OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 108. 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 2022-05-01 to 2026-05-01.)

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	8596
Interpreting and comparing neural activity across systems by geometric deep learning	1246
Tamir Gonen	1179
More dimensions of the 3D genome	1138
Exoskeleton empowers large-scale neural recordings in freely roaming mice	882
Modeling locomotion from environment to neurons	716
Analyzing submicron spatial transcriptomics data at their original resolution	615
SNAP-tag2 improves live-cell imaging	464
How noncoding RNAs began to leave the junkyard	436
Line-scanning speeds up Brillouin microscopy	435
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	418
Annotating unknown metabolites	415
Optimism for abundant whole-brain connectomes and connectomic screening	413
Method of the Year 2025: electron microscopy-based connectomics	403
Antibody stabilization for thermally accelerated deep immunostaining	401
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	379
Fast and efficient template-mediated synthesis of genetic variants	372
Chromoscope: interactive multiscale visualization for structural variation in human genomes	327
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	327
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	321
Maximum-likelihood model fitting for quantitative analysis of SMLM data	312
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus	311
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	311
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	310
Appeals: what, why, when, how	287

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	278
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	265
GWAS and eQTL disparity	264
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	260
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	255
MRIcroGL: voxel-based visualization for neuroimaging	254
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	253
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	231
Prediction of protein subcellular localization in single cells	229
Unlocking the power of spatial omics with AI	229
BIONIC: biological network integration using convolutions	209
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	205
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	203
Self-localized ultrafast pencil beam for volumetric multiphoton imaging	202
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	201
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	193
Quest: my postdoc home	187
BATTLES: high-throughput screening of antigen recognition under force	186
Using machine learning to predict the structure of proteins that bind to DNA and RNA	185
Setting standards for stem cells	183
Non-invasive metabolic imaging of brown adipose tissue	179
Sensitive protein analysis with plexDIA	173
Tracking gene transfer using RNA tools	173
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	172
One cell, two cell, dead cell, true cell	172
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	169
From GWAS to single-cell MPRA	168
Benchmarking genomic language models	166
Bat organoids at bat	160
Road trip home to start a lab	160
ENTERing the world of immune cells	158
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	158
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	158
Host–microbiome maps	157
Long-read sequencing in the era of epigenomics and epitranscriptomics	157
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	156
Peer review demystified: part 2	155
How developmental cell atlases inform stem cell embryo models	154
Trawling the ocean virome	153
When labs welcome under-represented groups	152
The Hodge Laplacian advances inference of single-cell trajectories	152
Tardigrades	151
Author Correction: Learning single-cell perturbation responses using neural optimal transport	148
Systematic scRNA-seq screens profile neural organoid response to morphogens	147
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	147
Mentoring echoes down the generations	146
Comparing classifier performance with baselines	145
The crustacean Parhyale	142
Indexing and searching petabase-scale nucleotide resources	142
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	141

InterPLM: discovering interpretable features in protein language models via sparse autoencoders	140
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	140
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	139
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	139
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	139
The tidyomics ecosystem: enhancing omic data analyses	136
Computational strategies for cross-species knowledge transfer	133
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	130
Nicheformer: a foundation model for single-cell and spatial omics	127
The placozoan Trichoplax	126
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	125
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	123
StayGold variants for molecular fusion and membrane-targeting applications	122
Deciphering subcellular organization with multiplexed imaging and deep learning	121
Combining compact human protein domains with CRISPR systems for robust gene activation	121
Neural networks built with biomolecules	121
Science while parenting	121
The LGBTQ+ job hunt	121
What makes a Nature Methods paper	119
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	115
MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony	115
Building an automated three-dimensional flight agent for neural network reconstruction	115
The future of bioimage analysis: a dialog between mind and machine	114
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	114
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	113
Vector choices, vector surprises	112
Differentiable simulation expands frontiers for biophysical neural models	112
Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences	111
CAD we share? Publishing reproducible microscope hardware	110
The evolution of embryo models	109
Enabling global image data sharing in the life sciences	109
Propensity score weighting	109
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	109
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108