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SaveExpression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration
Madrigal, Pedro; Thanki, Anil S.; Fexova, Silvie; Yu, Iris D.; Chatzigeorgiou, Arsenios; Zucchi, Ida; Marugan Calles, Jose C.; Vilmovsky, Liora; Khen, Amnon; Zhao, Lingyun; Erdos, Karoly; Kurri, Sandeep R.; Selvakumar, Sandeep; Kumbham, Upendra; Prakash, Ananth; Wang, Shengbo; Green, Andrew; Ribas, Carlos Eduardo; Sweeney, Blake; Alegbe, Tobi; Suveges, Daniel; Hemrom, Anmol; Gomez Gutierrez, David E.; Insua, Santiago; Jeffryes, Matt; Pearce, Matt; Basutkar, Prasad; Kaforou, Myrsini; Cunnington, Aubrey; Levin, Michael; Kumari, Sunita; Ware, Doreen; Goutte-Gattat, Damien; Roper, Katja; Brown, Nicholas H.; Hu, Yanhui; Perrimon, Norbert; Papatheodorou, Irene; Brazma, Alvis; Hermjakob, Henning; Harrison, Melissa; Ocana, David; Ochoa, David; McDonagh, Ellen M.; Bateman, Alex; Keane, Thomas; Vizcaino, Juan Antonio; Ernst, Christina Share Save Share Save Share Save Expression Atlas update: insights from sequencing data at both bulk and single cell levelGeorge, Nancy; Fexova, Silvie; Fuentes, Alfonso Munoz; Madrigal, Pedro; Bi, Yalan; Iqbal, Haider; Kumbham, Upendra; Nolte, Nadja Francesca; Zhao, Lingyun; Thanki, Anil S.; Yu, Iris D.; Marugan Calles, Jose C.; Erdos, Karoly; Vilmovsky, Liora; Kurri, Sandeep R.; Vathrakokoili-Pournara, Anna; Osumi-Sutherland, David; Prakash, Ananth; Wang, Shengbo; Tello-Ruiz, Marcela K.; Kumari, Sunita; Ware, Doreen; Goutte-Gattat, Damien; Hu, Yanhui; Brown, Nick; Perrimon, Norbert; Vizcaino, Juan Antonio; Burdett, Tony; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene Share Save Share Save High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (vol 11, 736, 2020)Zhang, Yiqun; Chen, Fengju; Fonseca, Nuno A.; He, Yao; Fujita, Masashi; Nakagawa, Hidewaki; Zhang, Zemin; Brazma, Alvis; Creighton, Chad J. Share Save Tumour gene expression signature in primary melanoma predicts long-term outcomes (vol 12, 1137, 2021)Garg, Manik; Couturier, Dominique-Laurent; Nsengimana, Jeremie; Fonseca, Nuno A.; Wongchenko, Matthew; Yan, Yibing; Lauss, Martin; Jonsson, Goran B.; Newton-Bishop, Julia; Parkinson, Christine; Middleton, Mark R.; Bishop, D. Timothy; McDonald, Sarah; Stefanos, Nikki; Tadross, John; Vergara, Ismael A.; Lo, Serigne; Newell, Felicity; Wilmott, James S.; Thompson, John F.; Long, Georgina V.; Scolyer, Richard A.; Corrie, Pippa; Adams, David J.; Brazma, Alvis; Rabbie, Roy Share Save Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different SeveritiesLi, Xu; Garg, Manik; Jia, Tingting; Liao, Qijun; Yuan, Lifang; Li, Mao; Wu, Zhengyu; Wu, Weihua; Bi, Yalan; George, Nancy; Papatheodorou, Irene; Brazma, Alvis; Luo, Huanle; Fang, Shisong; Miao, Zhichao; Shu, Yuelong Share Save Expression Atlas update: gene and protein expression in multiple speciesMoreno, Pablo; Fexova, Silvie; George, Nancy; Manning, Jonathan R.; Miao, Zhichiao; Mohammed, Suhaib; Munoz-Pomer, Alfonso; Fullgrabe, Anja; Bi, Yalan; Bush, Natassja; Iqbal, Haider; Kumbham, Upendra; Solovyev, Andrey; Zhao, Lingyun; Prakash, Ananth; Garcia-Seisdedos, David; Kundu, Deepti J.; Wang, Shengbo; Walzer, Mathias; Clarke, Laura; Osumi-Sutherland, David; Tello-Ruiz, Marcela Karey; Kumari, Sunita; Ware, Doreen; Eliasova, Jana; Arends, Mark J.; Nawijn, Martijn C.; Meyer, Kerstin; Burdett, Tony; Marioni, John; Teichmann, Sarah; Vizcaino, Juan Antonio; Brazma, Alvis; Papatheodorou, Irene Share Save The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidencesPerez-Riverol, Yasset; Bai, Jingwen; Bandla, Chakradhar; Garcia-Seisdedos, David; Hewapathirana, Suresh; Kamatchinathan, Selvakumar; Kundu, Deepti J.; Prakash, Ananth; Frericks-Zipper, Anika; Eisenacher, Martin; Walzer, Mathias; Wang, Shengbo; Brazma, Alvis; Vizcaino, Juan Antonio Share Save Share Save A proteomics sample metadata representation for multiomics integration and big data analysisDai, Chengxin; Fullgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M.; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; Gruening, Bjoern; Foell, Melanie