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Using clusterProfiler to characterize multiomics data
Using clusterProfiler to characterize multiomics data
With the advent of multiomics, software capable of multidimensional enrichment analysis has become increasingly crucial fo...
OBSERVE: guidelines for the refinement of rodent cancer models
OBSERVE: guidelines for the refinement of rodent cancer models
Existing guidelines on the preparation (Planning Research and Experimental Procedures on Animals: Recommendations for Exce...
Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method
Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activ...
A multi-glycomic platform for the analysis of food carbohydrates
A multi-glycomic platform for the analysis of food carbohydrates
Carbohydrates comprise the largest fraction of most diets and exert a profound impact on health. Components such as simple...
Observing isolated synaptic vesicle association and fusion ex vivo
Observing isolated synaptic vesicle association and fusion ex vivo
Here, we present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissu...
The OBSERVE guidelines provide refinement criteria for rodent oncology models
The OBSERVE guidelines provide refinement criteria for rodent oncology models
A consensus statement outlines the best practices to refine animal welfare in rodent models of cancer. Their adoption will...
Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test
Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test
The evolution and mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgent concerns as they pos...
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the depend...
Characterizing the structure of mouse behavior using Motion Sequencing
Characterizing the structure of mouse behavior using Motion Sequencing
Spontaneous mouse behavior is composed from repeatedly used modules of movement (e.g., rearing, running or grooming) that ...
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract
Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for pr...
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimenta...
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding
Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bact...
Electro-elution-based purification of covalent DNA–protein cross-links
Electro-elution-based purification of covalent DNA–protein cross-links
Covalent DNA–protein cross-links (DPCs) are pervasive DNA lesions that challenge genome stability and can be induced...
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification
Catalytic mechanism-based, light-activated traps have recently been developed to identify the substrates of cysteine or se...
Molecular recording using DNA Typewriter
Molecular recording using DNA Typewriter
Recording molecular information to genomic DNA is a powerful means of investigating topics ranging from multicellular deve...
Scanorama: integrating large and diverse single-cell transcriptomic datasets
Scanorama: integrating large and diverse single-cell transcriptomic datasets
Merging diverse single-cell RNA sequencing (scRNA-seq) data from numerous experiments, laboratories and technologies can u...
Author Correction: CRISPR-Cas9-based genome-wide screening of Toxoplasma gondii
Authors and AffiliationsWhitehead Institute for Biomedical Research, Cambridge, Massachusetts, USASaima M. Sidik, Diego Hu...
All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq
All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq
Neuronal pathways recruit large postsynaptic populations and maintain connections via distinct postsynaptic response types...
Real-time imaging of axonal membrane protein life cycles
Real-time imaging of axonal membrane protein life cycles
The construction of neuronal membranes is a dynamic process involving the biogenesis, vesicular packaging, transport, inse...
Morphological and molecular preservation through universal preparation of fresh-frozen tissue samples for multimodal imaging workflows
Morphological and molecular preservation through universal preparation of fresh-frozen tissue samples for multimodal imaging workflows
The landscape of tissue-based imaging modalities is constantly and rapidly evolving. While formalin-fixed, paraffin-embedd...
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development
Numerous toxins threaten humans, but specific antidotes are unavailable for most of them. Although CRISPR screening has ai...
Reproducible mass spectrometry data processing and compound annotation in MZmine 3
Reproducible mass spectrometry data processing and compound annotation in MZmine 3
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to in...
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy
Tutorial: design, production and testing of oncolytic viruses for cancer immunotherapy
Oncolytic viruses (OVs) represent a novel class of cancer immunotherapy agents that preferentially infect and kill cancer ...
ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets
ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets
Methods that measure the transcriptomic state of thousands of individual cells have transformed our understanding of cellu...
An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing
An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing
Technological advances in mass spectrometry and proteomics have made it possible to perform larger-scale and more-complex ...
Welcoming protocols.io
Springer Nature recently acquired protocols.io, an open-access platform for developing and sharing protocols, which will r...
High-throughput identification of gut microbiome-dependent metabolites
High-throughput identification of gut microbiome-dependent metabolites
A significant hurdle that has limited progress in microbiome science has been identifying and studying the diverse set of ...
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder
Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability a...
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries
These authors contributed equally: Sierra N. Henson, Evan A. Elko.These authors jointly supervised this work: John A. Alti...
A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials
A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials
Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in ...
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