Nature Biotechnology

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
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells	243
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains	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
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering	177
Fully implantable and bioresorbable cardiac pacemakers without leads or batteries	177
Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase	176
Deep Visual Proteomics defines single-cell identity and heterogeneity	169
Predicting the efficiency of prime editing guide RNAs in human cells	169
Dual base editor catalyzes both cytosine and adenine base conversions in human cells	167
Deep diversification of an AAV capsid protein by machine learning	167
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing	167
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging	165
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding	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
Detection of SARS-CoV-2 in nasal swabs using MALDI-MS	159
The delivery challenge: fulfilling the promise of therapeutic genome editing	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
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis	156
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED	156

Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA	155
Integrative analysis of multimodal mass spectrometry data in MZmine 3	155
Single-sequence protein structure prediction using a language model and deep learning	153
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling	152
CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity	152
Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy	151
Spatial components of molecular tissue biology	148
Haplotype-resolved assembly of diploid genomes without parental data	146
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing	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
High-dose AAV gene therapy deaths	137
Prediction of the sequence-specific cleavage activity of Cas9 variants	137
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore	137
Base editors for simultaneous introduction of C-to-T and A-to-G mutations	136
Deep brain optogenetics without intracranial surgery	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
Precise genomic deletions using paired prime editing	111
A comprehensive library of human transcription factors for cell fate engineering	110
Improved prediction of immune checkpoint blockade efficacy across multiple cancer types	110
Chromosome-scale, haplotype-resolved assembly of human genomes	109
Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing	109
CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells	108
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities	108
RNA demethylation increases the yield and biomass of rice and potato plants in field trials	107
Generation of paternal haploids in wheat by genome editing of the centromeric histone CENH3	107
Biopharmaceutical benchmarks 2022	107
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci	106
A knowledge graph to interpret clinical proteomics data	104
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long	103
Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement	101
Implications of antibody-dependent enhancement of infection for SARS-CoV-2 countermeasures	100
High-confidence structural annotation of metabolites absent from spectral libraries	100
Cell type prioritization in single-cell data	100
Optimization of AsCas12a for combinatorial genetic screens in human cells	100
Variability within rare cell states enables multiple paths toward drug resistance	99
Rapid image deconvolution and multiview fusion for optical microscopy	99
Quantifying the effect of experimental perturbations at single-cell resolution	98
Identification of tumor antigens with immunopeptidomics	97
Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection	96
COVID-19 antibodies on trial	96
The Organoid Cell Atlas	96
A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat	96
Increasing the throughput of sensitive proteomics by plexDIA	95
Learning protein fitness models from evolutionary and assay-labeled data	94
The expanding vistas of spatial transcriptomics	92
Targeting herpes simplex virus with CRISPR–Cas9 cures herpetic stromal keratitis in mice	91
Standardized annotation of translated open reading frames	91
Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI	91
Deletion and replacement of long genomic sequences using prime editing	91
Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy	91
A programmable encapsulation system improves delivery of therapeutic bacteria in mice	91
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL	91
An engineered prime editor with enhanced editing efficiency in plants	90
Saturation variant interpretation using CRISPR prime editing	90
An engineered ScCas9 with broad PAM range and high specificity and activity	89
Curated variation benchmarks for challenging medically relevant autosomal genes	88
A near-infrared genetically encoded calcium indicator for in vivo imaging	88
Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates	87
Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale	87

Compact RNA editors with small Cas13 proteins	86
DestVI identifies continuums of cell types in spatial transcriptomics data	85
A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity	85
Noncanonical open reading frames encode functional proteins essential for cancer cell survival	84
Telomere-to-telomere assembly of diploid chromosomes with Verkko	84
CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA	84
The PROTAC gold rush	84
Engineering circular RNA for enhanced protein production	81
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases	81
Genome-wide specificity of prime editors in plants	80
Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage	80
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data	80
Single-cell immunology of SARS-CoV-2 infection	80
GABA-enriched tomato is first CRISPR-edited food to enter market	79
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin	79
Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19	79
High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails	78
Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics	78
A split prime editor with untethered reverse transcriptase and circular RNA template	78
Monitoring deep-tissue oxygenation with a millimeter-scale ultrasonic implant	78
Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases	78
Efficient evolution of human antibodies from general protein language models	77
Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID	76
Send in the senolytics	76
Multiscale and integrative single-cell Hi-C analysis with Higashi	76
Sequence-specific prediction of the efficiencies of adenine and cytosine base editors	76
Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood–brain barrier and knock down genes in the rodent CNS	75
Assessing single-cell transcriptomic variability through density-preserving data visualization	75
Spatial charting of single-cell transcriptomes in tissues	75
A fluorescent sensor for spatiotemporally resolved imaging of endocannabinoid dynamics in vivo	75
The RNA Atlas expands the catalog of human non-coding RNAs	75
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning	74
A highly photostable and bright green fluorescent protein	73
Overcoming barriers to early disease intervention	73
Remote smartphone monitoring of Parkinson’s disease and individual response to therapy	73
High-throughput total RNA sequencing in single cells using VASA-seq	72
Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis	71
Determination of isoform-specific RNA structure with nanopore long reads	71
Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs	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
High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects	70
Bioinstructive implantable scaffolds for rapid in vivo manufacture and release of CAR-T cells	70
Engineered off-the-shelf therapeutic T cells resist host immune rejection	70
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution	70
Transplantation of a human liver following 3 days of ex situ normothermic preservation	70
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study	69
Prediction of drug efficacy from transcriptional profiles with deep learning	69
Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks	69
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems	67
The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing	67
A humanized mouse model of chronic COVID-19	66
Inferring gene expression from cell-free DNA fragmentation profiles	66
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing	66
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)	66
Plug-and-play control of a brain–computer interface through neural map stabilization	66
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine	65
Identification of highly selective covalent inhibitors by phage display	65
Oral delivery of systemic monoclonal antibodies, peptides and small molecules using gastric auto-injectors	65
Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase	64
Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo	64
A comprehensive SARS-CoV-2–human protein–protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets	64
High-throughput mapping of a whole rhesus monkey brain at micrometer resolution	63
Could mutations of SARS-CoV-2 suppress diagnostic detection?	62
Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes	62
Single-cell measurement of higher-order 3D genome organization with scSPRITE	62
Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters	61
Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins	60
A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples	60
Animal-free alternatives and the antibody iceberg	60
Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing	60
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics	59
Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq	59
Super-resolved spatial transcriptomics by deep data fusion	59
Uncovering the mode of action of engineered T cells in patient cancer organoids	58
Functional single-cell genomics of human cytomegalovirus infection	58
A unified haplotype-based method for accurate and comprehensive variant calling	57
A small and highly sensitive red/far-red optogenetic switch for applications in mammals	57
A network analysis of COVID-19 mRNA vaccine patents	56
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome	56
A tissue-engineered uterus supports live births in rabbits	56
Artificial intelligence, drug repurposing and peer review	56
Identification of mobile genetic elements with geNomad	56
Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity	56
Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination	56
Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing	55
Modeling intercellular communication in tissues using spatial graphs of cells	55
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue	55
The scverse project provides a computational ecosystem for single-cell omics data analysis	55
Epineural optogenetic activation of nociceptors initiates and amplifies inflammation	55
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants	55
Wireless closed-loop optogenetics across the entire dorsoventral spinal cord in mice	53
A genome and gene catalog of glacier microbiomes	53
Smartphone apps in the COVID-19 pandemic	52
Iterative single-cell multi-omic integration using online learning	52