OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 107. 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 2020-10-01 to 2024-10-01.)

Article	Citations
ColabFold: making protein folding accessible to all	4687
nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation	3444
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm	2331
Cellpose: a generalist algorithm for cellular segmentation	1873
Sensitive protein alignments at tree-of-life scale using DIAMOND	1821
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction	1000
Single-cell chromatin state analysis with Signac	805
Martini 3: a general purpose force field for coarse-grained molecular dynamics	702
Benchmarking atlas-level data integration in single-cell genomics	559
Method of the Year: spatially resolved transcriptomics	540
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices	531
Museum of spatial transcriptomics	527
metaFlye: scalable long-read metagenome assembly using repeat graphs	521
Effective gene expression prediction from sequence by integrating long-range interactions	504
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition	493
Cellpose 2.0: how to train your own model	435
TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines	433
SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network	430
Squidpy: a scalable framework for spatial omics analysis	424
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram	391
CellRank for directed single-cell fate mapping	387
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks	366
Spatial omics and multiplexed imaging to explore cancer biology	345
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells	331
Next-generation GRAB sensors for monitoring dopaminergic activity in vivo	326

Deciphering molecular interactions by proximity labeling	314
Joint probabilistic modeling of single-cell multi-omic data with totalVI	294
SLEAP: A deep learning system for multi-animal pose tracking	282
Evaluation and development of deep neural networks for image super-resolution in optical microscopy	251
Low-N protein engineering with data-efficient deep learning	251
Multi-animal pose estimation, identification and tracking with DeepLabCut	229
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing	226
The emerging landscape of single-molecule protein sequencing technologies	225
Critical assessment of protein intrinsic disorder prediction	219
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes	217
Screening for functional circular RNAs using the CRISPR–Cas13 system	214
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	213
SNT: a unifying toolbox for quantification of neuronal anatomy	206
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution	206
Spatially resolved transcriptomics adds a new dimension to genomics	204
AlphaFill: enriching AlphaFold models with ligands and cofactors	204
The power of imaging to understand extracellular vesicle biology in vivo	198
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning	198
Joint profiling of histone modifications and transcriptome in single cells from mouse brain	195
SpaceM reveals metabolic states of single cells	194
Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research	191
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	184
Predicting 3D genome folding from DNA sequence with Akita	183
Exosome detection via the ultrafast-isolation system: EXODUS	182
Protein structure predictions to atomic accuracy with AlphaFold	182
Critical Assessment of Metagenome Interpretation: the second round of challenges	172
The triumphs and limitations of computational methods for scRNA-seq	172
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data	166
High-throughput and single-cell T cell receptor sequencing technologies	166
Defining the carrier proteome limit for single-cell proteomics	164
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco	164
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads	162
Spatially resolved single-cell genomics and transcriptomics by imaging	154
Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels	152
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data	152
Deep learning enables fast and dense single-molecule localization with high accuracy	151
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations	150
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender	150
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing	149
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	149
neuromaps: structural and functional interpretation of brain maps	148
LIVECell—A large-scale dataset for label-free live cell segmentation	147
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes	146
An efficient KRAB domain for CRISPRi applications in human cells	144
FlyWire: online community for whole-brain connectomics	144
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	143
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning	141
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ	141
Systematic evaluation of chromosome conformation capture assays	140
DeepC: predicting 3D genome folding using megabase-scale transfer learning	137

Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography	137
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma	136
Single-molecule FRET imaging of GPCR dimers in living cells	135
A systematic evaluation of the design and context dependencies of massively parallel reporter assays	132
DOME: recommendations for supervised machine learning validation in biology	130
Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging	130
Metabolite discovery through global annotation of untargeted metabolomics data	129
Geometric deep learning enables 3D kinematic profiling across species and environments	127
A compact Cascade–Cas3 system for targeted genome engineering	126
The impact of AlphaFold2 one year on	125
Method of the year: long-read sequencing	120
Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI	119
Reproducibility standards for machine learning in the life sciences	118
Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM	118
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets	118
A practical guide to cancer subclonal reconstruction from DNA sequencing	118
Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes	117
DeepLC can predict retention times for peptides that carry as-yet unseen modifications	116
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy	116
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging	115
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration	113
Lineage recording in human cerebral organoids	113
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry	112
Screening cell–cell communication in spatial transcriptomics via collective optimal transport	112
Deep learning-based point-scanning super-resolution imaging	112
Alignment and integration of spatial transcriptomics data	112
Understudied proteins: opportunities and challenges for functional proteomics	111
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers	109
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms	108
Long-read mapping to repetitive reference sequences using Winnowmap2	107
Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation	107
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing	107