University of Dundee

2021

Bage MG, Almohammed R, Cowling VH, Pisliakov AV. 2021. A novel RNA Pol II CTD interaction site on the mRNA Capping Enzyme is essential for its allosteric activation. Nucleic Acids Research. 49(6):3109-3126. https://doi.org/10.1093/nar/gkab130

Bage, MG, Almohammed, R, Cowling, VH & Pisliakov, AV 2021, 'Molecular details of mRNA capping enzyme recruitment and activation: A computational study', European Biophysics Journal, vol. 50, no. Supplement 1, O-149, pp. S87. https://doi.org/10.1007/s00249-021-01558-w

Barton MI, MacGowan SA, Kutuzov MA, Dushek O, Barton GJ, van der Merwe PA. 2021. Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand the human ACE2 receptor on binding affinity and kinetics. eLife. 10:Article e70658. https://doi.org/10.7554/eLife.70658

Bartsch A, Ives C, Kattner C, Pein F, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C, Llabres S. 2021. An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding. BBA - Biomembranes. 1863(6):Article 183601. https://doi.org/10.1016/j.bbamem.2021.183601

Berta, D, Badaoui, M, Martino, SA, Buigues, PJ, Pisliakov, AV, Elghobashi-Meinhardt, N, Wells, G, Harris, SA, Frezza, E & Rosta, E 2021, 'Modelling the Active SARS-CoV-2 Helicase Complex as a Basis for Structurebased Inhibitor Design', Chemical Science, vol. 12, pp. 13492-13505. https://doi.org/10.1039/D1SC02775A

Blümli S, Wiechens N, Wu M-Y, Singh V, Gierlinski M, Schweikert G, Gilbert N, Naughton C, Sundaramoorthy R, Varghese J, Gourlay R, Soares R, Clark D, Owen-Hughes T. 2021. Acute depletion of the ARID1A subunit of SWI/SNF complexes reveals distinct pathways for activation and repression of transcription. Cell Reports. 37(5):1-17. https://doi.org/10.1016/j.celrep.2021.109943

Boehm U, Nelson G, Brown CM, Bagley S, Bajcsy P, Bischof J, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Nitschke R. 2021. QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. Nature Methods. https://doi.org/10.1038/s41592-021-01162-y

Bredeson JV, Lyon JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Goodstein D, Egesi CN, Featherston J, Simpson G, Doležel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS. 2021. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Cold Spring Harbor Laboratory: BioRxiv. pp. 1-36. https://doi.org/10.1101/2021.04.14.439117

MacGowan SA, Barton MI, Kutuzov M, Dushek O, Merwe PAVD, Barton GJ. 2021. Missense variants in human ACE2 modify binding to SARS-CoV-2 Spike. BioRxiv. https://doi.org/10.1101/2021.05.21.445118

Mironenko A, Zachariae U, de Groot BL, Kopec W. 2021. The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology. 433(17):Article 167002. https://doi.org/10.1016/j.jmb.2021.167002

Moore J, Allan C, Besson S, Burel J-M, Diel E, Gault D, Kozlowski K, Lindner D, Linkert M, Manz T, Moore W, Pape C, Tischer C, Swedlow JR. 2021. OME-NGFF: a next-generation file format for expanding bioimaging data access strategies . Nature Methods., (2021). DOI: 10.1038/s41592-021-01326-w

Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Ogg S, Spitaler M, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1):56-73. https://doi.org/10.1111/jmi.13041

Parker MT, Knop K, Barton GJ, Simpson GG. 2021. 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing. Genome Biology. 22(1):Article 72. https://doi.org/10.1186/s13059-021-02296-0

Parker M, Knop K, Zacharaki V, Sherwood A, Tomé D, Yu X, Martin P, Beynon J, Michaels S, Barton GJ, Simpson GG. 2021. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife. 10:Article e65537. https://doi.org/10.7554/eLife.65537

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. 1 ed. New York: Humana Press. pp. 203-224. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-0716-1036-7_13

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. Erratum: Correction to: Alignment of Biological Sequences with Jalview (Methods in molecular biology (Clifton, N.J.) (2021) 2231 (203-224)). Methods in Molecular Biology (Clifton, N.J.). 2231:C1. https://doi.org/10.1007/978-1-0716-1036-7_18

Redl E, Sheibani-Tezerji R, Cardona CDJ, Hamminger P, Timelthaler G, Hassler MR, Zrimšek M, Lagger S, Dillinger T, Hofbauer L, Draganić K, Tiefenbacher A, Kothmayer M, Dietz CH, Ramsahoye BH, Kenner L, Bock C, Seiser C, Ellmeier W, Schweikert G, Egger G. 2021. Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK-driven lymphomagenesis. Life Science Alliance. 4(2):Article e202000794. https://doi.org/10.26508/lsa.202000794

Saraswathibhatla, A, Henkes, S, Galles, EE, Sknepnek, R & Notbohm, J 2021, 'Coordinated tractions increase the size of a collectively moving pack in a cell monolayer', Extreme Mechanics Letters, vol. 48, 101438. https://doi.org/10.1016/j.eml.2021.101438

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché J-K, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. 2021. REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nature Methods. https://doi.org/10.1038/s41592-021-01166-8

Swedlow JR, Kankaanpää P, Sarkans U, Goscinski W, Galloway G, Malacrida L, Sullivan RP, Härtel S, Brown CM, Wood C, Keppler A, Paina F, Loos B, Zullino S, Longo DL, Aime S, Onami S. 2021. A global view of standards for open image data formats and repositories. Nature Methods. https://doi.org/10.1038/s41592-021-01113-7

Thomson NJ, Vickery ON, Ives CM, Zachariae U. 2021. Ion-water coupling controls class A GPCR signal transduction pathways. BioRxiv. https://doi.org/10.1101/2020.08.28.271510

Utgés JS, Tsenkov MI, Dietrich NJM, MacGowan SA, Barton GJ. 2021. Ankyrin repeats in context with human population variation. BioRxiv. https://doi.org/10.1101/2021.05.28.445974

Utgés JS, Tsenkov MI, Dietrich NJM, MacGowan SA, Barton GJ. 2021. Ankyrin repeats in context with human population variation. PLoS Computational Biology. 17(8):Article e1009335. https://doi.org/10.1371/journal.pcbi.1009335

Williamson G, Brito AS, Bizior A, Tamburrino G, Mirandela GD, Harris T, Hoskisson PA, Zachariae U, Marini AM, Boeckstaens M, Javelle A. 2021. A mechanistic switch from selective transporter to an ion channel impairs the filamentation signalling capability of ammonium transceptors in yeast. BioRxiv. https://doi.org/10.1101/2021.08.25.457613

Wittner R, Holub P, Müller H, Geiger J, Goble C, Soiland-Reyes S, Pireddu L, Frexia F, Mascia C, Fairweather E, Swedlow JR, Moore J, Strambio C, Grunwald D, Nakae H. 2021. ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. Glavic B, Braganholo V, Koop D, editors. In Provenance and Annotation of Data and Processes: 8th and 9th International Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021, Proceedings. 1 ed. Switzerland: Springer Nature Switzerland AG. pp. 222-225. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-030-80960-7_16