By Associate Professor Matthew Baker

Preprints

Philip JS; McNally L; Baker MAB, 2026, Evolutionary Coupling of Flagellar Motility and Type VI Secretion Systems Across Bacteria, http://dx.doi.org/10.64898/2026.06.16.732483

Matzke NJ; Puente-Lelievre C; Baker MAB, 2025, A Pipeline for Generating Datasets of 3-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics, http://dx.doi.org/10.31219/osf.io/5uhkx_v1

Feng X; Tachiyama S; He J; Zhu S; Zhao H; Botting JM; Liu Y; Chen Y; Hua C; Lara-Tejero M; Baker MAB; Gao X; Liu J; Gao B, 2025, The architecture, assembly, and evolution of a complex flagellar motor., http://dx.doi.org/10.1101/2025.02.19.638559

Ridone P; Baker MAB, 2025, A compact vector for scarless gene editing in E. coli, http://dx.doi.org/10.1101/2025.08.05.668820

Mason A; Wickham SFJ; Baker MAB, 2024, DIB-BOT: An open-source hardware approach for high throughput droplet interface bilayer deposition, http://dx.doi.org/10.1101/2024.01.26.577347

Mandal A; Priyam S; Chan HH; Gouveia BM; Guitera P; Song Y; Baker MAB; Vafaee F, 2022, Computer-aided diagnosis of reflectance confocal images to differentiate between lentigo maligna (LM) and atypical intraepidermal melanocytic proliferation (AIMP), http://dx.doi.org/10.1101/2022.05.10.491423

Baker M; Nieves D; Hilzenrat G; Berengut J; Gaus K; Lee L, 2019, Stoichiometric quantification of spatially dense assemblies with qPAINT, http://dx.doi.org/10.1101/525345

Nieves DJ; Hilzenrat G; Tran J; Yang Z; MacRae HH; Baker MAB; Gooding JJ; Gaus K, 2019, tagPAINT: covalent labelling of genetically encoded protein tags for DNA-PAINT imaging, http://dx.doi.org/10.1101/604462

Jaggers O; Ridone P; Martinac B; Baker M, 2018, Fluorescence Microscopy of Piezo1 in Droplet Hydrogel Bilayers, http://dx.doi.org/10.1101/508176

Islam I; Ridone P; Lin A; Michie KA; Matzke NJ; Hochberg G; Baker MA, Ancestral reconstruction of the MotA stator subunit reveals that conserved residues far from the pore are required to drive flagellar motility, http://dx.doi.org/10.1101/2022.10.17.512626

Singh JKD; Darley E; Ridone P; Gaston JP; Abbas A; Wickham SF; Baker MA, Binding of DNA origami to lipids: maximising yield and switching via strand-displacement, http://dx.doi.org/10.1101/2020.06.01.128686

Li J; Jamieson WD; Dimitriou P; Xu W; Rohde P; Martinac B; Baker M; Drinkwater BW; Castell OK; Barrow DA, Building programmable multicompartment artificial cells incorporating remotely activated protein channels using microfluidics and acoustic levitation, http://dx.doi.org/10.1101/2022.01.13.476178

Brown HJ; Islam I; Ruan J; Baker MAB; Ithurbide S; Duggin IG, CetZ1-dependent polar assembly of the archaeal motility machinery, http://dx.doi.org/10.1101/2024.05.02.592137

Matzke NJ; Lin A; Stone M; Baker MAB, Homology between the flagellar export apparatus and ATP synthetase: evidence from synteny predating the Last Universal Common Ancestor, http://dx.doi.org/10.1101/2021.01.01.425057

Ridone P; Baker MAB, Hybrid Exb/Mot stators require substitutions distant from the chimeric pore to power flagellar rotation, http://dx.doi.org/10.1101/2024.03.12.584617

Gurung JP; Ridone P; Biquet-Bisquert A; Bryant G; Pedaci F; Nord AL; Baker MA, Insertion of fluorescent proteins near the plug domain of MotB generates functional stator complex, http://dx.doi.org/10.1101/2024.09.27.615325

Philip JS; Grewal S; Scadden J; Puente-Lelievre C; Matzke NJ; McNally L; Baker MA, Mapping the loss of flagellar motility across the tree of life, http://dx.doi.org/10.1101/2024.12.05.626484

Gurung JP; Kashani MN; de Silva CM; Baker MA, Microbial stir bars: light-activated rotation of tethered bacterial cells to enhance mixing in stagnant fluids, http://dx.doi.org/10.1101/2023.01.26.525760

Puente-Lelievre C; Ridone P; Douglas J; Amritkar K; Kaçar B; Baker M; Matzke N, Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility, http://dx.doi.org/10.1101/2024.07.22.604496

Islam M; Bae J; Ishida T; Ridone P; Lin J; Kelso M; Sowa Y; Buckley B; Baker M, Novel amiloride derivatives that inhibit bacterial motility across multiple strains and stator types, http://dx.doi.org/10.1101/2021.04.13.439105

Scadden J; Ridone P; Pandit D; Sowa Y; Baker MA, Rescue of bacterial motility using two and three-species FliC chimeras, http://dx.doi.org/10.1101/2024.12.02.626473

Gurung JP; Kashani MN; Agarwal S; Peralta G; Gel M; Baker MA, Separation and enrichment of sodium-motile bacteria using cost-effective microfluidics, http://dx.doi.org/10.1101/2020.11.24.395772

Ishida T; Ito R; Clark J; Matzke NJ; Sowa Y; Baker MA, Sodium-powered stators of the bacterial flagellar motor can generate torque in the presence of phenamil with mutations near the peptidoglycan-binding region, http://dx.doi.org/10.1101/507533

Puente-Lelievre C; Malik AJ; Douglas J; Ascher D; Baker M; Allison J; Poole A; Lundin D; Fullmer M; Bouckert R; Kim H; Steinegger M; Matzke N, Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone, http://dx.doi.org/10.1101/2023.12.12.571181

Gaston J; Meepat S; Islam S; Singh JKD; Booth MJ; Wickham SF; Baker MA, The effect of PEGylation on surface tethering of liposomes via DNA nanotechnology, http://dx.doi.org/10.1101/2025.07.07.663613

Hamm JN; Liao Y; von Kügelgen A; Dombrowski N; Landers E; Brownlee C; Johansson EMV; Whan RM; Baker MAB; Baum B; Bharat TAM; Duggin IG; Spang A; Cavicchioli R, The parasitic lifestyle of an archaeal symbiont, http://dx.doi.org/10.1101/2023.02.24.529834

Ridone P; Ishida T; Lin A; Humphreys DT; Giannoulatou E; Sowa Y; Baker MAB, The rapid evolution of flagellar ion-selectivity in experimental populations of E. coli, http://dx.doi.org/10.1101/2021.01.26.427765

Ridone P; Winter DL; Baker MAB, Tuning the stator subunit of the flagellar motor with coiled-coil engineering, http://dx.doi.org/10.1101/2023.03.05.530362

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