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....
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...
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...
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...
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...
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...
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...
Published in Cell Systems
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...
Published in Cell systems
