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 2022-08-01 to 2026-08-01.)

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	1460
More dimensions of the 3D genome	1377
Exoskeleton empowers large-scale neural recordings in freely roaming mice	1130
Modeling locomotion from environment to neurons	818
Analyzing submicron spatial transcriptomics data at their original resolution	719
SNAP-tag2 improves live-cell imaging	543
Annotating unknown metabolites	520
Optimism for abundant whole-brain connectomes and connectomic screening	477
Appeals: what, why, when, how	474
GWAS and eQTL disparity	470
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	469
Chromoscope: interactive multiscale visualization for structural variation in human genomes	469
Line-scanning speeds up Brillouin microscopy	460
Self-localized ultrafast pencil beam for volumetric multiphoton imaging	424
How noncoding RNAs began to leave the junkyard	382
Fast and efficient template-mediated synthesis of genetic variants	369
BIONIC: biological network integration using convolutions	359
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	355
Method of the Year 2025: electron microscopy-based connectomics	351
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	341
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	302
Antibody stabilization for thermally accelerated deep immunostaining	301
EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control	295
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	294
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	282

Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus	278
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	262
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	237
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	236
Maximum-likelihood model fitting for quantitative analysis of SMLM data	236
Unlocking the power of spatial omics with AI	234
Prediction of protein subcellular localization in single cells	233
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	231
Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases	225
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	223
MRIcroGL: voxel-based visualization for neuroimaging	217
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	217
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	217
Inference of secreted protein signaling activities in intercellular communication	216
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	214
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	209
Quest: my postdoc home	207
BATTLES: high-throughput screening of antigen recognition under force	204
Using machine learning to predict the structure of proteins that bind to DNA and RNA	195
Non-invasive metabolic imaging of brown adipose tissue	192
Sensitive protein analysis with plexDIA	190
Tracking gene transfer using RNA tools	183
One cell, two cell, dead cell, true cell	182
From GWAS to single-cell MPRA	181
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	181
Benchmarking genomic language models	178
Road trip home to start a lab	177
ENTERing the world of immune cells	176
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	175
Host–microbiome maps	173
Peer review demystified: part 2	172
How developmental cell atlases inform stem cell embryo models	171
The Hodge Laplacian advances inference of single-cell trajectories	171
When labs welcome under-represented groups	170
Mentoring echoes down the generations	168
Author Correction: Learning single-cell perturbation responses using neural optimal transport	167
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	165
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	165
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	164
The placozoan Trichoplax	160
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	160
Setting standards for stem cells	158
The crustacean Parhyale	152
Systematic scRNA-seq screens profile neural organoid response to morphogens	151
Bridging complexity and accessibility in metabolomics with MetaboApps	151
Bat organoids at bat	144
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	143
Tardigrades	139
Computational strategies for cross-species knowledge transfer	134
Circuit manipulation with gap junctions	131

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	130
Quantum image transmission	130
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	128
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	128
Long-read sequencing in the era of epigenomics and epitranscriptomics	128
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	126
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	125
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	125
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	125
Nicheformer: a foundation model for single-cell and spatial omics	124
StayGold variants for molecular fusion and membrane-targeting applications	124
Indexing and searching petabase-scale nucleotide resources	124
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	121
Comparing classifier performance with baselines	121
The tidyomics ecosystem: enhancing omic data analyses	121
The LGBTQ+ job hunt	120
Deciphering subcellular organization with multiplexed imaging and deep learning	119
Neural networks built with biomolecules	117
Multimodal large language models for bioimage analysis	117
Vector choices, vector surprises	117
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	115
Challenges and recommendations in establishing national human diversity genomic projects	115
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	115
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	115
Science while parenting	112
A method for quantitative and base-resolution sequencing of pseudouridine	112
Inside the chase after those elusive proteoforms	112
Method of the Year: EM connectomics	112
Tackling tumor complexity with single-cell proteomics	109
Building an automated three-dimensional flight agent for neural network reconstruction	108
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	107
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	107
Differentiable simulation expands frontiers for biophysical neural models	107