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AlteredPQR is a software tool, available as an R package, to infer remodeling of protein functional modules from whole-cell or tissue lysate proteomic measurements.
A Ni2+-modified MspA nanopore construct can unambiguously discriminate the 20 proteogenic amino acids as well as several post-translational modifications.
Droplet-based microfluidics enable rapid mixing with millisecond dead times and allow single-molecule measurements of non-equilibrium binding kinetics on even challenging, strongly adsorptive samples, such as intrinsically disordered proteins.
Modern high-throughput metagenomics is producing hundreds of thousands of metagenome-assembled genomes (MAGs), which is overwhelming traditional sequence-similarity search methods. We present a computational method, skani, that efficiently compares MAGs on a terabyte scale while being robust to the inherent noise in MAGs, enabling larger and more accurate analyses.
skani achieves fast calculation of average nucleotide identity (ANI) between metagenome-assembled genomes (MAGs), with improved robustness against incomplete and fragmented MAGs.
EzMechanism is a tool for automated prediction of the catalytic mechanisms of enzymes using their three-dimensional structures and chemical reactions as input.
veloVI enhances RNA velocity analysis with uncertainty quantification and extensibility by deep generative modeling of gene-specific transcriptional dynamics.
To capture expansive, seamless fields of view from frozen hydrated specimens by cryo-electron tomography, we developed methods for the collection and processing of montage data. This approach enables rapid acquisition of contiguous regions of specimens using a montaged tilt series collection scheme.
We introduce GelMap, a flexible workflow for reporting deformations and anisotropy in expansion microscopy. By intrinsically calibrating the expansion hydrogel using a fluorescent grid that scales with expansion and deforms with anisotropy, GelMap enables the reliable quantification of expansion factors and correction of deformations.
The GelMap workflow adds a fluorescent grid into samples before expansion, allowing for precise determination of expansion factor and subsequent deformation correction in ExM. GelMap works with diverse samples and expansion methods.
Montage parallel array cryo-tomography adopts principles of montage tomography via regular array beam-image-shift montage acquisition and is robust for imaging large fields of view while retaining high-resolution structural information in cryo-electron tomography.
The Clivias are a series of small, monomeric fluorescent RNAs that emit with a large Stokes shift in the orange–red. They enable multiplexed RNA imaging in live cells and BRET-based detection of protein–RNA interactions in mice.
Statistically unbiased prediction utilizing spatiotemporal information in imaging data (SUPPORT) is a self-supervised deep learning approach to accurately denoise voltage and calcium imaging data while preserving true dynamic signals.
This Review discusses statistical and computational strategies for analyzing various spatial and temporal omics data types, with an emphasis on the common modeling principles.
This work introduces a wet lab and computational pipeline, Napu, for small variant calling and de novo assembly of Nanopore sequencing data, which leads to comparable performances to short-read sequencing and allows for large-scale long-read sequencing projects.
