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Empowering materials science with VASPKIT: a toolkit for enhanced simulation and analysis
Empowering materials science with VASPKIT: a toolkit for enhanced simulation and analysis
Driven by rapid advances in high-performance supercomputing, computational materials science has emerged as a powerful app...
Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR
Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR
Immunoglobulin gene analysis provides fundamental insight into B cell receptor structure and function. In B cell tumors, i...
Thioether-mediated protein ubiquitination in constructing affinity- and activity-based ubiquitinated protein probes
Thioether-mediated protein ubiquitination in constructing affinity- and activity-based ubiquitinated protein probes
Protein ubiquitination, a critical regulatory mechanism and post-translational modification in eukaryotic cells, involves ...
Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq
Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq
Formalin-fixed paraffin-embedded (FFPE) samples represent a vast and valuable resource of patient material, often linked t...
Establishment of human expanded potential stem cell lines via preimplantation embryo cultivation and somatic cell reprogramming
Establishment of human expanded potential stem cell lines via preimplantation embryo cultivation and somatic cell reprogramming
We previously reported the derivation of expanded potential stem cells (EPSCs) by modulating signaling pathways involved i...
Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST
Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST
The characterization of antimicrobial susceptibility and other relevant phenotypes in large collections of microbial isola...
Achieving transient and reversible optical transparency in live mice with tartrazine
Achieving transient and reversible optical transparency in live mice with tartrazine
Optical imaging provides real-time visualization of tissues and cells at high spatial and temporal resolutions through tec...
Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery
Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery
Genomes and proteomes constitute a rich reservoir of molecular diversity. However, they have remained underexplored becaus...
Design, performance, processing, and validation of a pooled CRISPR perturbation screen for bacterial toxins
Design, performance, processing, and validation of a pooled CRISPR perturbation screen for bacterial toxins
Unbiased forward genetic screens have been extensively employed in biological research to elucidate functional genomics. I...
Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells
Life-long functional regeneration of in vivo airway epithelium by the engraftment of airway basal stem cells
Durable and functional regeneration of the airway epithelium in vivo with transplanted stem cells has the potential to rec...
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes
Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes
Described herein is a protocol for producing a synthetic extracellular matrix that can be modified in situ during three-di...
Using the Chemotion repository to deposit and access FAIR research data for chemistry experiments
Using the Chemotion repository to deposit and access FAIR research data for chemistry experiments
We are thankful for the support of the Ministry of Science, Research and the Arts of Baden-Württemberg (MWK Baden-Württemb...
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units
Versatile synthesis of uniform mesoporous superparticles from stable monomicelle units
Superstructures with architectural complexity and unique functionalities are promising for a variety of practical applicat...
High-throughput glycosaminoglycan extraction and UHPLC-MS/MS quantification in human biofluids
High-throughput glycosaminoglycan extraction and UHPLC-MS/MS quantification in human biofluids
Glycosaminoglycans (GAGs) are linear, unbranched heteropolysaccharides whose structural complexity determines their functi...
RNA sample optimization for cryo-EM analysis
RNA sample optimization for cryo-EM analysis
RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily de...
Host circuit engagement of human cortical organoids transplanted in rodents
Host circuit engagement of human cortical organoids transplanted in rodents
Human neural organoids represent promising models for studying neural function; however, organoids grown in vitro lack cer...
High-resolution topographic surveying and change detection with the iPhone LiDAR
High-resolution topographic surveying and change detection with the iPhone LiDAR
This paper introduces a comprehensive protocol leveraging open-access techniques to create small- to medium-scale 3D repre...
A network control theory pipeline for studying the dynamics of the structural connectome
A network control theory pipeline for studying the dynamics of the structural connectome
Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains the dy...
Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq
Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq
Transcription factors (TFs) bind specific DNA sequences to regulate transcription. Apart from DNA sequences, local factors...
Flux synthesis of two-dimensional covalent organic frameworks
Flux synthesis of two-dimensional covalent organic frameworks
Covalent organic frameworks (COFs) are crystalline porous polymers constructed from organic building blocks into ordered t...
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP
Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivi...
Optimizing the standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes
Optimizing the standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes
Nanozymes are nanomaterials with enzyme-like catalytic properties. They are attractive reagents because they do not have t...
Proximity sequencing for the detection of mRNA, extracellular proteins and extracellular protein complexes in single cells
Proximity sequencing for the detection of mRNA, extracellular proteins and extracellular protein complexes in single cells
Complex cellular functions occur via the coordinated formation and dissociation of protein complexes. Functions such as th...
Light-mediated intracellular polymerization
Light-mediated intracellular polymerization
The synthesis of synthetic intracellular polymers offers groundbreaking possibilities in cellular biology and medical rese...
Generating human bone marrow organoids for disease modeling and drug discovery
Generating human bone marrow organoids for disease modeling and drug discovery
The bone marrow supports and regulates hematopoiesis, responding to physiological requirements for blood cell production o...
A practical guide for the preparation of C1-labeled α-amino acids using aldehyde catalysis with isotopically labeled CO2
A practical guide for the preparation of C1-labeled α-amino acids using aldehyde catalysis with isotopically labeled CO2
Isotopically carbon-labeled α-amino acids are valuable synthetic targets that are increasingly needed in pharmacology...
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks
A promising cell-therapy approach for heart failure aims at differentiating human pluripotent stem cells (hPSCs) into func...
Packaging and containerization of computational methods
Packaging and containerization of computational methods
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts ...
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins
Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution unders...
Control of DNA replication in vitro using a reversible replication barrier
Control of DNA replication in vitro using a reversible replication barrier
A major obstacle to studying DNA replication is that it involves asynchronous and highly delocalized events. A reversible ...
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