Methods & Resources
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq dataA systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.
Harnessing reaction-based probes to preferentially target pancreatic β-cells and β-like cellsThe study uses a reaction probe to target insulin-expressing pancreatic β-cells and β-like cells derived from pluripotent stem cells by harnessing high intracellular Zn(II) concentration.
A FIJI macro for quantifying pattern in extracellular matrixThis work provides a quantitative tool for the analysis of fibrillar patterns in biology. We demonstrates its utility on in vitro generated extracellular matrices, mouse tissues, and patient samples. The tool is already publicly available to the research community.
FIREWORKS: a bottom-up approach to integrative coessentiality network analysisA tool to create bias-adjusted coessentiality networks reveals functional relationships between genes, context-specific rewiring of genetic networks, determinants of essentiality, and therapeutic targets for challenging proteins.
ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomesA simple and efficient recombineering-based method for introducing point mutations into bacterial artificial chromosomes using an artificial intron cassette.
Predicting gene regulatory networks from cell atlasesIntegrated single-cell gene regulatory network from three mouse cell atlases captures global and cell type–specific regulatory modules and crosstalk, important for cellular identity.
Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortalityAffinity-based proteomics assays identify particular profiles of the circulating histidine-rich glycoprotein to increase with age and elevated levels to indicate a higher risk of all-cause mortality.
Prion infection, transmission, and cytopathology modeled in a low-biohazard human cell lineExpanding the toolbox of prion research to a low-biohazard, scalable human cell model.
Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondriaA novel, machine-learning approach to quantify cristae density and architecture in live-cell super-resolution imaging characterizes the ultrastructural parameters of individual mitochondria over time.
Ubiquitin and SUMO conjugation as biomarkers of acute myeloid leukemias response to chemotherapiesThis study describes the identification of a new class of biomarkers of cancer response to therapies based on protein modification by ubiquitin and SUMO and developed tools to validate them in acute myeloid leukemia patient samples.