Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data von Wolock, Samuel L., Lopez, Romain, Klein, Allon M.

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Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models von Xu, Chenling, Lopez, Romain, Mehlman, Edouard, Regier, Jeffrey, Jordan, Michael I, Yosef, Nir

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Enhancing scientific discoveries in molecular biology with deep generative models von Lopez, Romain, Gayoso, Adam, Yosef, Nir

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A Python library for probabilistic analysis of single-cell omics data von Gayoso, Adam, Lopez, Romain, Xing, Galen, Boyeau, Pierre, Valiollah Pour Amiri, Valeh, Hong, Justin, Wu, Katherine, Jayasuriya, Michael, Mehlman, Edouard, Langevin, Maxime, Liu, Yining, Samaran, Jules, Misrachi, Gabriel, Nazaret, Achille, Clivio, Oscar, Xu, Chenling, Ashuach, Tal, Gabitto, Mariano, Lotfollahi, Mohammad, Svensson, Valentine, da Veiga Beltrame, Eduardo, Kleshchevnikov, Vitalii, Talavera-López, Carlos, Pachter, Lior, Theis, Fabian J., Streets, Aaron, Jordan, Michael I., Regier, Jeffrey, Yosef, Nir

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Deep generative modeling for single-cell transcriptomics von Lopez, Romain, Regier, Jeffrey, Cole, Michael B., Jordan, Michael I., Yosef, Nir

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Managing marine socio-ecological systems: picturing the future von Thébaud, Olivier, Link, Jason S., Kohler, Bas, Kraan, Marloes, López, Romain, Poos, Jan Jaap, Schmidt, Jörn O., Smith, David C.

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What can exploratory modelling tell us about the ecobiology of European sea bass (Dicentrarchus labrax): a comprehensive overview von López, Romain, de Pontual, Hélène, Bertignac, Michel, Mahévas, Stéphanie

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Deep generative modeling for single-cell transcriptomics von Lopez, Romain, Regier, Jeffrey, Cole, Michael B., Jordan, Michael I., Yosef, Nir

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Joint probabilistic modeling of single-cell multi-omic data with totalVI von Gayoso, Adam, Steier, Zoë, Lopez, Romain, Regier, Jeffrey, Nazor, Kristopher L., Streets, Aaron, Yosef, Nir

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The Quilt of Sustainable Ocean Governance: Patterns for Practitioners von Stephenson, Robert L., Hobday, Alistair J., Allison, Edward H., Armitage, Derek, Brooks, Kate, Bundy, Alida, Cvitanovic, Christopher, Dickey-Collas, Mark, Grilli, Natalia de Miranda, Gomez, Catalina, Jarre, Astrid, Kaikkonen, Laura, Kelly, Rachel, Lopez, Romain, Muhl, Ella-Kari, Pennino, Maria Grazia, Tam, Jamie C., van Putten, Ingrid

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DestVI identifies continuums of cell types in spatial transcriptomics data von Lopez, Romain, Li, Baoguo, Keren-Shaul, Hadas, Boyeau, Pierre, Kedmi, Merav, Pilzer, David, Jelinski, Adam, Yofe, Ido, David, Eyal, Wagner, Allon, Ergen, Can, Addadi, Yoseph, Golani, Ofra, Ronchese, Franca, Jordan, Michael I., Amit, Ido, Yosef, Nir

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An empirical Bayes method for differential expression analysis of single cells with deep generative models von Boyeau, Pierre, Regier, Jeffrey, Gayoso, Adam, Jordan, Michael I, Lopez, Romain, Yosef, Nir

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe’er, Dana, Regev, Aviv, Teichmann, Sarah A., Finotello, Francesca, Wolf, F. Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J.

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Occurrence of Neocyttus helgae (Zeiformes, Oreosomatidae) in the Cantabrian Sea (Northern Spain) von ARRONTE, Juan Carlos, LOPEZ, Romain

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe'er, Dana, Regev, Aviv, Teichmann, Sarah A, Finotello, Francesca, Wolf, F Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J

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Testosterone deficiency in men surviving childhood acute leukemia after treatment with hematopoietic stem cell transplantation or testicular radiation: an L.E.A. study von Lopez, Romain, Plat, Geneviève, Bertrand, Yves, Ducassou, Stéphane, Saultier, Paul, Berbis, Julie, Pochon, Cécile, Hamidou, Zeinab, Poiree, Marilyne, Tabone, Marie-Dominique, Kanold, Justyna, Dalle, Jean-Hugues, Gandemer, Virginie, Paillard, Catherine, Sirvent, Nicolas, Plantaz, Dominique, Thouvenin, Sandrine, Pellier, Isabelle, Ansoborlo, Sophie, Leverger, Guy, Baruchel, André, Auquier, Pascal, Michel, Gérard

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Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors von Huang, Kexin, Lopez, Romain, Hütter, Jan-Christian, Kudo, Takamasa, Rios, Antonio, Regev, Aviv

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hca_heart_LV_stereoscope_subset_raw_ctl201217.h5ad von Lopez, Romain

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10x left ventricle data von Lopez, Romain

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Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport von Ryu, Jayoung, Bunne, Charlotte, Pinello, Luca, Regev, Aviv, Lopez, Romain

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