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This Registered Report presents the results of the Long-read RNA-Seq Genome Annotation Assessment Project, which is a community effort for benchmarking long-read methods for transcriptome analyses, including transcript isoform detection, quantification and de novo transcript detection.
Deconwolf is a computationally efficient and user-friendly software tool for fluorescence microscopy image deconvolution that improves the analysis of diverse fluorescence in situ hybridization methods and can handle large datasets.
scFoundation, with 100 million parameters covering about 20,000 genes, pretrained on over 50 million single-cell transcriptomics profiles, is a foundation model for diverse tasks of single-cell analysis.
Integrative and reference-informed tissue segmentation (IRIS) harnesses single-cell RNA sequencing data for the accurate identification of spatial domains in spatially resolved transcriptomics. IRIS is computationally efficient and uniquely suited for analyzing large datasets.
In targeted-illumination confocal microscopy, the combination of targeted illumination with confocal detection allows one-photon voltage imaging across large fields of view with a high signal-to-noise ratio.
Photoconversion of popular organic dyes results in blue-shifted emission and altered fluorescence lifetimes that can cause artifacts in quantitative microscopy. These can be avoided through proper labeling strategies such as using exchangeable dyes.
uiPSF (universal inverse modeling of point spread functions) offers a versatile solution for inferring accurate PSF models from images of beads and blinking fluorophores, enabling improved imaging and image processing in localization microscopy.
This resource presents a high-resolution diffusion MRI dataset of a chimpanzee brain, which should be useful for evolutionary studies of primate brain evolution.
PdCO is a switchable optogenetic tool for inhibiting synaptic transmission in neuronal terminals in vivo, as demonstrated in a variety of contexts mainly in the mouse.
FluidFM-based force-controlled nanopipettes enable control of mechanical stimuli for the investigation of Piezo1-induced mechanosensation in cell membranes.
Using a dependency-aware deep generative framework, spaVAE efficiently models spatially resolved transcriptomics data and advances diverse analysis tasks. Following similar strategies, spaPeakVAE and spaMultiVAE enable spatial ATAC-seq data and spatial multi-omics data modeling and analysis, respectively.
The Consortium for Top-Down Proteomics conducted a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. They report the summary of the outcomes and their recommendations in this Analysis.
OpenFold is a trainable open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.
By effective and efficient integration of PacBio HiFi, Oxford Nanopore Technologies ultra-long and other sequencing data types, hifiasm (UL) enables telomere-to-telomere diploid and polyploid genome assembly at a population scale.
By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference and batch effect mitigation.
Single-cell quantitative expression reporters enable high-sensitivity quantitative characterization of cis-regulatory elements at the single-cell level in multicellular systems.
Molecular Pixelation is an optics-free method that uses DNA-tagged antibodies to enable identification of the relative location of proteins on single cells.