By Mr Thomas Litfin

Preprints

Zhou Y; lang M; Litfin T; Chen K; Zhan J, 2023, Deep learning models of RNA base-pairing structures generalize to unseen folds and make accurate zero-shot predictions of base-base interactions of RNA complexes, http://dx.doi.org/10.21203/rs.3.rs-3387481/v1

Atack J; Guo C; Litfin T; Yang L; Blackall P; Zhou Y; Jennings M, 2020, Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination, http://dx.doi.org/10.1101/2020.06.18.137471

Lang M; Litfin T; Chen K; Zhan J; Zhou Y, Deep learning models of RNA base-pairing structures make accurate zero-shot predictions of base-base interactions of RNA complexes, http://dx.doi.org/10.1101/2023.09.26.559463

Singh J; Paliwal K; Singh J; Litfin T; Zhou Y, Improved RNA homology detection and alignment by automatic iterative search in an expanded database, http://dx.doi.org/10.1101/2022.10.03.510702

Litfin T; Caley JS; Michie KA, LMI4Boltz: Optimising VRAM utilisation to predict large macromolecular complexes with consumer grade hardware, http://dx.doi.org/10.1101/2025.10.29.684571

Zhang Y; Lang M; Jiang J; Gao Z; Xu F; Litfin T; Chen K; Singh J; Huang X; Song G; Tian Y; Zhan J; Chen J; Zhou Y, Multiple sequence-alignment-based RNA language model and its application to structural inference, http://dx.doi.org/10.1101/2023.03.15.532863

Zhang T; Singh J; Litfin T; Zhan J; Paliwal K; Zhou Y, RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis, http://dx.doi.org/10.1101/2020.08.08.242636

Singh J; Litfin T; Singh J; Paliwal K; Zhou Y, SPOT-Contact-Single: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model, http://dx.doi.org/10.1101/2021.06.19.449089

Chen K; Litfin T; Singh J; Zhan J; Zhou Y, The Master Database of All Possible RNA Sequences and Its Integration with RNAcmap for RNA Homology Search, http://dx.doi.org/10.1101/2023.02.01.526559

Litfin T; Zhou Y; von Itzstein M, Ultra-fast and highly sensitive protein structure alignment with segment-level representations and block-sparse optimization, http://dx.doi.org/10.1101/2025.03.14.643159

Meltzer J; Vázquez-Campos X; Johnson MD; Litfin T; Valova V; Luque D; Syrmalis M-C; Rowell K; Hewitt L; Paul B; Michie KA; Pitt ME; Ghosal D; Ferrari BC; Burns BP, Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions, http://dx.doi.org/10.64898/2026.08.12.739948

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