OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Biotechnology is 114. 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
PICRUSt2 for prediction of metagenome functions	2567
Visualizing and interpreting cancer genomics data via the Xena platform	1968
CRISPR–Cas12-based detection of SARS-CoV-2	1811
Generalizing RNA velocity to transient cell states through dynamical modeling	1417
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors	1257
A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction	995
SignalP 6.0 predicts all five types of signal peptides using protein language models	896
COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis	850
A complete domain-to-species taxonomy for Bacteria and Archaea	833
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics	747
A unified catalog of 204,938 reference genomes from the human gut microbiome	603
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2	561
CheckV assesses the quality and completeness of metagenome-assembled viral genomes	544
Nanopore sequencing technology, bioinformatics and applications	520
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods	512
Multiplex digital spatial profiling of proteins and RNA in fixed tissue	504
A genomic catalog of Earth’s microbiomes	433
A lipidome atlas in MS-DIAL 4	425
Single-cell RNA counting at allele and isoform resolution using Smart-seq3	389
Robust decomposition of cell type mixtures in spatial transcriptomics	350
Cell2location maps fine-grained cell types in spatial transcriptomics	339
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes	333
CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells	315
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra	313
Spatial transcriptomics at subspot resolution with BayesSpace	312

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects	305
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes	302
Directed evolution of adenine base editors with increased activity and therapeutic application	300
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning	292
Engineered pegRNAs improve prime editing efficiency	282
Wearable materials with embedded synthetic biology sensors for biomolecule detection	282
Glycosylase base editors enable C-to-A and C-to-G base changes	268
A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants	264
Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening	262
Fast and accurate protein structure search with Foldseek	259
The clinical progress of mRNA vaccines and immunotherapies	255
Modular, efficient and constant-memory single-cell RNA-seq preprocessing	250
Improved metagenome binning and assembly using deep variational autoencoders	247
A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells	242
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells	236
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	233
Differential abundance testing on single-cell data using k-nearest neighbor graphs	233
Mapping single-cell data to reference atlases by transfer learning	229
A robust benchmark for detection of germline large deletions and insertions	225
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues	222
Large language models generate functional protein sequences across diverse families	219
Efficient production of male Wolbachia-infected Aedes aegypti mosquitoes enables large-scale suppression of wild populations	218
Tracking COVID-19 with wastewater	218
Computational principles and challenges in single-cell data integration	216
Cell-free biosensors for rapid detection of water contaminants	214
Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing	211
Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children	208
Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells	207
A Python library for probabilistic analysis of single-cell omics data	207
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance	206
Readfish enables targeted nanopore sequencing of gigabase-sized genomes	197
In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels	197
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale	195
High-efficiency prime editing with optimized, paired pegRNAs in plants	185
Human heart-forming organoids recapitulate early heart and foregut development	178
Single-cell metabolic profiling of human cytotoxic T cells	177
Morphing electronics enable neuromodulation in growing tissue	174
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering	174
Ultra-fast proteomics with Scanning SWATH	173
Long-term wireless streaming of neural recordings for circuit discovery and adaptive stimulation in individuals with Parkinson’s disease	173
Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase	168
Deep diversification of an AAV capsid protein by machine learning	165
Fully implantable and bioresorbable cardiac pacemakers without leads or batteries	165
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing	164
Predicting the efficiency of prime editing guide RNAs in human cells	162
Dual base editor catalyzes both cytosine and adenine base conversions in human cells	162
Deep Visual Proteomics defines single-cell identity and heterogeneity	162
Mitochondrial copper depletion suppresses triple-negative breast cancer in mice	160
Detection of SARS-CoV-2 in nasal swabs using MALDI-MS	157
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding	156

The delivery challenge: fulfilling the promise of therapeutic genome editing	155
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED	154
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis	151
CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity	148
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling	147
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA	147
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging	146
Spatial components of molecular tissue biology	144
Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries	144
Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy	143
Identification of antimicrobial peptides from the human gut microbiome using deep learning	143
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing	141
A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae	140
Single-sequence protein structure prediction using a language model and deep learning	140
Initialization is critical for preserving global data structure in both t-SNE and UMAP	139
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4	139
Integrative analysis of multimodal mass spectrometry data in MZmine 3	136
Base editors for simultaneous introduction of C-to-T and A-to-G mutations	135
Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells	134
High-dose AAV gene therapy deaths	134
Prediction of the sequence-specific cleavage activity of Cas9 variants	133
Haplotype-resolved assembly of diploid genomes without parental data	131
Deep brain optogenetics without intracranial surgery	131
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore	130
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data	128
Using deep learning to annotate the protein universe	127
Spatially informed cell-type deconvolution for spatial transcriptomics	123
Design and analysis of CRISPR–Cas experiments	122
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer	121
Targeted, efficient sequence insertion and replacement in rice	121
Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents	121
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression	120
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology	120
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads	120
Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus	119
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19	117
Dictionary learning for integrative, multimodal and scalable single-cell analysis	117
Cell segmentation in imaging-based spatial transcriptomics	116
Efficient gene editing of human long-term hematopoietic stem cells validated by clonal tracking	115
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome	114