024. The 57 full papers included in this book were carefully reviewed and selected from 352 submissions. They were organized in topical sections as follows: theoretical and foundational algorithm contributions and more applied directions that engage with new technologies and intriguing biological questions.