OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Biotechnology is 110. 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
SignalP 6.0 predicts all five types of signal peptides using protein language models	1309
Nanopore sequencing technology, bioinformatics and applications	824
CheckV assesses the quality and completeness of metagenome-assembled viral genomes	777
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2	759
Dictionary learning for integrative, multimodal and scalable single-cell analysis	679
Fast and accurate protein structure search with Foldseek	653
Cell2location maps fine-grained cell types in spatial transcriptomics	550
Robust decomposition of cell type mixtures in spatial transcriptomics	547
A genomic catalog of Earth’s microbiomes	523
Spatial transcriptomics at subspot resolution with BayesSpace	493
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning	438
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes	431
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra	408
Large language models generate functional protein sequences across diverse families	405
Engineered pegRNAs improve prime editing efficiency	392
The clinical progress of mRNA vaccines and immunotherapies	377
Differential abundance testing on single-cell data using k-nearest neighbor graphs	354
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4	334
Wearable materials with embedded synthetic biology sensors for biomolecule detection	333
A Python library for probabilistic analysis of single-cell omics data	330
Improved metagenome binning and assembly using deep variational autoencoders	329
Integrative analysis of multimodal mass spectrometry data in MZmine 3	325
Mapping single-cell data to reference atlases by transfer learning	308
Modular, efficient and constant-memory single-cell RNA-seq preprocessing	306
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	295

High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging	292
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells	290
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues	288
A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells	279
Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing	276
Computational principles and challenges in single-cell data integration	275
Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells	267
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale	261
Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children	248
Readfish enables targeted nanopore sequencing of gigabase-sized genomes	243
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding	238
Haplotype-resolved assembly of diploid genomes without parental data	235
Deep Visual Proteomics defines single-cell identity and heterogeneity	230
Identification of antimicrobial peptides from the human gut microbiome using deep learning	228
In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels	226
High-efficiency prime editing with optimized, paired pegRNAs in plants	221
Human heart-forming organoids recapitulate early heart and foregut development	219
Spatially informed cell-type deconvolution for spatial transcriptomics	218
Single-sequence protein structure prediction using a language model and deep learning	215
Long-term wireless streaming of neural recordings for circuit discovery and adaptive stimulation in individuals with Parkinson’s disease	215
Unlocking the promise of mRNA therapeutics	212
Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells	209
Fully implantable and bioresorbable cardiac pacemakers without leads or batteries	208
Ultra-fast proteomics with Scanning SWATH	205
Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases	202
Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing	198
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data	198
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis	198
Biopharmaceutical benchmarks 2022	197
Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries	194
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering	193
Deep diversification of an AAV capsid protein by machine learning	192
Spatial components of molecular tissue biology	185
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA	181
Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy	179
Cell segmentation in imaging-based spatial transcriptomics	178
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing	176
Initialization is critical for preserving global data structure in both t-SNE and UMAP	176
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED	175
Using deep learning to annotate the protein universe	174
Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size	169
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore	168
Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus	162
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome	158
Identification of mobile genetic elements with geNomad	158
MaxDIA enables library-based and library-free data-independent acquisition proteomics	157
The expanding vistas of spatial transcriptomics	151
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer	149
Efficient evolution of human antibodies from general protein language models	147
Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI	147

RNA demethylation increases the yield and biomass of rice and potato plants in field trials	145
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression	143
Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents	142
Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning	142
Improved prediction of immune checkpoint blockade efficacy across multiple cancer types	142
Precise genomic deletions using paired prime editing	138
A knowledge graph to interpret clinical proteomics data	137
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology	137
Telomere-to-telomere assembly of diploid chromosomes with Verkko	137
CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells	136
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads	136
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities	134
A highly photostable and bright green fluorescent protein	133
Increasing the throughput of sensitive proteomics by plexDIA	132
Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement	131
Learning protein fitness models from evolutionary and assay-labeled data	130
Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale	129
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19	128
A comprehensive library of human transcription factors for cell fate engineering	127
Chromosome-scale, haplotype-resolved assembly of human genomes	127
Quantifying the effect of experimental perturbations at single-cell resolution	124
Generation of paternal haploids in wheat by genome editing of the centromeric histone CENH3	124
A programmable encapsulation system improves delivery of therapeutic bacteria in mice	119
Engineering circular RNA for enhanced protein production	118
Variability within rare cell states enables multiple paths toward drug resistance	118
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution	117
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long	117
High-confidence structural annotation of metabolites absent from spectral libraries	116
Curated variation benchmarks for challenging medically relevant autosomal genes	116
An engineered prime editor with enhanced editing efficiency in plants	116
Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage	113
Standardized annotation of translated open reading frames	113
The Organoid Cell Atlas	111
High-throughput total RNA sequencing in single cells using VASA-seq	110
Identification of tumor antigens with immunopeptidomics	110