Nature Biotechnology

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
Wearable materials with embedded synthetic biology sensors for biomolecule detection	282
Engineered pegRNAs improve prime editing efficiency	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
Differential abundance testing on single-cell data using k-nearest neighbor graphs	233
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	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
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering	174
Morphing electronics enable neuromodulation in growing tissue	174
Long-term wireless streaming of neural recordings for circuit discovery and adaptive stimulation in individuals with Parkinson’s disease	173
Ultra-fast proteomics with Scanning SWATH	173
Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase	168
Fully implantable and bioresorbable cardiac pacemakers without leads or batteries	165
Deep diversification of an AAV capsid protein by machine learning	165
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing	164
Dual base editor catalyzes both cytosine and adenine base conversions in human cells	162
Deep Visual Proteomics defines single-cell identity and heterogeneity	162
Predicting the efficiency of prime editing guide RNAs in human cells	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
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA	147
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling	147
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging	146
Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries	144
Spatial components of molecular tissue biology	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
Single-sequence protein structure prediction using a language model and deep learning	140
A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae	140
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4	139
Initialization is critical for preserving global data structure in both t-SNE and UMAP	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
Deep brain optogenetics without intracranial surgery	131
Haplotype-resolved assembly of diploid genomes without parental data	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
Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents	121
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer	121
Targeted, efficient sequence insertion and replacement in rice	121
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads	120
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
Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus	119
Dictionary learning for integrative, multimodal and scalable single-cell analysis	117
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19	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
MaxDIA enables library-based and library-free data-independent acquisition proteomics	113
Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning	113
Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size	111
Developing therapeutic monoclonal antibodies at pandemic pace	111
Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases	111
Improved prediction of immune checkpoint blockade efficacy across multiple cancer types	108
Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradient	108
Unlocking the promise of mRNA therapeutics	108
CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells	105
Precise genomic deletions using paired prime editing	105
A comprehensive library of human transcription factors for cell fate engineering	105
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci	104
Chromosome-scale, haplotype-resolved assembly of human genomes	104
Generation of paternal haploids in wheat by genome editing of the centromeric histone CENH3	103
RNA demethylation increases the yield and biomass of rice and potato plants in field trials	103
Viral contamination in biologic manufacture and implications for emerging therapies	102
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long	102
Implications of antibody-dependent enhancement of infection for SARS-CoV-2 countermeasures	100
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities	99
A knowledge graph to interpret clinical proteomics data	98
Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection	96
Quantifying the effect of experimental perturbations at single-cell resolution	96
Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement	96
Optimization of AsCas12a for combinatorial genetic screens in human cells	95
The Organoid Cell Atlas	95
Rapid image deconvolution and multiview fusion for optical microscopy	95
Identification of tumor antigens with immunopeptidomics	94
Biopharmaceutical benchmarks 2022	94
A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat	94
Cell type prioritization in single-cell data	93
Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing	93
COVID-19 antibodies on trial	93
High-confidence structural annotation of metabolites absent from spectral libraries	92
Variability within rare cell states enables multiple paths toward drug resistance	92
Learning protein fitness models from evolutionary and assay-labeled data	91
Targeting herpes simplex virus with CRISPR–Cas9 cures herpetic stromal keratitis in mice	90
A programmable encapsulation system improves delivery of therapeutic bacteria in mice	89
Plants with genetically encoded autoluminescence	88
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL	88
Increasing the throughput of sensitive proteomics by plexDIA	88

Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy	88
Standardized annotation of translated open reading frames	88
An engineered ScCas9 with broad PAM range and high specificity and activity	87
Sci-fate characterizes the dynamics of gene expression in single cells	87
An engineered prime editor with enhanced editing efficiency in plants	86
Deletion and replacement of long genomic sequences using prime editing	85
A near-infrared genetically encoded calcium indicator for in vivo imaging	85
