OOIR: Observatory of International Research

Papers

(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.)

Article	Citations
Fast, sensitive and accurate integration of single-cell data with Harmony	1755
ilastik: interactive machine learning for (bio)image analysis	1155
fMRIPrep: a robust preprocessing pipeline for functional MRI	1109
U-Net: deep learning for cell counting, detection, and morphometry	905
Moving beyond P values: data analysis with estimation graphics	851
Fast and accurate long-read assembly with wtdbg2	609
High-performance calcium sensors for imaging activity in neuronal populations and microcompartments	582
Real-time cryo-electron microscopy data preprocessing with Warp	581
Deep learning for cellular image analysis	575
NicheNet: modeling intercellular communication by linking ligands to target genes	512
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information	495
High-definition spatial transcriptomics for in situ tissue profiling	495
Unified rational protein engineering with sequence-based deep representation learning	449
Promoting transparency and reproducibility in enhanced molecular simulations	420
Flow-enhanced vascularization and maturation of kidney organoids in vitro	418
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput	412
Engineering of human brain organoids with a functional vascular-like system	403
Deep learning enables cross-modality super-resolution in fluorescence microscopy	399
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning	398
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs	387
Machine-learning-guided directed evolution for protein engineering	383
Fast animal pose estimation using deep neural networks	333
Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments	328
Nanopore native RNA sequencing of a human poly(A) transcriptome	297
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl	279
Software tools for automated transmission electron microscopy	273
Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data	273
Orchestrating single-cell analysis with Bioconductor	271
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells	267
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices	264
Reliability of human cortical organoid generation	254
FPbase: a community-editable fluorescent protein database	236
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data	236
Supervised classification enables rapid annotation of cell atlases	235
Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction	227
Imaging cellular ultrastructures using expansion microscopy (U-ExM)	227
FRET as a biomolecular research tool — understanding its potential while avoiding pitfalls	226
Expansion microscopy: principles and uses in biological research	220
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning	217
A test metric for assessing single-cell RNA-seq batch correction	206
Single-cell chromatin state analysis with Signac	204
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues	199
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments	199
Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software	190
DART-seq: an antibody-free method for global m6A detection	184
Nuclear pores as versatile reference standards for quantitative superresolution microscopy	183
Best practices and benchmarks for intact protein analysis for top-down mass spectrometry	181
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling	179
FEAST: fast expectation-maximization for microbial source tracking	178
A genetically encoded fluorescent sensor for in vivo imaging of GABA	176
Joint analysis of heterogeneous single-cell RNA-seq dataset collections	175
Methods to study RNA–protein interactions	174
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold	166
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry	166
scGen predicts single-cell perturbation responses	164
A dream of single-cell proteomics	161
High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis	161
Brillouin microscopy: an emerging tool for mechanobiology	160
Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution	160
idtracker.ai: tracking all individuals in small or large collectives of unmarked animals	156
Exploring single-cell data with deep multitasking neural networks	156
Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0	154
Assessment of network module identification across complex diseases	154
BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples	151
Biological imaging of chemical bonds by stimulated Raman scattering microscopy	145
Evaluation of variability in human kidney organoids	143
A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms	141
Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts	137
Probabilistic cell typing enables fine mapping of closely related cell types in situ	136
The cryo-EM method microcrystal electron diffraction (MicroED)	133
Learning representations of microbe–metabolite interactions	130
Parameter-free image resolution estimation based on decorrelation analysis	129
Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning	128
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells	125
A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue	125
The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue	122
Biological plasticity rescues target activity in CRISPR knock outs	121
Metagenomic engineering of the mammalian gut microbiome in situ	121
A complete data processing workflow for cryo-ET and subtomogram averaging	120
Light-sheet microscopy in the near-infrared II window	119
A genetically encoded near-infrared fluorescent calcium ion indicator	119
Joint profiling of DNA methylation and chromatin architecture in single cells	118
Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification	114
Data denoising with transfer learning in single-cell transcriptomics	114
High-density multi-fiber photometry for studying large-scale brain circuit dynamics	109
Long-read sequence and assembly of segmental duplications	108
In vivo RNA editing of point mutations via RNA-guided adenosine deaminases	106
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics	101
Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution	101
CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer	99
An online resource for GPCR structure determination and analysis	99
Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning	98
Comprehensive mapping of neurotransmitter networks by MALDI–MS imaging	98
Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution	97
A pH-correctable, DNA-based fluorescent reporter for organellar calcium	97
Kilohertz frame-rate two-photon tomography	96
Localization microscopy at doubled precision with patterned illumination	96
A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM	95
Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells	94
Laser phase plate for transmission electron microscopy	91
All the light that we can see: a new era in miniaturized microscopy	91
LADL: light-activated dynamic looping for endogenous gene expression control	90
4D functional ultrasound imaging of whole-brain activity in rodents	89
FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control	88
ImJoy: an open-source computational platform for the deep learning era	85
trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data	83
High throughput discovery of functional protein modifications by Hotspot Thermal Profiling	83
A discriminative learning approach to differential expression analysis for single-cell RNA-seq	81
T cell antigen discovery via trogocytosis	81
An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions	80
Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity	80
T cell antigen discovery via signaling and antigen-presenting bifunctional receptors	78
Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins	77
CLIJ: GPU-accelerated image processing for everyone	77
Time-resolved serial femtosecond crystallography at the European XFEL	77
Evaluating measures of association for single-cell transcriptomics	76
Molecular resolution imaging by repetitive optical selective exposure	76
An efficient auxin-inducible degron system with low basal degradation in human cells	76
Selene: a PyTorch-based deep learning library for sequence data	74