Nature Methods

(The TQCC of Nature Methods 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.)
Fast, sensitive and accurate integration of single-cell data with Harmony1755
ilastik: interactive machine learning for (bio)image analysis1155
fMRIPrep: a robust preprocessing pipeline for functional MRI1109
U-Net: deep learning for cell counting, detection, and morphometry905
Moving beyond P values: data analysis with estimation graphics851
Fast and accurate long-read assembly with wtdbg2609
High-performance calcium sensors for imaging activity in neuronal populations and microcompartments582
Real-time cryo-electron microscopy data preprocessing with Warp581
Deep learning for cellular image analysis575
NicheNet: modeling intercellular communication by linking ligands to target genes512
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information495
High-definition spatial transcriptomics for in situ tissue profiling495
Unified rational protein engineering with sequence-based deep representation learning449
Promoting transparency and reproducibility in enhanced molecular simulations420
Flow-enhanced vascularization and maturation of kidney organoids in vitro418
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput412
Engineering of human brain organoids with a functional vascular-like system403
Deep learning enables cross-modality super-resolution in fluorescence microscopy399
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning398
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs387
Machine-learning-guided directed evolution for protein engineering383
Fast animal pose estimation using deep neural networks333
Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments328
Nanopore native RNA sequencing of a human poly(A) transcriptome297
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl279
Software tools for automated transmission electron microscopy273
Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data273
Orchestrating single-cell analysis with Bioconductor271
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells267
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices264
Reliability of human cortical organoid generation254
FPbase: a community-editable fluorescent protein database236
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data236
Supervised classification enables rapid annotation of cell atlases235
Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction227
Imaging cellular ultrastructures using expansion microscopy (U-ExM)227
FRET as a biomolecular research tool — understanding its potential while avoiding pitfalls226
Expansion microscopy: principles and uses in biological research220
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning217
A test metric for assessing single-cell RNA-seq batch correction206
Single-cell chromatin state analysis with Signac204
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues199
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments199
Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software190
DART-seq: an antibody-free method for global m6A detection184
Nuclear pores as versatile reference standards for quantitative superresolution microscopy183
Best practices and benchmarks for intact protein analysis for top-down mass spectrometry181
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling179
FEAST: fast expectation-maximization for microbial source tracking178
A genetically encoded fluorescent sensor for in vivo imaging of GABA176
Joint analysis of heterogeneous single-cell RNA-seq dataset collections175
Methods to study RNA–protein interactions174
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold166
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry166
scGen predicts single-cell perturbation responses164
A dream of single-cell proteomics161
High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis161
Brillouin microscopy: an emerging tool for mechanobiology160
Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution160 tracking all individuals in small or large collectives of unmarked animals156
Exploring single-cell data with deep multitasking neural networks156
Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0154
Assessment of network module identification across complex diseases154
BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples151
Biological imaging of chemical bonds by stimulated Raman scattering microscopy145
Evaluation of variability in human kidney organoids143
A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms141
Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts137
Probabilistic cell typing enables fine mapping of closely related cell types in situ136
The cryo-EM method microcrystal electron diffraction (MicroED)133
Learning representations of microbe–metabolite interactions130
Parameter-free image resolution estimation based on decorrelation analysis129
Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning128
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells125
A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue125
The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue122
Biological plasticity rescues target activity in CRISPR knock outs121
Metagenomic engineering of the mammalian gut microbiome in situ121
A complete data processing workflow for cryo-ET and subtomogram averaging120
Light-sheet microscopy in the near-infrared II window119
A genetically encoded near-infrared fluorescent calcium ion indicator119
Joint profiling of DNA methylation and chromatin architecture in single cells118
Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification114
Data denoising with transfer learning in single-cell transcriptomics114
High-density multi-fiber photometry for studying large-scale brain circuit dynamics109
Long-read sequence and assembly of segmental duplications108
In vivo RNA editing of point mutations via RNA-guided adenosine deaminases106
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics101
Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution101
CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer99
An online resource for GPCR structure determination and analysis99
Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning98
Comprehensive mapping of neurotransmitter networks by MALDI–MS imaging98
Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution97
A pH-correctable, DNA-based fluorescent reporter for organellar calcium97
Kilohertz frame-rate two-photon tomography96
Localization microscopy at doubled precision with patterned illumination96
A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM95
Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells94
Laser phase plate for transmission electron microscopy91
All the light that we can see: a new era in miniaturized microscopy91
LADL: light-activated dynamic looping for endogenous gene expression control90
4D functional ultrasound imaging of whole-brain activity in rodents89
FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control88
ImJoy: an open-source computational platform for the deep learning era85
trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data83
High throughput discovery of functional protein modifications by Hotspot Thermal Profiling83
A discriminative learning approach to differential expression analysis for single-cell RNA-seq81
T cell antigen discovery via trogocytosis81
An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions80
Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity80
T cell antigen discovery via signaling and antigen-presenting bifunctional receptors78
Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins77
CLIJ: GPU-accelerated image processing for everyone77
Time-resolved serial femtosecond crystallography at the European XFEL77
Evaluating measures of association for single-cell transcriptomics76
Molecular resolution imaging by repetitive optical selective exposure76
An efficient auxin-inducible degron system with low basal degradation in human cells76
Selene: a PyTorch-based deep learning library for sequence data74