OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 104. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)

Article	Citations
ColabFold: making protein folding accessible to all	3511
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	2603
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	1767
Cellpose: a generalist algorithm for cellular segmentation	1455
Sensitive protein alignments at tree-of-life scale using DIAMOND	1311
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction	843
Feature-based molecular networking in the GNPS analysis environment	667
Single-cell chromatin state analysis with Signac	634
Martini 3: a general purpose force field for coarse-grained molecular dynamics	585
Macromolecular modeling and design in Rosetta: recent methods and frameworks	512
Method of the Year: spatially resolved transcriptomics	445
metaFlye: scalable long-read metagenome assembly using repeat graphs	438
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	425
Benchmarking atlas-level data integration in single-cell genomics	420
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition	406
Effective gene expression prediction from sequence by integrating long-range interactions	394
Museum of spatial transcriptomics	380
Advances and challenges for fluorescence nanothermometry	351
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	315
Squidpy: a scalable framework for spatial omics analysis	313
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	308
CellRank for directed single-cell fate mapping	301
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	295
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	293
Next-generation GRAB sensors for monitoring dopaminergic activity in vivo	289

Spatial omics and multiplexed imaging to explore cancer biology	288
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	280
Philosopher: a versatile toolkit for shotgun proteomics data analysis	271
Cellpose 2.0: how to train your own model	268
Deciphering molecular interactions by proximity labeling	266
Joint probabilistic modeling of single-cell multi-omic data with totalVI	249
Improvement of cryo-EM maps by density modification	244
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes	239
An optimized acetylcholine sensor for monitoring in vivo cholinergic activity	222
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	220
Low-N protein engineering with data-efficient deep learning	216
SLEAP: A deep learning system for multi-animal pose tracking	210
The emerging landscape of single-molecule protein sequencing technologies	198
Critical assessment of protein intrinsic disorder prediction	195
DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning	193
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	192
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	192
Screening for functional circular RNAs using the CRISPR–Cas13 system	185
Multi-animal pose estimation, identification and tracking with DeepLabCut	179
SpaceM reveals metabolic states of single cells	175
Spatially resolved transcriptomics adds a new dimension to genomics	173
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	171
The power of imaging to understand extracellular vesicle biology in vivo	168
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	163
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing	163
A general method to optimize and functionalize red-shifted rhodamine dyes	161
Protein structure predictions to atomic accuracy with AlphaFold	156
Exosome detection via the ultrafast-isolation system: EXODUS	156
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	152
AlphaFill: enriching AlphaFold models with ligands and cofactors	151
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	151
SNT: a unifying toolbox for quantification of neuronal anatomy	149
Predicting 3D genome folding from DNA sequence with Akita	149
Critical Assessment of Metagenome Interpretation: the second round of challenges	143
The triumphs and limitations of computational methods for scRNA-seq	141
An expanded palette of dopamine sensors for multiplex imaging in vivo	141
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	141
Defining the carrier proteome limit for single-cell proteomics	140
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco	140
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	137
Targeted Perturb-seq enables genome-scale genetic screens in single cells	137
High-throughput and single-cell T cell receptor sequencing technologies	136
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq	135
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing	135
Spatially resolved single-cell genomics and transcriptomics by imaging	133
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	129
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	127
Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals	126
Deep learning enables fast and dense single-molecule localization with high accuracy	126
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	125

Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	125
Up to 100-fold speed-up and multiplexing in optimized DNA-PAINT	122
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	121
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures	121
LIVECell—A large-scale dataset for label-free live cell segmentation	120
An efficient KRAB domain for CRISPRi applications in human cells	120
The SEIRS model for infectious disease dynamics	117
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	117
Metabolite discovery through global annotation of untargeted metabolomics data	116
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	115
Systematic evaluation of chromosome conformation capture assays	115
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma	115
Intelligent image-based deformation-assisted cell sorting with molecular specificity	114
Geometric deep learning enables 3D kinematic profiling across species and environments	114
Single-molecule FRET imaging of GPCR dimers in living cells	114
DeepC: predicting 3D genome folding using megabase-scale transfer learning	111
Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins	111
SMAP: a modular super-resolution microscopy analysis platform for SMLM data	111
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI	110
A systematic evaluation of the design and context dependencies of massively parallel reporter assays	110
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	109
The impact of AlphaFold2 one year on	108
DOME: recommendations for supervised machine learning validation in biology	108
FlyWire: online community for whole-brain connectomics	107
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	106
A practical guide to cancer subclonal reconstruction from DNA sequencing	106
METLIN MS2 molecular standards database: a broad chemical and biological resource	105
A compact Cascade–Cas3 system for targeted genome engineering	104
Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq	104