OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 105. 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 2022-01-01 to 2026-01-01.)

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	7933
Interpreting and comparing neural activity across systems by geometric deep learning	1076
Tamir Gonen	984
More dimensions of the 3D genome	952
Exoskeleton empowers large-scale neural recordings in freely roaming mice	882
Modeling locomotion from environment to neurons	823
Analyzing submicron spatial transcriptomics data at their original resolution	666
Annotating unknown metabolites	636
SNAP-tag2 improves live-cell imaging	628
How noncoding RNAs began to leave the junkyard	560
Line-scanning speeds up Brillouin microscopy	502
Fast and efficient template-mediated synthesis of genetic variants	454
Detecting and correcting false transients in calcium imaging	391
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	390
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	386
Chromoscope: interactive multiscale visualization for structural variation in human genomes	359
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	344
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	335
Optimism for abundant whole-brain connectomes and connectomic screening	334
Method of the Year 2025: electron microscopy-based connectomics	291
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	285
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	284
Antibody stabilization for thermally accelerated deep immunostaining	281
BIONIC: biological network integration using convolutions	274
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	273

GWAS and eQTL disparity	265
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	264
Prediction of protein subcellular localization in single cells	261
Maximum-likelihood model fitting for quantitative analysis of SMLM data	258
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	257
Unlocking the power of spatial omics with AI	246
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	246
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	236
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	228
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	228
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	222
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	211
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	201
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	197
Efficient targeted insertion of large DNA fragments without DNA donors	194
MRIcroGL: voxel-based visualization for neuroimaging	185
BATTLES: high-throughput screening of antigen recognition under force	183
Quest: my postdoc home	183
Using machine learning to predict the structure of proteins that bind to DNA and RNA	173
Setting standards for stem cells	170
Sensitive protein analysis with plexDIA	164
Non-invasive metabolic imaging of brown adipose tissue	164
Tracking gene transfer using RNA tools	159
One cell, two cell, dead cell, true cell	158
The placozoan Trichoplax	154
Benchmarking genomic language models	154
Road trip home to start a lab	152
Author Correction: Learning single-cell perturbation responses using neural optimal transport	151
Bat organoids at bat	149
Peer review demystified: part 2	147
ENTERing the world of immune cells	147
From GWAS to single-cell MPRA	145
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	145
The crustacean Parhyale	143
The Hodge Laplacian advances inference of single-cell trajectories	140
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	138
Trawling the ocean virome	137
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	136
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	135
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	135
Computational strategies for cross-species knowledge transfer	134
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	132
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	131
Publisher Correction: Museum of spatial transcriptomics	131
Indexing and searching petabase-scale nucleotide resources	130
Systematic scRNA-seq screens profile neural organoid response to morphogens	130
When labs welcome under-represented groups	130
Long-read sequencing in the era of epigenomics and epitranscriptomics	129
How developmental cell atlases inform stem cell embryo models	127
Nicheformer: a foundation model for single-cell and spatial omics	126

The tidyomics ecosystem: enhancing omic data analyses	125
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	123
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	122
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	122
Comparing classifier performance with baselines	122
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	121
Tardigrades	120
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	120
StayGold variants for molecular fusion and membrane-targeting applications	118
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	117
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	116
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	115
A graph neural network that combines scRNA-seq and protein–protein interaction data	115
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	115
A method for quantitative and base-resolution sequencing of pseudouridine	115
The LGBTQ+ job hunt	114
Neural networks built with biomolecules	114
Deciphering subcellular organization with multiplexed imaging and deep learning	114
Science while parenting	113
Combining compact human protein domains with CRISPR systems for robust gene activation	112
What makes a Nature Methods paper	110
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	109
Genomics beyond complete genomes	108
Building an automated three-dimensional flight agent for neural network reconstruction	108
Mackenzie Weygandt Mathis	108
Merging conformational landscapes in a single consensus space with FlexConsensus algorithm	107
Vector choices, vector surprises	106
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	106
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	106
The future of bioimage analysis: a dialog between mind and machine	106
Analyzing single-cell bisulfite sequencing data with MethSCAn	105
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	105