OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Protocols is 69. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)

Article	Citations
Tutorial: a guide to performing polygenic risk score analyses	919
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data	610
A scalable SCENIC workflow for single-cell gene regulatory network analysis	519
Reproducible molecular networking of untargeted mass spectrometry data using GNPS	354
Establishment of patient-derived cancer organoids for drug-screening applications	315
The trRosetta server for fast and accurate protein structure prediction	308
Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay	295
Tutorial: design and fabrication of nanoparticle-based lateral-flow immunoassays	246
CODEX multiplexed tissue imaging with DNA-conjugated antibodies	239
A practical guide to large-scale docking	222
Design, fabrication and applications of tetrahedral DNA nanostructure-based multifunctional complexes in drug delivery and biomedical treatment	221
Isolation and characterization of extracellular vesicle subpopulations from tissues	204
Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results	198
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays	197
Efficient low-cost chromatin profiling with CUT&Tag	186
Tutorial: multivariate classification for vibrational spectroscopy in biological samples	185
Proximity labeling in mammalian cells with TurboID and split-TurboID	180
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data	177
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2	154
Tutorial: guidelines for standardized performance tests for electrodes intended for neural interfaces and bioelectronics	147
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures	139
Metagenome analysis using the Kraken software suite	136
Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry	134
Engineering SARS-CoV-2 using a reverse genetic system	134
Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development	127

Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles	125
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking	123
Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation	122
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction	118
Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography	116
Optimization of metabolomic data processing using NOREVA	114
Standardized bacteriophage purification for personalized phage therapy	112
Chromatin accessibility profiling by ATAC-seq	112
Multiplexed single-cell proteomics using SCoPE2	110
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	109
High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method	107
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods	105
3D bioprinted silk fibroin hydrogels for tissue engineering	104
Intestinal organoid cocultures with microbes	101
Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA	101
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality	99
Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids	99
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	98
High-throughput cultivation and identification of bacteria from the plant root microbiota	96
Precision genome editing using cytosine and adenine base editors in mammalian cells	96
Algorithmic assessment of cellular senescence in experimental and clinical specimens	95
Ligand binding free-energy calculations with funnel metadynamics	93
Jointly defining cell types from multiple single-cell datasets using LIGER	92
A standardized social preference protocol for measuring social deficits in mouse models of autism	91
High-yield, green and scalable methods for producing MOF-303 for water harvesting from desert air	90
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing	89
RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19	89
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	87
Measuring DNA modifications with the comet assay: a compendium of protocols	86
Establishment and differentiation of long-term trophoblast organoid cultures from the human placenta	85
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	83
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	83
Analysis of task-based functional MRI data preprocessed with fMRIPrep	83
Microfluidic integration of regeneratable electrochemical affinity-based biosensors for continual monitoring of organ-on-a-chip devices	83
Analyzing high-dimensional cytometry data using FlowSOM	81
Rolling circle amplification (RCA)-based DNA hydrogel	77
Generation of insulin-producing pancreatic β cells from multiple human stem cell lines	77
A dynamic DNA tetrahedron framework for active targeting	75
Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap	74
Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks	73
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	72
Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver	72
3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert	71
Identifying unknown metabolites using NMR-based metabolic profiling techniques	70