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PCprophet: a framework for protein complex prediction and differential analysis using proteomic data

期刊: NATURE METHODS, 2021; 18 (5)

Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. A......

Universal Spectrum Identifier for mass spectra

期刊: NATURE METHODS, 2021; 18 (7)

Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to mass spectra deposited to public repositories or ......

Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution

期刊: NATURE METHODS, 2021; 18 (6)

The combination of adaptive optics with an improved isoSTED nanoscope allows imaging of cells and tissues with sub-50-nm isotropic resolution. Underst......

A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis

期刊: NATURE METHODS, 2021; 18 (8)

A protein expression atlas of transcription factors charted onto cell lineage maps of Caenorhabditiselegans development that uncovers mechanisms of sp......

Challenges in benchmarking metagenomic profilers

期刊: NATURE METHODS, 2021; 18 (6)

Many computational tools for metagenomic profiling have been developed, with different algorithms and features. This analysis shows that, when compari......

StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy

期刊: NATURE METHODS, 2021; 18 (8)

Precision mapping of glycans at structural and site-specific level is still one of the most challenging tasks in the glycobiology field. Here, we desc......

Metabolomic profiling of single enlarged lysosomes

期刊: NATURE METHODS, 2021; 18 (7)

Single-lysosome mass spectrometry (SLMS) integrates lysosomal patch-clamp recording and induced nanoESI/MS for concurrent metabolic and electrophysiol......

Molecular-scale axial localization by repetitive optical selective exposure

期刊: NATURE METHODS, 2021; 18 (4)

We introduce an axial localization with repetitive optical selective exposure (ROSE-Z) method for super-resolution imaging. By using an asymmetric opt......

Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions

期刊: NATURE METHODS, 2021; 18 (6)

This paper reports CoTECH, which couples chromatin binding enrichment with RNA sequencing for concurrent measurements of histone modification and tran......

The emerging landscape of single-molecule protein sequencing technologies

期刊: NATURE METHODS, 2021; 18 (6)

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explo......

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

期刊: NATURE METHODS, 2021; 18 (6)

This work presents NeoLoopFinder, a computational method, for identifying chromatin interactions of structurally rearranged genomes. NeoLoopFinder was......

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data

期刊: NATURE METHODS, 2021; 18 (9)

SnapHiC offers a computational tool for improving detection of chromatin loops from single-cell Hi-C data. Single-cell Hi-C (scHi-C) analysis has been......

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

期刊: NATURE METHODS, 2021; 18 (6)

We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in alpha beta/gamma delta T cells and B cells from RNA......

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