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.