Titlebook: Research in Computational Molecular Biology; 28th Annual Internat Jian Ma Conference proceedings 2024 The Editor(s) (if applicable) and The

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,Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ss, representing short sequences of (modified) nucleotides, are individually docked as poses onto the protein surface using a force field. Compatible poses are then assembled while optimizing for an additive notion of energy, to obtain stable conformations that can either be constrained to represent

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,Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching,tures that define a series of searches, each of which specifies lower and upper bounds on the number of errors in each part of a partitioned search pattern, and the processing order of these parts. Collectively, these searches guarantee that all approximate occurrences of a search pattern up to a pr

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,Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning,erdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulati

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,Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decompositiog. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (.) criterion under the Turner model. In this paper, we address

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