OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Protocols is 67. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data	867
The trRosetta server for fast and accurate protein structure prediction	395
CODEX multiplexed tissue imaging with DNA-conjugated antibodies	342
A practical guide to large-scale docking	274
Isolation and characterization of extracellular vesicle subpopulations from tissues	264
Metagenome analysis using the Kraken software suite	236
Proximity labeling in mammalian cells with TurboID and split-TurboID	230
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction	225
Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays	224
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data	208
Chromatin accessibility profiling by ATAC-seq	198
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures	186
Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking	167
Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles	162
Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development	158
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	158
Engineering SARS-CoV-2 using a reverse genetic system	153
Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation	149
Measuring DNA modifications with the comet assay: a compendium of protocols	145
Optimization of metabolomic data processing using NOREVA	141
High-yield, green and scalable methods for producing MOF-303 for water harvesting from desert air	138
Multiplexed single-cell proteomics using SCoPE2	138
3D bioprinted silk fibroin hydrogels for tissue engineering	137
High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method	136
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods	131

An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality	127
High-throughput cultivation and identification of bacteria from the plant root microbiota	123
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling	123
Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids	122
Engineered human blood–brain barrier microfluidic model for vascular permeability analyses	119
Intestinal organoid cocultures with microbes	118
Microfluidic integration of regeneratable electrochemical affinity-based biosensors for continual monitoring of organ-on-a-chip devices	113
Algorithmic assessment of cellular senescence in experimental and clinical specimens	113
A dynamic DNA tetrahedron framework for active targeting	109
Generation of insulin-producing pancreatic β cells from multiple human stem cell lines	109
Precision genome editing using cytosine and adenine base editors in mammalian cells	109
Rolling circle amplification (RCA)-based DNA hydrogel	105
Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases	104
RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19	101
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing	99
Microtiter plate assays to assess antibiofilm activity against bacteria	98
Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	97
3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert	94
Analyzing high-dimensional cytometry data using FlowSOM	93
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)	92
The normative modeling framework for computational psychiatry	90
Establishment of human fetal hepatocyte organoids and CRISPR–Cas9-based gene knockin and knockout in organoid cultures from human liver	87
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	87
Bioconjugates of photon-upconversion nanoparticles for cancer biomarker detection and imaging	87
Generic acquisition protocol for quantitative MRI of the spinal cord	78
Engineering brain assembloids to interrogate human neural circuits	77
Comprehensive isolation of extracellular vesicles and nanoparticles	75
Detection of aberrant gene expression events in RNA sequencing data	75
Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages	73
Genetic circuit design automation with Cello 2.0	72
Measuring the elastic modulus of soft culture surfaces and three-dimensional hydrogels using atomic force microscopy	72
Fabrication, characterization and applications of graphene electronic tattoos	71
Tools for experimental and computational analyses of off-target editing by programmable nucleases	70
A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei	70
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport	69
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome	69
Nanocarriers based on bacterial membrane materials for cancer vaccine delivery	69
Digital postprocessing and image segmentation for objective analysis of colorimetric reactions	68
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	67
Transplantation of intestinal organoids into a mouse model of colitis	67
Antigen retrieval and clearing for whole-organ immunofluorescence by FLASH	67
Whole-brain functional ultrasound imaging in awake head-fixed mice	67