Compact RNA editors with small Cas13 proteins	82
A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity	82
Curated variation benchmarks for challenging medically relevant autosomal genes	82
Noncanonical open reading frames encode functional proteins essential for cancer cell survival	82
The expanding vistas of spatial transcriptomics	82
Saturation variant interpretation using CRISPR prime editing	82
The PROTAC gold rush	81
CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA	80
Genome-wide specificity of prime editors in plants	80
Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale	80
Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI	79
Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19	79
Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates	79
Monitoring deep-tissue oxygenation with a millimeter-scale ultrasonic implant	78
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases	78
Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage	78
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin	78
Engineering circular RNA for enhanced protein production	77
Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases	77
DestVI identifies continuums of cell types in spatial transcriptomics data	77
Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics	77
GABA-enriched tomato is first CRISPR-edited food to enter market	76
Single-cell immunology of SARS-CoV-2 infection	76
Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID	76
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data	75
Send in the senolytics	75
Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood–brain barrier and knock down genes in the rodent CNS	74
Spatial charting of single-cell transcriptomes in tissues	74
Telomere-to-telomere assembly of diploid chromosomes with Verkko	74
The RNA Atlas expands the catalog of human non-coding RNAs	73
High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails	72
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning	72
Assessing single-cell transcriptomic variability through density-preserving data visualization	72
Sequence-specific prediction of the efficiencies of adenine and cytosine base editors	72
A split prime editor with untethered reverse transcriptase and circular RNA template	72
Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis	71
Remote smartphone monitoring of Parkinson’s disease and individual response to therapy	71
Multiscale and integrative single-cell Hi-C analysis with Higashi	71
A fluorescent sensor for spatiotemporally resolved imaging of endocannabinoid dynamics in vivo	71
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker	70
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin	70
A highly photostable and bright green fluorescent protein	70
Overcoming barriers to early disease intervention	69
High-throughput total RNA sequencing in single cells using VASA-seq	69
Determination of isoform-specific RNA structure with nanopore long reads	69
Engineered off-the-shelf therapeutic T cells resist host immune rejection	69
Transplantation of a human liver following 3 days of ex situ normothermic preservation	68
Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs	67
Prediction of drug efficacy from transcriptional profiles with deep learning	67
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study	67
The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing	67
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution	67
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems	66
High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects	66
Generation of pancreatic β cells from CD177+ anterior definitive endoderm	66
Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks	65
Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase–tRNA pairs	64
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing	64
Identification of highly selective covalent inhibitors by phage display	63
Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo	63
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)	63
Plug-and-play control of a brain–computer interface through neural map stabilization	63
A humanized mouse model of chronic COVID-19	63
Bioinstructive implantable scaffolds for rapid in vivo manufacture and release of CAR-T cells	63
Oral delivery of systemic monoclonal antibodies, peptides and small molecules using gastric auto-injectors	62
Efficient evolution of human antibodies from general protein language models	62
Single-cell measurement of higher-order 3D genome organization with scSPRITE	61
Inferring gene expression from cell-free DNA fragmentation profiles	61
Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase	60
Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters	60
Could mutations of SARS-CoV-2 suppress diagnostic detection?	60
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine	59
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics	59
A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples	59
A comprehensive SARS-CoV-2–human protein–protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets	59
Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins	58
High-throughput mapping of a whole rhesus monkey brain at micrometer resolution	58
Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes	58
Animal-free alternatives and the antibody iceberg	57
A network analysis of COVID-19 mRNA vaccine patents	56
Super-resolved spatial transcriptomics by deep data fusion	56
Functional single-cell genomics of human cytomegalovirus infection	55
Uncovering the mode of action of engineered T cells in patient cancer organoids	55
Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing	55
Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq	55
A unified haplotype-based method for accurate and comprehensive variant calling	55
A small and highly sensitive red/far-red optogenetic switch for applications in mammals	54
Artificial intelligence, drug repurposing and peer review	54