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This work presents CalicoST for inferring allele-specific copy numbers and reconstructing spatial tumor evolution by using spatial transcriptomics data.
Microscopy artifacts and tissue imperfections interfere with single-cell analysis. CyLinter software offers quality control for high-plex tissue profiling by removing artifactual cells, thereby facilitating accuracy of biological interpretation.
CryoSTAR is a deep neural network model that resolves continuous conformational heterogeneity from cryo-EM datasets using an initial atomic model as the reference to generate both density maps and reasonable coarse-grained models for different conformations.
The accuracy of SCUBA-D, a protein backbone structure diffusion model trained independently and orthogonally to existing protein structure prediction networks, is confirmed by the X-ray structures of 16 designed proteins and a protein complex, and by experimental validation of designed heme-binding proteins and Ras-binding proteins.
Cryo-electron microscopy with energy resolution, using the EELS-STEM method, allows researchers to identify the approximate locations of certain heavier atoms within single frozen, hydrated protein particles.
An approach combining electron energy-loss spectroscopy with image processing tools from single-particle cryo-electron microscopy enables elemental mapping in macromolecular complexes, paving the way for the accurate assignment of metals, ions, ligands and lipids.
A protocol for differentiating visceral sensory ganglion organoids from induced pluripotent stem cells allows the establishment of an in vitro model for the gut–visceral nerve–brain axis and study of the propagation of pathogenic proteins involved in Alzheimer’s disease along the vagus nerve.
A systematic analysis of the influence of different sample preparation steps on proteoform identification by top-down proteomics serves as a useful reference for designing appropriate workflows for specific research questions.
We developed LABEL-seq, a platform that enables measurement of protein properties and functions at scale by leveraging the intracellular self-assembly of an RNA-binding domain (RBD) and protein-encoding RNA barcode. Enrichment of RBD–protein fusions, followed by high-throughput sequencing of the co-enriched barcodes, enables the profiling of protein abundance, activity, interactions and druggability at scale.
DiffModeler is a fully automated structure fitting method for modeling large protein complex structures in cryo-EM maps with resolutions up to 15 Å.
Labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq) enables massively parallel profiling of thousands of pooled protein variants in cells, yielding insight into protein function, interactions and druggability.
Very high-resolution images of the human brain obtained in vivo in a few minutes with MRI at an ultra-high magnetic field of 11.7 T reveal exquisite details. Biological and behavioral tests confirm the safety of the method, opening the door for human brain exploration at mesoscale resolution.
In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.
PetaKit5D offers versatile processing workflows for light sheet microscopy data including performant image input/output, geometric transformations, deconvolution and stitching. The software is efficient and scalable to petabyte-size datasets.
