Nature Biotechnology

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
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis	198
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
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
Initialization is critical for preserving global data structure in both t-SNE and UMAP	176
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing	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
Identification of mobile genetic elements with geNomad	158
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome	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
Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI	147
Efficient evolution of human antibodies from general protein language models	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
Improved prediction of immune checkpoint blockade efficacy across multiple cancer types	142
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
Precise genomic deletions using paired prime editing	138
Telomere-to-telomere assembly of diploid chromosomes with Verkko	137
A knowledge graph to interpret clinical proteomics data	137
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology	137
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads	136
CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells	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
Chromosome-scale, haplotype-resolved assembly of human genomes	127
A comprehensive library of human transcription factors for cell fate engineering	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
Standardized annotation of translated open reading frames	113
Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage	113
The Organoid Cell Atlas	111
Identification of tumor antigens with immunopeptidomics	110
High-throughput total RNA sequencing in single cells using VASA-seq	110
DestVI identifies continuums of cell types in spatial transcriptomics data	109
A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat	109
GABA-enriched tomato is first CRISPR-edited food to enter market	108
Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing	108
Targeting herpes simplex virus with CRISPR–Cas9 cures herpetic stromal keratitis in mice	108
Saturation variant interpretation using CRISPR prime editing	108
Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates	108
The scverse project provides a computational ecosystem for single-cell omics data analysis	108
Deletion and replacement of long genomic sequences using prime editing	108
Inferring gene expression from cell-free DNA fragmentation profiles	106
High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects	104
High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails	104
Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection	103
CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA	102
Spatial charting of single-cell transcriptomes in tissues	101
Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase	101
Multiscale and integrative single-cell Hi-C analysis with Higashi	100
Compact RNA editors with small Cas13 proteins	99
Noncanonical open reading frames encode functional proteins essential for cancer cell survival	98
Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID	98
Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity	98
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine	97
Modeling intercellular communication in tissues using spatial graphs of cells	96
Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs	95
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq	95
Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo	95
Assessing single-cell transcriptomic variability through density-preserving data visualization	95
The PROTAC gold rush	94
Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes	94
A split prime editor with untethered reverse transcriptase and circular RNA template	94
The RNA Atlas expands the catalog of human non-coding RNAs	93
Remote smartphone monitoring of Parkinson’s disease and individual response to therapy	93
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin	92
Monitoring deep-tissue oxygenation with a millimeter-scale ultrasonic implant	91
Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins	91
Bioinstructive implantable scaffolds for rapid in vivo manufacture and release of CAR-T cells	91
Single-cell immunology of SARS-CoV-2 infection	90
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data	90
A fluorescent sensor for spatiotemporally resolved imaging of endocannabinoid dynamics in vivo	89
Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood–brain barrier and knock down genes in the rodent CNS	89
Prediction of drug efficacy from transcriptional profiles with deep learning	89
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin	89
Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics	88
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing	87
Genome-wide specificity of prime editors in plants	86

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning	86
High-throughput microbial culturomics using automation and machine learning	86
Greengenes2 unifies microbial data in a single reference tree	85
Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks	85
A comprehensive SARS-CoV-2–human protein–protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets	84
Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing	83
Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19	83
Global detection of human variants and isoforms by deep proteome sequencing	83
Send in the senolytics	82
Transplantation of a human liver following 3 days of ex situ normothermic preservation	82
An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts	82
Super-resolved spatial transcriptomics by deep data fusion	82
Uncovering the mode of action of engineered T cells in patient cancer organoids	81
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome	81
Oral delivery of systemic monoclonal antibodies, peptides and small molecules using gastric auto-injectors	80
Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit	80
Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination	78
A fully integrated wearable ultrasound system to monitor deep tissues in moving subjects	77
High-throughput mapping of a whole rhesus monkey brain at micrometer resolution	77
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study	76
Identification of highly selective covalent inhibitors by phage display	75
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)	74
Single-cell measurement of higher-order 3D genome organization with scSPRITE	73
A genome and gene catalog of glacier microbiomes	72
A humanized mouse model of chronic COVID-19	72
Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing	70
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations	70
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue	70
A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples	70
Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq	70
A small and highly sensitive red/far-red optogenetic switch for applications in mammals	69
Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing	69
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants	69
Could mutations of SARS-CoV-2 suppress diagnostic detection?	67
Efficient prime editing in mouse brain, liver and heart with dual AAVs	66
A unified haplotype-based method for accurate and comprehensive variant calling	66
Functional single-cell genomics of human cytomegalovirus infection	66
Microfluidics-free single-cell genomics with templated emulsification	66
Integration of whole transcriptome spatial profiling with protein markers	65
Magnify is a universal molecular anchoring strategy for expansion microscopy	65
Adenine base editor engineering reduces editing of bystander cytosines	65
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress	65
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro	65
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning	64
Accurate isoform discovery with IsoQuant using long reads	64
Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition	64
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data	63
SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data	63
Smartphone apps in the COVID-19 pandemic	63
Predicting prime editing efficiency and product purity by deep learning	63
Fast nanopore sequencing data analysis with SLOW5	63
Wireless closed-loop optogenetics across the entire dorsoventral spinal cord in mice	62
Unidirectional single-file transport of full-length proteins through a nanopore	61
A network analysis of COVID-19 mRNA vaccine patents	61
Development of spirulina for the manufacture and oral delivery of protein therapeutics	61
Improved cytosine base editors generated from TadA variants	60
Massively parallel phenotyping of coding variants in cancer with Perturb-seq	60
Iterative single-cell multi-omic integration using online learning	60
Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes	60
Personalized phosphoproteomics identifies functional signaling	59
Genotoxic effects of base and prime editing in human hematopoietic stem cells	59
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning	59
CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo	58
High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs	58
Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens	58
Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes	57
In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice	57
Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria	57
A proteome-wide atlas of drug mechanism of action	57
Integrative spatial analysis of cell morphologies and transcriptional states with MUSE	57
Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides	56
The lag in SARS-CoV-2 genome submissions to GISAID	56
Precision targeting of autoantigen-specific B cells in muscle-specific tyrosine kinase myasthenia gravis with chimeric autoantibody receptor T cells	56
Bioorthogonal information storage in l-DNA with a high-fidelity mirror-image Pfu DNA polymerase	56
Pangenome graph construction from genome alignments with Minigraph-Cactus	56
Sensitive identification of neoantigens and cognate TCRs in human solid tumors	55
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE	55
CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information	55
Sustainable manufacturing with synthetic biology	55
Bayesian inference of gene expression states from single-cell RNA-seq data	55
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing	54
A genetically encoded sensor measures temporal oxytocin release from different neuronal compartments	53
Bioengineered corneal tissue for minimally invasive vision restoration in advanced keratoconus in two clinical cohorts	53
Engineered human hepatocyte organoids enable CRISPR-based target discovery and drug screening for steatosis	53
Cell types of origin of the cell-free transcriptome	53
Building a high-quality Human Cell Atlas	53
Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads	53
Detection of mosaic and population-level structural variants with Sniffles2	52
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing	52
Prediction of peptide mass spectral libraries with machine learning	52
Soil microbiome engineering for sustainability in a changing environment	50
Engineered CRISPR prime editors with compact, untethered reverse transcriptases	50
Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction	49
Quantitative mapping of the cellular small RNA landscape with AQRNA-seq	49
RNA-responsive elements for eukaryotic translational control	49