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 2022-06-01 to 2026-06-01.)

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	1273
Interpreting and comparing neural activity across systems by geometric deep learning	1244
More dimensions of the 3D genome	1169
Exoskeleton empowers large-scale neural recordings in freely roaming mice	935
Modeling locomotion from environment to neurons	747
Analyzing submicron spatial transcriptomics data at their original resolution	644
SNAP-tag2 improves live-cell imaging	482
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	445
Annotating unknown metabolites	442
Optimism for abundant whole-brain connectomes and connectomic screening	440
Method of the Year 2025: electron microscopy-based connectomics	429
Antibody stabilization for thermally accelerated deep immunostaining	429
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	423
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	401
Prediction of protein subcellular localization in single cells	396
GWAS and eQTL disparity	339
Appeals: what, why, when, how	339
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	338
Chromoscope: interactive multiscale visualization for structural variation in human genomes	337
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	330
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	323
Line-scanning speeds up Brillouin microscopy	322
Self-localized ultrafast pencil beam for volumetric multiphoton imaging	292
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	283
How noncoding RNAs began to leave the junkyard	276

MARBLE: interpretable representations of neural population dynamics using geometric deep learning	272
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	272
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	264
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	263
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	239
Fast and efficient template-mediated synthesis of genetic variants	238
Maximum-likelihood model fitting for quantitative analysis of SMLM data	217
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	216
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	213
Unlocking the power of spatial omics with AI	209
MRIcroGL: voxel-based visualization for neuroimaging	209
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	204
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus	198
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	197
BIONIC: biological network integration using convolutions	185
Quest: my postdoc home	184
Using machine learning to predict the structure of proteins that bind to DNA and RNA	182
BATTLES: high-throughput screening of antigen recognition under force	182
Setting standards for stem cells	182
Non-invasive metabolic imaging of brown adipose tissue	180
Sensitive protein analysis with plexDIA	178
Tracking gene transfer using RNA tools	173
One cell, two cell, dead cell, true cell	169
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	167
From GWAS to single-cell MPRA	166
Benchmarking genomic language models	165
Road trip home to start a lab	164
Bat organoids at bat	164
ENTERing the world of immune cells	163
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	162
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	161
Host–microbiome maps	158
Peer review demystified: part 2	157
How developmental cell atlases inform stem cell embryo models	156
Indexing and searching petabase-scale nucleotide resources	155
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	154
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	153
The Hodge Laplacian advances inference of single-cell trajectories	152
Trawling the ocean virome	152
Computational strategies for cross-species knowledge transfer	148
When labs welcome under-represented groups	148
The crustacean Parhyale	147
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	145
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	145
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	145
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	145
Mentoring echoes down the generations	143
Comparing classifier performance with baselines	139
Author Correction: Learning single-cell perturbation responses using neural optimal transport	135
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	129

Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	127
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	127
The tidyomics ecosystem: enhancing omic data analyses	124
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	124
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	124
The placozoan Trichoplax	123
Systematic scRNA-seq screens profile neural organoid response to morphogens	121
Long-read sequencing in the era of epigenomics and epitranscriptomics	121
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	120
Tardigrades	120
StayGold variants for molecular fusion and membrane-targeting applications	119
Nicheformer: a foundation model for single-cell and spatial omics	119
The LGBTQ+ job hunt	118
Deciphering subcellular organization with multiplexed imaging and deep learning	117
What makes a Nature Methods paper	115
Neural networks built with biomolecules	115
A method for quantitative and base-resolution sequencing of pseudouridine	114
Science while parenting	113
Inside the chase after those elusive proteoforms	113
Method of the Year: EM connectomics	112
Analyzing single-cell bisulfite sequencing data with MethSCAn	112
Tackling tumor complexity with single-cell proteomics	110
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	110
Differentiable simulation expands frontiers for biophysical neural models	109
The future of bioimage analysis: a dialog between mind and machine	109
Building an automated three-dimensional flight agent for neural network reconstruction	109
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	108
Vector choices, vector surprises	107
Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences	107
Multimodal large language models for bioimage analysis	106