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 2022-07-01 to 2026-07-01.)

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	1360
More dimensions of the 3D genome	1331
Exoskeleton empowers large-scale neural recordings in freely roaming mice	1035
Modeling locomotion from environment to neurons	786
Analyzing submicron spatial transcriptomics data at their original resolution	691
SNAP-tag2 improves live-cell imaging	502
Annotating unknown metabolites	490
Optimism for abundant whole-brain connectomes and connectomic screening	459
Appeals: what, why, when, how	456
GWAS and eQTL disparity	455
Chromoscope: interactive multiscale visualization for structural variation in human genomes	454
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	443
Line-scanning speeds up Brillouin microscopy	442
Self-localized ultrafast pencil beam for volumetric multiphoton imaging	430
How noncoding RNAs began to leave the junkyard	384
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	361
Fast and efficient template-mediated synthesis of genetic variants	357
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	342
Maximum-likelihood model fitting for quantitative analysis of SMLM data	340
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	334
Prediction of protein subcellular localization in single cells	323
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	296
BIONIC: biological network integration using convolutions	290
Method of the Year 2025: electron microscopy-based connectomics	289
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	284

Unlocking the power of spatial omics with AI	274
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	255
EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control	250
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	225
Antibody stabilization for thermally accelerated deep immunostaining	224
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	223
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	221
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	219
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	214
MRIcroGL: voxel-based visualization for neuroimaging	214
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	213
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus	209
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	201
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	199
Quest: my postdoc home	197
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	197
BATTLES: high-throughput screening of antigen recognition under force	195
Non-invasive metabolic imaging of brown adipose tissue	194
Using machine learning to predict the structure of proteins that bind to DNA and RNA	194
Sensitive protein analysis with plexDIA	182
Tracking gene transfer using RNA tools	180
One cell, two cell, dead cell, true cell	179
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	175
From GWAS to single-cell MPRA	175
Benchmarking genomic language models	174
Bat organoids at bat	172
Road trip home to start a lab	172
ENTERing the world of immune cells	168
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	167
Peer review demystified: part 2	165
Host–microbiome maps	165
Trawling the ocean virome	163
How developmental cell atlases inform stem cell embryo models	163
The Hodge Laplacian advances inference of single-cell trajectories	160
When labs welcome under-represented groups	160
The tidyomics ecosystem: enhancing omic data analyses	158
Mentoring echoes down the generations	157
Author Correction: Learning single-cell perturbation responses using neural optimal transport	157
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	154
Computational strategies for cross-species knowledge transfer	153
Systematic scRNA-seq screens profile neural organoid response to morphogens	153
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	153
Comparing classifier performance with baselines	152
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	152
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	149
The placozoan Trichoplax	148
Setting standards for stem cells	136
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	133
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	133
Tardigrades	129

Indexing and searching petabase-scale nucleotide resources	127
StayGold variants for molecular fusion and membrane-targeting applications	127
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	127
Long-read sequencing in the era of epigenomics and epitranscriptomics	127
Nicheformer: a foundation model for single-cell and spatial omics	125
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	124
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	124
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	122
The crustacean Parhyale	122
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	121
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	120
Deciphering subcellular organization with multiplexed imaging and deep learning	120
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	120
The LGBTQ+ job hunt	120
Neural networks built with biomolecules	119
What makes a Nature Methods paper	116
A method for quantitative and base-resolution sequencing of pseudouridine	115
Inside the chase after those elusive proteoforms	114
Science while parenting	113
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	113
Method of the Year: EM connectomics	113
Tackling tumor complexity with single-cell proteomics	112
Building an automated three-dimensional flight agent for neural network reconstruction	111
Vector choices, vector surprises	110
The future of bioimage analysis: a dialog between mind and machine	110
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	110
Differentiable simulation expands frontiers for biophysical neural models	110
Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences	107
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	106
A graph neural network that combines scRNA-seq and protein–protein interaction data	105
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	105