Directed evolution of proteins often involves a greedy optimization in which the mutation in the highest-fitness variant identified in each round of single-site mutagenesis is fixed. The efficiency of such a single-step greedy walk depends on the ord...
Deep learning has emerged as the technique of choice for identifying hidden patterns in cell imaging data but is often criticized as "black box." Here, we employ a generative neural network in combination with supervised machine learning to classify ...
Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides informative data resources for constructing computational models of cell biology. Models that generalize well beyond training data ...
Changes in stem cell activity may underpin aging. However, these changes are not completely understood. Here, we combined single-cell profiling with machine learning and in vivo functional studies to explore how hematopoietic stem cell (HSC) division...
Subunit vaccines induce immunity to a pathogen by presenting a component of the pathogen and thus inherently limit the representation of pathogen peptides for cellular immunity-based memory. We find that severe acute respiratory syndrome coronavirus ...
Machine learning can infer how protein sequence maps to function without requiring a detailed understanding of the underlying physical or biological mechanisms. It is challenging to apply existing supervised learning frameworks to large-scale experim...
We performed RNA-seq and high-resolution mass spectrometry on 128 blood samples from COVID-19-positive and COVID-19-negative patients with diverse disease severities and outcomes. Quantified transcripts, proteins, metabolites, and lipids were associa...
Epidemiological studies show that SARS-CoV-2 infection leads to severe symptoms only in a fraction of patients, but the determinants of individual susceptibility to the virus are still unknown. The major histocompatibility complex (MHC) class I expos...
Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer pro...
Single-cell RNA sequencing (scRNA-seq) measurements of gene expression enable an unprecedented high-resolution view into cellular state. However, current methods often result in two or more cells that share the same cell-identifying barcode; these "d...