By Scott Berry

Journal articles

Yin JA; Frick L; Scheidmann MC; Liu T; Trevisan C; Dhingra A; Spinelli A; Wu Y; Yao L; Vena DL; Knapp B; Guo J; De Cecco E; Ging K; Armani A; Oakeley EJ; Nigsch F; Jenzer J; Haegele J; Pikusa M; Täger J; Rodriguez-Nieto S; Bouris V; Ribeiro R; Baroni F; Bedi MS; Berry S; Losa M; Hornemann S; Kampmann M; Pelkmans L; Hoepfner D; Heutink P; Aguzzi A, 2025, 'Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes', Nature Biomedical Engineering, 9, pp. 127 - 148, http://dx.doi.org/10.1038/s41551-024-01278-4

Cacioppo R; Gillis A; Shlamovitz I; Zeller A; Castiblanco D; Crisp A; Haworth B; Arabiotorre A; Abyaneh P; Bao Y; Sale JE; Berry S; Tufegdžić Vidaković A, 2024, 'CRL3^ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription', Molecular Cell, 84, pp. 4808 - 4823.e13, http://dx.doi.org/10.1016/j.molcel.2024.11.024

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

Conference Abstracts

Michniewicz F; Cazzoli R; Bell J; Saletta F; Poursani E; Rouaen JR; Shai-Hee T; Vu P; Jue TR; Biery M; Bramberger L; Lim T; Khan A; Giorgi FM; Mercatelli D; Mayoh C; Cirillo G; Macmillan A; Whan R; Barlow CT; Tsoli M; Vitanza N; Berry S; Faridi P; Ziegler D; Vittorio O, 2024, 'A comprehensive approach: Copper chelation therapy modulates epigenetic, kinase signaling and metabolic pathways in diffuse midline gliomas (DMG)', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, CA, San Diego, Vol. 84, presented at Annual Meeting of the American-Association-for-Cancer-Research (AACR), CA, San Diego, 05 April 2024 - 10 April 2024, http://dx.doi.org/10.1158/1538-7445.AM2024-525

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

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