Christine; Griss, Johannes; Vaudel, Marc; Audain, Enrique; Locard-Paulet, Marie; Turewicz, Michael; Eisenacher, Martin; Uszkoreit, Julian; Van den Bossche, Tim; Schwammle, Veit; Webel, Henry; Schulze, Stefan; Bouyssie, David; Jayaram, Savita; Duggineni, Vinay Kumar; Samaras, Patroklos; Wilhelm, Mathias; Choi, Meena; Wang, Mingxun; Kohlbacher, Oliver; Brazma, Alvis; Papatheodorou, Irene; Bandeira, Nuno; Deutsch, Eric W.; Vizcaino, Juan Antonio; Bai, Mingze; Sachsenberg, Timo; Levitsky, Lev I.; Perez-Riverol, Yasset Share Save REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biologySarkans, Ugis; Chiu, Wah; Collinson, Lucy; Darrow, Michele C.; Ellenberg, Jan; Grunwald, David; Heriche, Jean-Karim; Iudin, Andrii; Martins, Gabriel G.; Meehan, Terry; Narayan, Kedar; Patwardhan, Ardan; Russell, Matthew Robert Geoffrey; Saibil, Helen R.; Strambio-De-Castillia, Caterina; Swedlow, Jason R.; Tischer, Christian; Uhlmann, Virginie; Verkade, Paul; Barlow, Mary; Bayraktar, Omer; Birney, Ewan; Catavitello, Cesare; Cawthorne, Christopher; Wagner-Conrad, Stephan; Duke, Elizabeth; Paul-Gilloteaux, Perrine; Gustin, Emmanuel; Harkiolaki, Maria; Kankaanpaa, Pasi; Lemberger, Thomas; McEntyre, Jo; Moore, Josh; Nicholls, Andrew W.; Onami, Shuichi; Parkinson, Helen; Parsons, Maddy; Romanchikova, Marina; Sofroniew, Nicholas; Swoger, Jim; Utz, Nadine; Voortman, Lenard M.; Wong, Frances; Zhang, Peijun; Kleywegt, Gerard J.; Brazma, Alvis Share Save User-friendly, scalable tools and workflows for single-cell RNA-seq analysisMoreno, Pablo; Huang, Ni; Manning, Jonathan R.; Mohammed, Suhaib; Solovyev, Andrey; Polanski, Krzysztof; Bacon, Wendi; Chazarra, Ruben; Talavera-Lopez, Carlos; Doyle, Maria A.; Marnier, Guilhem; Gruening, Bjoern; Rasche, Helena; George, Nancy; Fexova, Silvie Korena; Alibi, Mohamed; Miao, Zhichao; Perez-Riverol, Yasset; Haeussler, Maximilian; Brazma, Alvis; Teichmann, Sarah; Meyer, Kerstin B.; Papatheodorou, Irene Share Save Tumour gene expression signature in primary melanoma predicts long-term outcomesGarg, Manik; Couturier, Dominique-Laurent; Nsengimana, Jeremie; Fonseca, Nuno A.; Wongchenko, Matthew; Yan, Yibing; Lauss, Martin; Jonsson, Goeran B.; Newton-Bishop, Julia; Parkinson, Christine; Middleton, Mark R.; Bishop, D. Timothy; McDonald, Sarah; Stefanos, Nikki; Tadross, John; Vergara, Ismael A.; Lo, Serigne; Newell, Felicity; Wilmott, James S.; Thompson, John F.; Long, Georgina V.; Scolyer, Richard A.; Corrie, Pippa; Adams, David J.; Brazma, Alvis; Rabbie, Roy Share Save Urinary metabolic phenotyping for Alzheimer's diseaseKurbatova, Natalja; Garg, Manik; Whiley, Luke; Chekmeneva, Elena; Jimenez, Beatriz; Gomez-Romero, Maria; Pearce, Jake; Kimhofer, Torben; D'Hondt, Ellie; Soininen, Hilkka; Kloszewska, Iwona; Mecocci, Patrizia; Tsolaki, Magda; Vellas, Bruno; Aarsland, Dag; Nevado-Holgado, Alejo; Liu, Benjamine; Snowden, Stuart; Proitsi, Petroula; Ashton, Nicholas J.; Hye, Abdul; Legido-Quigley, Cristina; Lewis, Matthew R.; Nicholson, Jeremy K.; Holmes, Elaine; Brazma, Alvis; Lovestone, Simon Share Save From ArrayExpress to BioStudiesSarkans, Ugis; Fullgrabe, Anja; Ali, Ahmed; Athar, Awais; Behrangi, Ehsan; Diaz, Nestor; Fexova, Silvie; George, Nancy; Iqbal, Haider; Kurri, Sandeep; Munoz, Jhoan; Rada, Juan; Papatheodorou, Irene; Brazma, Alvis Share Save Guidelines for reporting single-cell RNA-seq experimentsFullgrabe, Anja; George, Nancy; Green, Matthew; Nejad, Parisa; Aronow, Bruce; Fexova, Silvie Korena; Fischer, Clay; Freeberg, Mallory Ann; Huerta, Laura; Morrison, Norman; Scheuermann, Richard H.; Taylor, Deanne; Vasilevsky, Nicole; Clarke, Laura; Gehlenborg, Nils; Kent, Jim; Marioni, John; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene Share Save Using Deep Learning to Extrapolate Protein Expression MeasurementsBarzine, Mitra Parissa; Freivalds, Karlis; Wright, James C.; Opmanis, Martins; Rituma, Darta; Ghavidel, Fatemeh Zamanzad; Jarnuczak, Andrew F.; Celms, Edgars; Cerans, Karlis; Jonassen, Inge; Lace, Lelde; Antonio Vizcaino, Juan; Choudhary, Jyoti Sharma; Brazma, Alvis; Viksna, Juris Share Save 
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