Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones

Authors: Cheung, Stephanie ^{1, 7}, Bredikhin, Danila ^{2, 3, 7}, Gerber, Tobias ^{1, 2, 7}, Steenbergen, Petrus J. ^{1, 7}, Basu, Soham ^{1, 7}, Bailleul, Richard ¹, Hansen, Pauline ¹, Paix, Alexandre ¹, Benton, Matthew A. ¹, Korswagen, Hendrik C. ⁴, Arendt, Detlev ¹, Stegle, Oliver ^{2, 3, 5, 6, ∗}, Ikmi, Aissam ^{1, 8, ∗∗}

Source: In Developmental Cell 10 March 2025 60(5):780-793

Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Authors: Kolbasova, Glafira, Schmidt-Rhaesa, Andreas, Syomin, Vitaly, Bredikhin, Danila, Morozov, Taras, Neretina, Tatiana

Source: Zoologischer Anzeiger. 302:113-130

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181224030.0x000001&indx=1&recIds=ETOCvdc_100181224030.0x000001

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

Authors: Alda-Catalinas, Celia, Bredikhin, Danila, Hernando-Herraez, Irene, Santos, Fátima, Kubinyecz, Oana, Eckersley-Maslin, Mélanie A., Stegle, Oliver, Reik, Wolf

Source: In Cell Systems 22 July 2020 11(1):25-41

Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.

Authors: Ban, Maria¹ (AUTHOR) mb531@medschl.cam.ac.uk, Bredikhin, Danila^2,3 (AUTHOR), Huang, Yuanhua^1,4 (AUTHOR), Bonder, Marc Jan^2,3 (AUTHOR), Katarzyna, Kania⁵ (AUTHOR), Oliver, Amanda J⁶ (AUTHOR), Wilson, Nicola K^7,8 (AUTHOR), Coupland, Paul⁵ (AUTHOR), Hadfield, James⁵ (AUTHOR), Göttgens, Berthold^7,8 (AUTHOR), Madissoon, Elo^4,6 (AUTHOR), Stegle, Oliver^2,3,4 (AUTHOR), Sawcer, Stephen¹ (AUTHOR)

Source: Brain: A Journal of Neurology. Feb2024, Vol. 147 Issue 2, p554-565. 12p.

Subject Terms: *GENE expression, *MULTIPLE sclerosis, *CEREBROSPINAL fluid, *LOCUS (Genetics), *AUTOIMMUNE diseases, *RNA splicing

The scverse project provides a computational ecosystem for single-cell omics data analysis.

Authors: Virshup, Isaac¹ (AUTHOR) steering-council@scverse.org, Bredikhin, Danila^2,3,4 (AUTHOR) steering-council@scverse.org, Heumos, Lukas^1,5,6 (AUTHOR) steering-council@scverse.org, Palla, Giovanni^1,6 (AUTHOR), Sturm, Gregor⁷ (AUTHOR), Gayoso, Adam⁸ (AUTHOR), Kats, Ilia³ (AUTHOR), Koutrouli, Mikaela⁹ (AUTHOR), Scverse Community (AUTHOR), Angerer, Philipp¹⁰ (AUTHOR), Bergen, Volker^1,10 (AUTHOR), Boyeau, Pierre¹¹ (AUTHOR), Büttner, Maren^1,12 (AUTHOR), Eraslan, Gokcen¹³ (AUTHOR), Fischer, David^1,6 (AUTHOR), Frank, Max² (AUTHOR), Hong, Justin^8,11 (AUTHOR), Klein, Michal¹ (AUTHOR), Lange, Marius^1,14 (AUTHOR), Lopez, Romain^13,15 (AUTHOR)

Source: Nature Biotechnology. May2023, Vol. 41 Issue 5, p604-606. 3p.

MUON: multimodal omics analysis framework.

Authors: Bredikhin, Danila, Kats, Ilia, Stegle, Oliver

Source: Genome Biology; 2/1/2022, Vol. 23 Issue 1, p1-12, 12p

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Authors: Velten, Britta, Braunger, Jana M., Argelaguet, Ricard, Arnol, Damien, Wirbel, Jakob, Bredikhin, Danila, Zeller, Georg, Stegle, Oliver

Source: Nature Methods; February 2022, Vol. 19 Issue: 2 p179-186, 8p

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.

Authors: Argelaguet, Ricard, Arnol, Damien, Bredikhin, Danila, Deloro, Yonatan, Velten, Britta, Marioni, John C., Stegle, Oliver

Source: Genome Biology; 5/11/2020, Vol. 21 Issue 1, p1-17, 17p