P724: Expanding the matched annotation from NCBI and EMBL-EBI (MANE) dataset to include MANE Select for non-coding genes by Shashikant Pujar, Jane Loveland, Alex Astashyn, Ruth Bennett, Andrew Berry, Eric Cox, Claire Davidson, Olga Ermolaeva, Reham Fatima, Tamara Goldfarb, Jose Gonzalez, Diana Haddad, Matthew Hardy, Toby Hunt, John Jackson, Vinita Joardar, Michael Kay, Vamsi Kodali, Kelly McGarvey, Jonathan Mudge, Michael Murphy, Sanjida Rangwala, Françoise Thibaud-Nissen, Anjana Vatsan, Craig Wallin, David Webb, Adam Frankish, Mallory Freeberg, Terence Murphy

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Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival by Abel Sousa, Aurelien Dugourd, Danish Memon, Borgthor Petursson, Evangelia Petsalaki, Julio Saez‐Rodriguez, Pedro Beltrao

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The BioStudies database by Jo McEntyre, Ugis Sarkans, Alvis Brazma

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Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets by Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle

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A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages by Varsha Kale, Germana Baldi, Martin Beracochea, Cecilie Clausen, Alejandra Escobar-Zepeda, Sabina Leanti La Rosa, Laurène A. Lecaudey, Sen Li, Sarah S. T. Mak, Michael D. Martin, Garazi Martin Bideguren, Louisa A. Pless, Jacob A. Rasmussen, Alexander B. Rogers, Harald Sveier, Arturo Vera-Ponce de León, Ana Verissimo, M. Thomas P. Gilbert, Lorna Richardson, Morten T. Limborg, Robert D. Finn

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CEN‐tools: an integrative platform to identify the contexts of essential genes by Sumana Sharma, Cansu Dincer, Paula Weidemüller, Gavin J Wright, Evangelia Petsalaki

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EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays by Stathis Megas, Valentina Lorenzi, John C. Marioni

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CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq by Anna S E Cuomo, Tobias Heinen, Danai Vagiaki, Danilo Horta, John C Marioni, Oliver Stegle

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High-throughput tomography correlated with light and electron microscopy for multi-scale imaging of human kidney tissue by Lawson Matthew, Burrell Alana, Albers Jonas, Xiong Xioafan, Uhlmann Virginie, Schwab Yannick, Roufosse Candice, Collinson Lucy, Duke Elizabeth

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Fifteen years of ChEMBL and its role in cheminformatics and drug discovery by Barbara Zdrazil

“…Abstract In October 2024 we celebrated the 15th anniversary of the first launch of ChEMBL, Europe’s most impactful, open-access drug discovery database, hosted by EMBL’s European Bioinformatics Institute (EMBL-EBI). This is a good moment to reflect on ChEMBL’s history, the role that ChEMBL plays in Cheminformatics and Drug Discovery as well as innovations accelerated using data extracted from it. …”
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A compound-target pairs dataset: differences between drugs, clinical candidates and other bioactive compounds by A. Lina Heinzke, Barbara Zdrazil, Paul D. Leeson, Robert J. Young, Axel Pahl, Herbert Waldmann, Andrew R. Leach

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Enabling pan-repository reanalysis for big data science of public metabolomics data by Yasin El Abiead, Michael Strobel, Thomas Payne, Eoin Fahy, Claire O’Donovan, Shankar Subramamiam, Juan Antonio Vizcaíno, Ozgur Yurekten, Victoria Deleray, Simone Zuffa, Shipei Xing, Helena Mannochio-Russo, Ipsita Mohanty, Haoqi Nina Zhao, Andres M. Caraballo-Rodriguez, Paulo Wender P. Gomes, Nicole E. Avalon, Trent R. Northen, Benjamin P. Bowen, Katherine B. Louie, Pieter C. Dorrestein, Mingxun Wang

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Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research by Muskan Kapoor, Enrique Sapena Ventura, Amy Walsh, Alexey Sokolov, Nancy George, Sunita Kumari, Nicholas J. Provart, Benjamin Cole, Marc Libault, Timothy Tickle, Wesley C. Warren, James E. Koltes, Irene Papatheodorou, Irene Papatheodorou, Doreen Ware, Doreen Ware, Peter W. Harrison, Christine Elsik, Galabina Yordanova, Tony Burdett, Christopher K. Tuggle

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega by Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson, Desmond G Higgins

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Natural genetic variation quantitatively regulates heart rate and dimension by Jakob Gierten, Bettina Welz, Tomas Fitzgerald, Thomas Thumberger, Rashi Agarwal, Oliver Hummel, Adrien Leger, Philipp Weber, Kiyoshi Naruse, David Hassel, Norbert Hübner, Ewan Birney, Joachim Wittbrodt

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The evolution of standards and data management practices in systems biology by Natalie J Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble

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Deep learning for computational biology by Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle

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Phosphoproteomic analyses reveal novel cross‐modulation mechanisms between two signaling pathways in yeast by Stefania Vaga, Marti Bernardo‐Faura, Thomas Cokelaer, Alessio Maiolica, Christopher A Barnes, Ludovic C Gillet, Björn Hegemann, Frank van Drogen, Hoda Sharifian, Edda Klipp, Matthias Peter, Julio Saez‐Rodriguez, Ruedi Aebersold

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Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes by Georgy Smyshlyaev, Alex Bateman, Orsolya Barabas

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Clustering phenotype populations by genome‐wide RNAi and multiparametric imaging by Florian Fuchs, Gregoire Pau, Dominique Kranz, Oleg Sklyar, Christoph Budjan, Sandra Steinbrink, Thomas Horn, Angelika Pedal, Wolfgang Huber, Michael Boutros

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