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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