Nature Biotechnology

(The TQCC of Nature Biotechnology is 74. The table below lists those papers that are above that threshold based on CrossRef citation counts. The publications cover those that have been published in the past four years, i.e., from 2019-03-01 to 2023-03-01.)
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 26843
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype3782
SignalP 5.0 improves signal peptide predictions using deep neural networks2429
Dimensionality reduction for visualizing single-cell data using UMAP2246
Assembly of long, error-prone reads using repeat graphs1612
Determining cell type abundance and expression from bulk tissues with digital cytometry1405
Wearable biosensors for healthcare monitoring1338
A comparison of single-cell trajectory inference methods757
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome593
CRISPResso2 provides accurate and rapid genome editing sequence analysis549
Deep learning enables rapid identification of potent DDR1 kinase inhibitors473
A laser-engraved wearable sensor for sensitive detection of uric acid and tyrosine in sweat460
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion432
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice425
Breeding crops to feed 10 billion403
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell378
Visualizing structure and transitions in high-dimensional biological data378
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama376
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks362
Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients339
Broad-spectrum resistance to bacterial blight in rice using genome editing331
Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing321
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2320
A human gut bacterial genome and culture collection for improved metagenomic analyses320
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses300
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)296
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection279
In vivo molecular imaging for immunotherapy using ultra-bright near-infrared-IIb rare-earth nanoparticles277
Minimum Information about an Uncultivated Virus Genome (MIUViG)275
Accessing analytes in biofluids for peripheral biochemical monitoring271
Predicting the mutations generated by repair of Cas9-induced double-strand breaks270
CAR-T cells secreting BiTEs circumvent antigen escape without detectable toxicity268
Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation257
Characterization of cell fate probabilities in single-cell data with Palantir251
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery248
Plant gene editing through de novo induction of meristems245
Toward a new generation of smart skins237
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility228
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia226
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues225
A large peptidome dataset improves HLA class I epitope prediction across most of the human population225
Tubuloids derived from human adult kidney and urine for personalized disease modeling222
Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore219
An open resource for accurately benchmarking small variant and reference calls212
The International Cancer Genome Consortium Data Portal200
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2199
Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution196
Resistance gene cloning from a wild crop relative by sequence capture and association genetics195
Increasing the specificity of CRISPR systems with engineered RNA secondary structures194
Multi-omic measurements of heterogeneity in HeLa cells across laboratories194
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance190
The functional landscape of the human phosphoproteome189
Best practices for benchmarking germline small-variant calls in human genomes187
CRISPR DNA base editors with reduced RNA off-target and self-editing activities187
Specification of positional identity in forebrain organoids182
Complete, closed bacterial genomes from microbiomes using nanopore sequencing182
Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)181
Protection of tissue physicochemical properties using polyfunctional crosslinkers176
One-step genome editing of elite crop germplasm during haploid induction174
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages168
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics168
Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes166
FAIRsharing as a community approach to standards, repositories and policies165
Predicting HLA class II antigen presentation through integrated deep learning158
Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors158
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes155
Continuous evolution of base editors with expanded target compatibility and improved activity153
Blood metabolome predicts gut microbiome α-diversity in humans152
Probing and engineering liquid-phase organelles151
Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index151
Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts149
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes149
Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification149
Errors in long-read assemblies can critically affect protein prediction145
Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs141
Design of stapled antimicrobial peptides that are stable, nontoxic and kill antibiotic-resistant bacteria in mice136
Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides132
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay130
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes129
Genome-wide target specificity of CRISPR RNA-guided adenine base editors128
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters125
Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency125
The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2124
Antigen-specific therapeutic approaches for autoimmunity120
Gene editing for immune cell therapies117
Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs115
Regenerating the field of cardiovascular cell therapy113
Emerging technologies for improved deep brain stimulation111
Single-cell metabolic profiling of human cytotoxic T cells109
Next-generation interfaces for studying neural function109
NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells107
Phage combination therapies for bacterial wilt disease in tomato107
Interleukin-23 engineering improves CAR T cell function in solid tumors105
Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration102
TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets99
Ultrafast search of all deposited bacterial and viral genomic data96
Precise gene replacement in rice by RNA transcript-templated homologous recombination95
Overcoming genetic heterogeneity in industrial fermentations94
Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing94
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics93
Real-time measurement of protein–protein interactions at single-molecule resolution using a biological nanopore92
Self-organizing neuruloids model developmental aspects of Huntington’s disease in the ectodermal compartment88
Rapid customization of Solanaceae fruit crops for urban agriculture87
Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays86
In vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma85
Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces85
Supercooling extends preservation time of human livers82
Co-regulation map of the human proteome enables identification of protein functions80
A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system80
ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification80
Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations78
A DNA-of-things storage architecture to create materials with embedded memory78
Spatial metagenomic characterization of microbial biogeography in the gut77
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design77
Diagnostic kit for rice blight resistance75
Engineered immune cells as highly sensitive cancer diagnostics74