OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Biotechnology is 112. 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
PICRUSt2 for prediction of metagenome functions	2676
Visualizing and interpreting cancer genomics data via the Xena platform	2035
Generalizing RNA velocity to transient cell states through dynamical modeling	1463
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors	1299
A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction	1008
SignalP 6.0 predicts all five types of signal peptides using protein language models	945
COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis	865
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics	758
A unified catalog of 204,938 reference genomes from the human gut microbiome	618
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2	585
CheckV assesses the quality and completeness of metagenome-assembled viral genomes	566
Nanopore sequencing technology, bioinformatics and applications	559
Multiplex digital spatial profiling of proteins and RNA in fixed tissue	525
A lipidome atlas in MS-DIAL 4	445
A genomic catalog of Earth’s microbiomes	444
Single-cell RNA counting at allele and isoform resolution using Smart-seq3	397
Robust decomposition of cell type mixtures in spatial transcriptomics	379
Cell2location maps fine-grained cell types in spatial transcriptomics	365
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes	341
Spatial transcriptomics at subspot resolution with BayesSpace	331
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra	329
CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells	325
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes	323
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning	308
Fast and accurate protein structure search with Foldseek	303

Engineered pegRNAs improve prime editing efficiency	299
Wearable materials with embedded synthetic biology sensors for biomolecule detection	290
Glycosylase base editors enable C-to-A and C-to-G base changes	277
A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants	271
The clinical progress of mRNA vaccines and immunotherapies	269
Improved metagenome binning and assembly using deep variational autoencoders	261
Modular, efficient and constant-memory single-cell RNA-seq preprocessing	258
A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells	248
Differential abundance testing on single-cell data using k-nearest neighbor graphs	246
Large language models generate functional protein sequences across diverse families	245
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	243
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells	243
Mapping single-cell data to reference atlases by transfer learning	237
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues	232
A robust benchmark for detection of germline large deletions and insertions	230
Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing	226
Cell-free biosensors for rapid detection of water contaminants	221
Computational principles and challenges in single-cell data integration	220
Tracking COVID-19 with wastewater	220
Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children	219
A Python library for probabilistic analysis of single-cell omics data	218
Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells	214
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance	207
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale	205
Readfish enables targeted nanopore sequencing of gigabase-sized genomes	204
In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels	201
High-efficiency prime editing with optimized, paired pegRNAs in plants	191
Human heart-forming organoids recapitulate early heart and foregut development	185
Single-cell metabolic profiling of human cytotoxic T cells	180
Ultra-fast proteomics with Scanning SWATH	179
Long-term wireless streaming of neural recordings for circuit discovery and adaptive stimulation in individuals with Parkinson’s disease	178
Fully implantable and bioresorbable cardiac pacemakers without leads or batteries	177
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering	177
Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase	176
Predicting the efficiency of prime editing guide RNAs in human cells	169
Deep Visual Proteomics defines single-cell identity and heterogeneity	169
Deep diversification of an AAV capsid protein by machine learning	167
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing	167
Dual base editor catalyzes both cytosine and adenine base conversions in human cells	167
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding	165
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging	165
Mitochondrial copper depletion suppresses triple-negative breast cancer in mice	164
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4	163
Identification of antimicrobial peptides from the human gut microbiome using deep learning	160
The delivery challenge: fulfilling the promise of therapeutic genome editing	159
Detection of SARS-CoV-2 in nasal swabs using MALDI-MS	159
Dictionary learning for integrative, multimodal and scalable single-cell analysis	158
Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries	157
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED	156
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis	156

Integrative analysis of multimodal mass spectrometry data in MZmine 3	155
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA	155
Single-sequence protein structure prediction using a language model and deep learning	153
CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity	152
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling	152
Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy	151
Spatial components of molecular tissue biology	148
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing	146
Haplotype-resolved assembly of diploid genomes without parental data	146
Initialization is critical for preserving global data structure in both t-SNE and UMAP	145
Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells	143
Using deep learning to annotate the protein universe	140
A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae	139
Prediction of the sequence-specific cleavage activity of Cas9 variants	137
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore	137
High-dose AAV gene therapy deaths	137
Deep brain optogenetics without intracranial surgery	136
Base editors for simultaneous introduction of C-to-T and A-to-G mutations	136
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data	135
Spatially informed cell-type deconvolution for spatial transcriptomics	134
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer	127
Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus	125
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression	124
Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents	123
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads	123
Targeted, efficient sequence insertion and replacement in rice	122
Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases	121
Cell segmentation in imaging-based spatial transcriptomics	121
Unlocking the promise of mRNA therapeutics	120
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology	120
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19	119
Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning	119
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome	119
MaxDIA enables library-based and library-free data-independent acquisition proteomics	118
Efficient gene editing of human long-term hematopoietic stem cells validated by clonal tracking	118
Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size	115
Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradient	112