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Arxiv|March 31, 2025
Differentiable Folding for Nearest Neighbor Model OptimizationRyan K Krueger, Sharon Aviran, David H Mathews, et al.Biorxiv : the Preprint Server for Biology|November 24, 2025
Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional MethodsMarcell Szikszai, Ting-Yuan Wang, Ryan Krueger, et al.RNA (New York, N.Y.)|January 9, 2026
Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional MethodsMarcell Szikszai, Ting-Yuan Wang, Ryan Krueger, et al.Bioinformatics (Oxford, England)|April 25, 2025
JAX-RNAfold: scalable differentiable foldingRyan K Krueger, Max WardRNA (New York, N.Y.)|April 7, 2019
Estimating uncertainty in predicted folding free energy changes of RNA secondary structuresJeffrey Zuber, David H MathewsMethods in Molecular Biology (Clifton, N.J.)|May 23, 2024
Estimating RNA Secondary Structure Folding Free Energy Changes with efn2Jeffrey Zuber, David H MathewsMicroorganisms|August 26, 2023
Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted MutantsJeffrey Zuber, Sudisht K Sah, David H Mathews, et al.Journal of Molecular Biology|October 20, 2024
memerna: Sparse RNA folding including coaxial stackingEliot Courtney, Amitava Datta, David H Mathews, et al.Nucleic Acids Research|June 7, 2017
Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is bestMax Ward, Amitava Datta, Michael Wise, et al.Biorxiv : the Preprint Server for Biology|October 28, 2024
DecoyFinder: Identification of Contaminants in Sets of Homologous RNA SequencesMingyi Zhu, Jeffrey Zuber, Zhen Tan, et al.Pageof 29