University of Dundee

Computational Biology 2020

Alghamdi AH, Munday JC, Campagnaro GD, Gurvic D, Svensson F, Okpara CE, Kumar A, Quintana JF, Abril MEM, Milić P, Watson L, Paape D, Settimo L, Dimitriou A, Wielinska J, Smart G, Anderson LF, Woodley CM, Kelley SPY, Ibrahim HMS, Hulpia F, Al-Salabi MI, Eze AA, Gudin S, Field M, Dardonville C, Tidwell RR, Carrington M, O'Neill PM, Boykin DW, Zachariae U, de Koning HP. 2020. Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei. eLife. 9:1-33. https://doi.org/10.7554/eLife.56416

Bage MG, Almohammed R, Cowling VH, Pisliakov AV. Identification of novel RNA Polymerase II CTD interaction sites on the mRNA Capping Enzyme. bioRxiv (2020). https://doi.org/10.1101/2020.02.25.964700

Berta D et al. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. bioRxiv (2020). https://doi.org/10.1101/2020.11.03.366609

Das, A., Bhat, A., Sknepnek, R., Koster, D., Mayor, S., & Rao, M. (2020). Stratification relieves constraints from steric hindrance in the generation of compact acto-myosin asters at the membrane cortex. Science Advances, 6(11), [eaay6093]. https://doi.org/10.1126/sciadv.aay6093

Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker G-J, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Le Dévédec SE, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Strömblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone S-A, Martens L. 2020. Community standards for open cell migration data. GigaScience. 9(5):1-11. https://doi.org/10.1093/gigascience/giaa041

Henkes, S., Kostanjevec, K., Collinson, J. M., Sknepnek, R., & Bertin, E. (2020). Dense active matter model of motion patterns in confluent cell monolayers. Nature Communications, 11, [1405]. https://doi.org/10.1038/s41467-020-15164-5

Krah A, Huber RG, Zachariae U, Bond PJ. 2020. On the ion coupling mechanism of the MATE transporter ClbM. Biochimica et Biophysica Acta - Biomembranes. 1862(2):1-9. https://doi.org/10.1016/j.bbamem.2019.183137

Llabrés S, Tsenkov MI, MacGowan S, Barton G, Zachariae U. 2020. Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain. Journal of Structural Biology. 209(1):1-8. https://doi.org/10.1016/j.jsb.2019.107405

MacGowan S, Madeira F, Britto-Borges T, Warowny M, Drozdetskiy A, Procter J, Barton G. 2020. The Dundee Resource for Sequence Analysis and Structure Prediction. Protein Science. 29(1):277-297. https://doi.org/10.1002/pro.3783

MacGowan SA, Barton GJ. 2020. Missense variants in ACE2 are predicted to encourage and inhibit interaction with SARS-CoV-2 Spike and contribute to genetic risk in COVID-19. BioRxiv. https://doi.org/10.1101/2020.05.03.074781

Matoz-Fernandez, D., Davidson, F., Stanley-Wall, N., & Sknepnek, R. (2020). Wrinkle patterns in active viscoelastic thin sheets. Physical Review Research, 2, 1-13. [013165]. https://doi.org/10.1103/PhysRevResearch.2.013165

Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD, Hall AJW, Barton GJ, Simpson GG. 2020. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife. 9:1-35. https://doi.org/10.7554/eLife.49658

Parker MT, Barton GJ, Simpson GG. 2020. Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing. BioRxiv.

PDBe-KB consortium. 2020. PDBE-KB: A community-driven resource for structural and functional annotations. Nucleic Acids Research. 48(D1):D344-D353. https://doi.org/10.1093/nar/gkz853

Procter JB, Carstairs GM, Soares B, Mourão K, Ofoegbu TC, Barton D, Lui L, Menard A, Sherstnev N, Roldan-Martinez D, Duce S, Martin DMA, Barton GJ. 2021. Alignment of Biological Sequences with Jalview. Katoh K, editor. In Multiple Sequence Alignment: Methods and Protocols. New York: Humana Press. pp. 203-224. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-0716-1036-7_13

Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, Stepniewski TM, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo JC, Gonzalez A, Gutiérrez-de-Terán H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas MT, Miszta P, Olivella M, Perez-Benito L, Provasi D, Ríos S, Torrecillas IR, Sallander J, Sztyler A, Vasile S, Weinstein H, Zachariae U, Hildebrand PW, De Fabritiis G, Sanz F, Gloriam DE, Cordomi A, Guixà-González R, Selent J. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods. 17(8):777-787. https://doi.org/10.1038/s41592-020-0884-y

Sievers F, Barton GJ, Higgins DG. 2020. Multiple Sequence Alignments. Baxevanis AD, Bader GD, Wishart DS, editors. In Bioinformatics. 4 ed. Wiley. pp. 227-250.

Swedlow J. 2020. Open Microscopy Environment: OME is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. [Software].

Williamson G, Tamburrino G, Bizior A, Boeckstaens M, Dias Mirandela G, Bage M, Pisliakov A, Ives CM, Terras E, Hoskisson PA, Marini A-M, Zachariae U, Javelle A. 2020. A two-lane mechanism for selective biological ammonium transport. eLife. 9:Article e57183. https://doi.org/10.7554/eLife.57183

Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. 2020. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS Nano. 14(1):394-405. https://doi.org/10.1021/acsnano.9b05891