By Scott Berry

Journal articles

Gillis A; Berry S, 2024, 'Global control of RNA polymerase II', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1867, pp. 195024, http://dx.doi.org/10.1016/j.bbagrm.2024.195024

Antoniou-Kourounioti RL; Meschichi A; Reeck S; Berry S; Menon G; Zhao Y; Fozard J; Holmes T; Zhao L; Wang H; Hartley M; Dean C; Rosa S; Howard M, 2023, 'Integrating analog and digital modes of gene expression at Arabidopsis FLC', eLife, 12, http://dx.doi.org/10.7554/eLife.79743

Spitzer H; Berry S; Donoghoe M; Pelkmans L; Theis FJ, 2023, 'Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps', Nature Methods, 20, pp. 1058 - 1069, http://dx.doi.org/10.1038/s41592-023-01894-z

Berry S; Pelkmans L, 2022, 'Mechanisms of cellular mRNA transcript homeostasis', Trends in Cell Biology, 32, pp. 655 - 668, http://dx.doi.org/10.1016/j.tcb.2022.05.003

Berry S; Müller M; Rai A; Pelkmans L, 2022, 'Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells', Cell Systems, 13, pp. 454 - 470.e15, http://dx.doi.org/10.1016/j.cels.2022.04.005

Müller M; Avar M; Heinzer D; Emmenegger M; Aguzzi A; Pelkmans L; Berry S, 2021, 'Author Correction: High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production (Scientific Data, (2021), 8, 1, (162), 10.1038/s41597-021-00944-5)', Scientific Data, 8, http://dx.doi.org/10.1038/s41597-021-01096-2

Müller M; Pelkmans L; Berry S, 2021, 'High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production', Scientific Data, 8, pp. 162, http://dx.doi.org/10.1038/s41597-021-00944-5

Berry S; Rosa S; Howard M; Bühler M; Dean C, 2017, 'Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression', Genes and Development, 31, pp. 2115 - 2120, http://dx.doi.org/10.1101/gad.305227.117

Yang H; Berry S; Olsson TSG; Hartley M; Howard M; Dean C, 2017, 'Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis', Science, 357, pp. 1142 - 1145, http://dx.doi.org/10.1126/science.aan1121

Berry S; Dean C; Howard M, 2017, 'Slow Chromatin Dynamics Allow Polycomb Target Genes to Filter Fluctuations in Transcription Factor Activity', Cell Systems, 4, pp. 445 - 457.e8, http://dx.doi.org/10.1016/j.cels.2017.02.013

Berry S; Dean C, 2015, 'Environmental perception and epigenetic memory: Mechanistic insight through FLC', Plant Journal, 83, pp. 133 - 148, http://dx.doi.org/10.1111/tpj.12869

Berry S; Hartley M; Olsson TSG; Dean C; Howard M, 2015, 'Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance', eLife, 4, http://dx.doi.org/10.7554/eLife.07205

King JD; Berry S; Clarke BR; Morris RJ; Whitfield C, 2014, 'Lipopolysaccharide O antigen size distribution is determined by a chain extension complex of variable stoichiometry in Escherichia coli O9a', Proceedings of the National Academy of Sciences of the United States of America, 111, pp. 6407 - 6412, http://dx.doi.org/10.1073/pnas.1400814111

Richards D; Berry S; HOward M, 2012, 'Illustrations of mathematical modeling in biology: Epigenetics, meiosis, and an outlook', Cold Spring Harbor Symposia on Quantitative Biology, 77, pp. 175 - 181, http://dx.doi.org/10.1101/sqb.2013.77.015941

Berry SD; Bourke P; Wang JB, 2011, 'QwViz: Visualisation of quantum walks on graphs', Computer Physics Communications, 182, pp. 2295 - 2302, http://dx.doi.org/10.1016/j.cpc.2011.06.002

Berry SD; Wang JB, 2011, 'Two-particle quantum walks: Entanglement and graph isomorphism testing', Physical Review A - Atomic, Molecular, and Optical Physics, 83, http://dx.doi.org/10.1103/PhysRevA.83.042317

Berry SD; Wang JB, 2010, 'Quantum-walk-based search and centrality', Physical Review A - Atomic, Molecular, and Optical Physics, 82, http://dx.doi.org/10.1103/PhysRevA.82.042333

Software / Code

Berry S, 2024, blimp, Image analysis, Published: 26 August 2024, Software / Code, http://dx.doi.org/10.5281/zenodo.12559364

Spitzer H; Berry S, 2022, CAMPA, GitHub, Published: 09 May 2022, Software / Code, https://github.com/theislab/campa

Preprints

Yin J-A; Frick L; Scheidmann MC; Liu T; Trevisan C; Dhingra A; Spinelli A; Wu Y; Yao L; Vena DL; Knapp B; Cecco ED; Ging K; Armani A; Oakeley E; Nigsch F; Jenzer J; Haegele J; Pikusa M; Täger J; Rodriguez-Nieto S; Guo J; Bouris V; Ribeiro R; Baroni F; Bedi MS; Berry S; Losa M; Hornemann S; Kampmann M; Pelkmans L; Hoepfner D; Heutink P; Aguzzi A, 2022, Robust and Versatile Arrayed Libraries for Human Genome-Wide CRISPR Activation, Deletion and Silencing, http://dx.doi.org/10.1101/2022.05.25.493370

Spitzer H; Berry S; Donoghoe M; Pelkmans L; Theis F, 2022, Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps, http://dx.doi.org/10.1101/2022.05.07.490900

Berry S; Müller M; Pelkmans L, 2021, Nuclear RNA concentration coordinates RNA production with cell size in human cells, http://dx.doi.org/10.1101/2021.05.17.444432

Back to profile page