Zhang, Sai Cooper-Knock, Johnathan Weimer, Annika K Shi, Minyi Kozhaya, Lina Unutmaz, Derya Harvey, Calum Julian, Thomas H Furini, Simone Frullanti, Elisa
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Published in
Cell systems
The determinants of severe COVID-19 in healthy adults are poorly understood, which limits the opportunity for early intervention. We present a multiomic analysis using machine learning to characterize the genomic basis of COVID-19 severity. We use single-cell multiome profiling of human lungs to link genetic signals to cell-type-specific functions....
Ciani, Yari Fedrizzi, Tarcisio Prandi, Davide Lorenzin, Francesca Locallo, Alessio Gasperini, Paola Franceschini, Gian Marco Benelli, Matteo Elemento, Olivier Fava, Luca L
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Published in
Cell systems
Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients across 27 tumor types from the Cancer Genome Atlas (TCGA). Leveraging allele-specific data, we reclassified as loss of heterozygosity (LOH) 9% and 7% of apparent copy-number wild-typ...
Sáez, Meritxell Blassberg, Robert Camacho-Aguilar, Elena Siggia, Eric D. Rand, David A. Briscoe, James
Published in
Cell Systems
Fate decisions in developing tissues involve cells transitioning between discrete cell states. We developed an approach to construct a dynamical landscape from quantitative gene expression data, in which the development of a cell is represented by a trajectory through the landscape. Applying it to pluripotent stem cells exposed to different combina...
Bondt, Albert Hoek, Max Tamara, Sem de Graaf, Bastiaan Peng, Weiwei Schulte, Douwe van Rijswijck, Danique M.H. den Boer, Maurits A. Greisch, Jean-François Varkila, Meri R.J.
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Published in
Cell Systems
The human body produces immunoglobulins (Igs) to help combat pathogens. The number of distinct IgG molecules our body can produce exceeds several billions. In contrast to this near-infinite theoretical number, we reveal here, as monitored directly by LC-MS, that only a few dozen distinct clones dominate in abundance the total spectrum of plasma IgG...
Larkins-Ford, Jonah Greenstein, Talia Van, Nhi Degefu, Yonatan N Olson, Michaela C Sokolov, Artem Aldridge, Bree B
Published in
Cell systems
Lengthy multidrug chemotherapy is required to achieve a durable cure in tuberculosis. However, we lack well-validated, high-throughput in vitro models that predict animal outcomes. Here, we provide an extensible approach to rationally prioritize combination therapies for testing in in vivo mouse models of tuberculosis. We systematically measured My...
Hamelin, David J Fournelle, Dominique Grenier, Jean-Christophe Schockaert, Jana Kovalchik, Kevin A Kubiniok, Peter Mostefai, Fatima Duquette, Jérôme D Saab, Frederic Sirois, Isabelle
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Published in
Cell systems
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled ac...
Demichev, Vadim Tober-Lau, Pinkus Lemke, Oliver Nazarenko, Tatiana Thibeault, Charlotte Whitwell, Harry Röhl, Annika Freiwald, Anja Szyrwiel, Lukasz Ludwig, Daniela
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Published in
Cell systems
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma prot...
Karikó, Katalin Whitehead, Kathryn van der Meel, Roy
Published in
Cell Systems
Chustecki, Joanna M. Gibbs, Daniel J. Bassel, George W. Johnston, Iain G.
Published in
Cell Systems
Mitochondria in plant cells are highly motile and move as individuals (in contrast to the often highly connected networks in other taxa). The reasons for this motion remain unclear. This study uses single-cell live imaging of Arabidopsis to characterize “social” networks of encounters between mitochondria. Network analysis and modeling reveal a cel...
van Dorp, Lucy Shey, Muki S Ghedin, Elodie Michor, Franziska Koonin, Eugene V Hampson, Katie
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Cell systems