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 2020-04-01 to 2024-04-01.)

Article	Citations
Tutorial: a guide to performing polygenic risk score analyses	893
The HDOCK server for integrated protein–protein docking	639
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data	571
A scalable SCENIC workflow for single-cell gene regulatory network analysis	495
Reproducible molecular networking of untargeted mass spectrometry data using GNPS	338
Establishment of patient-derived cancer organoids for drug-screening applications	310
The trRosetta server for fast and accurate protein structure prediction	293
Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay	287
Tutorial: design and fabrication of nanoparticle-based lateral-flow immunoassays	238
CODEX multiplexed tissue imaging with DNA-conjugated antibodies	226
Design, fabrication and applications of tetrahedral DNA nanostructure-based multifunctional complexes in drug delivery and biomedical treatment	212
A practical guide to large-scale docking	209
Isolation and characterization of extracellular vesicle subpopulations from tissues	194
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays	192
Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results	190
Efficient low-cost chromatin profiling with CUT&Tag	178
Tutorial: multivariate classification for vibrational spectroscopy in biological samples	177
Proximity labeling in mammalian cells with TurboID and split-TurboID	169
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data	167
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2	145
Tutorial: guidelines for standardized performance tests for electrodes intended for neural interfaces and bioelectronics	142
Engineering SARS-CoV-2 using a reverse genetic system	131
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures	131
Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry	129
Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development	125

Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles	120
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking	116
Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation	115
Optimization of metabolomic data processing using NOREVA	113
Metagenome analysis using the Kraken software suite	112
Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography	112
Standardized bacteriophage purification for personalized phage therapy	110
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction	108
Chromatin accessibility profiling by ATAC-seq	104
High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method	104
Multiplexed single-cell proteomics using SCoPE2	104
Generation of synthetic nanobodies against delicate proteins	103
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods	99
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	98
Intestinal organoid cocultures with microbes	97
3D bioprinted silk fibroin hydrogels for tissue engineering	97
Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids	96
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	94
High-throughput cultivation and identification of bacteria from the plant root microbiota	92
Precision genome editing using cytosine and adenine base editors in mammalian cells	92
Jointly defining cell types from multiple single-cell datasets using LIGER	91
Ligand binding free-energy calculations with funnel metadynamics	91
Algorithmic assessment of cellular senescence in experimental and clinical specimens	90
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	89
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality	89
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing	88
A standardized social preference protocol for measuring social deficits in mouse models of autism	86
RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19	85
Establishment and differentiation of long-term trophoblast organoid cultures from the human placenta	84
High-yield, green and scalable methods for producing MOF-303 for water harvesting from desert air	84
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	83
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	81
Measuring DNA modifications with the comet assay: a compendium of protocols	80
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	80
Microfluidic integration of regeneratable electrochemical affinity-based biosensors for continual monitoring of organ-on-a-chip devices	79
Analyzing high-dimensional cytometry data using FlowSOM	78
Analysis of task-based functional MRI data preprocessed with fMRIPrep	75
Cellular thermal shift assay for the identification of drug–target interactions in the Plasmodium falciparum proteome	75
Generation of insulin-producing pancreatic β cells from multiple human stem cell lines	73
A dynamic DNA tetrahedron framework for active targeting	73
Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks	72
Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver	71
Rolling circle amplification (RCA)-based DNA hydrogel	70
Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap	70
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	69
Identifying unknown metabolites using NMR-based metabolic profiling techniques	69