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HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.
A straightforward method and tool, MetaMass, utilizes a list of subcellular markers to analyze and classify subcellular proteomics data from multiple experiments. An accompanying analysis reveals a wide variation in the results of subcellular fractionation protocols.
Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data.
A suite of tools and resources for Vibrio natriegens introduces the bacterium as a faster-growing alternative to E. coli for molecular biology and biotechnology applications.
sc-GEM enables the dissection of cellular heterogeneity by simultaneously assaying the status of DNA mutations, gene expression and DNA methylation at multiple targeted loci in individual cells.
Double-strand DNA breaks capture (DSBCapture) identifies in situ DSBs via the ligation of an Illumina adaptor into the break site and shows no bias for chromatin state or base composition. A genome-wide DSB profile shows breaks occurring more frequently in euchromatin and transcriptionally active regions.
Virtual microfluidics uses hydrogel entrapment to make high-throughput single-cell and single-molecule amplification broadly accessible without the need for special equipment.
LOVTRAP enables rapid optogenetic control of protein dissociation and is complementary to related optogenetic tools that mediate light-induced protein association. LOVTRAP is applied to the study of oscillatory processes at the cell membrane.
PALM and STORM are powerful methods for studying membrane-protein clustering. However, fluorophore blinking can lead to miscounting artifacts. A new method shows that varying label density works for artifact-free analysis of membrane-protein nanoclusters.
Structural Variant Search, a combination of a chimera-free library preparation and a non-consensus-based SV-calling algorithm, enables the quantitative detection of rare somatic variants.
Correlation fluorescent in situ hybridization (corrFISH) makes it possible to quantify abundant transcripts using sequential barcoded hybridization, despite high spot density in images.
For multiple hypothesis testing in genomics and other large-scale data analyses, the independent hypothesis weighting (IHW) approach uses data-driven P-value weight assignment to improve power while controlling the false discovery rate.
DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide.
The open-source Single Cell Genotyper software addresses common artifacts in single-cell sequencing data in order to robustly infer clonal genotypes, enabling the study of tumor heterogeneity and evolution.
X-shift software allows automated mapping of phenotypic space from large mass cytometry data sets. X-shift and the new representation algorithm Divisive Marker Tree provide a rapid, deterministic approach to navigating complex cellular systems.
Flyception is a tracking and imaging system that enables the monitoring of brain activity in freely walking fruit flies, making the analysis of calcium dynamics possible in studies of neural mechanisms such as those that underlie social behaviors.
Conventional metrics for assessing antiproliferative drug effect have time-dependent biases that may skew results. The drug-induced proliferation rate can be used as an alternative metric for accurate and reproducible assessment of drug performance.