OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 103. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Chromoscope: interactive multiscale visualization for structural variation in human genomes	6528
Interpreting and comparing neural activity across systems by geometric deep learning	1146
Tamir Gonen	823
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	778
Modeling locomotion from environment to neurons	736
More dimensions of the 3D genome	716
Exoskeleton empowers large-scale neural recordings in freely roaming mice	715
Analyzing submicron spatial transcriptomics data at their original resolution	703
GWAS and eQTL disparity	626
Annotating unknown metabolites	621
Line-scanning speeds up Brillouin microscopy	549
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	516
Antibody stabilization for thermally accelerated deep immunostaining	469
Unlocking the power of spatial omics with AI	466
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	431
Fast and efficient template-mediated synthesis of genetic variants	346
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	343
Prediction of protein subcellular localization in single cells	318
Best practices and tools for reporting reproducible fluorescence microscopy methods	317
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	316
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	292
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	291
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	268
Maximum-likelihood model fitting for quantitative analysis of SMLM data	264
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	256

SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	250
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	243
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	241
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	233
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	228
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	225
Efficient targeted insertion of large DNA fragments without DNA donors	224
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	218
How noncoding RNAs began to leave the junkyard	207
BIONIC: biological network integration using convolutions	205
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	203
Detecting and correcting false transients in calcium imaging	203
Using machine learning to predict the structure of proteins that bind to DNA and RNA	202
When labs welcome under-represented groups	197
ENTERing the world of immune cells	195
BATTLES: high-throughput screening of antigen recognition under force	194
Quest: my postdoc home	191
Non-invasive metabolic imaging of brown adipose tissue	190
Sensitive protein analysis with plexDIA	188
Setting standards for stem cells	178
The tidyomics ecosystem: enhancing omic data analyses	178
Trawling the ocean virome	178
The crustacean Parhyale	171
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	171
Comparing classifier performance with baselines	170
Peer review demystified: part 2	168
The placozoan Trichoplax	167
Author Correction: Learning single-cell perturbation responses using neural optimal transport	165
How developmental cell atlases inform stem cell embryo models	164
One cell, two cell, dead cell, true cell	163
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	163
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	162
Tardigrades	162
Publisher Correction: Museum of spatial transcriptomics	161
Tracking gene transfer using RNA tools	159
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	156
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	154
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	153
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	152
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	151
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	151
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	146
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	145
StayGold variants for molecular fusion and membrane-targeting applications	145
Long-read sequencing in the era of epigenomics and epitranscriptomics	144
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	141
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	139
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	138
Indexing and searching petabase-scale nucleotide resources	135
From GWAS to single-cell MPRA	135

LIVECell—A large-scale dataset for label-free live cell segmentation	135
The LGBTQ+ job hunt	131
Deciphering subcellular organization with multiplexed imaging and deep learning	131
A method for quantitative and base-resolution sequencing of pseudouridine	130
Neural networks built with biomolecules	130
A graph neural network that combines scRNA-seq and protein–protein interaction data	130
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	127
Enabling global image data sharing in the life sciences	127
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	124
Propensity score weighting	124
The future of bioimage analysis: a dialog between mind and machine	124
Science while parenting	123
Multimodal large language models for bioimage analysis	122
Combining compact human protein domains with CRISPR systems for robust gene activation	122
What makes a Nature Methods paper	122
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	120
Building an automated three-dimensional flight agent for neural network reconstruction	118
Method of the Year: protein structure prediction	117
Mackenzie Weygandt Mathis	115
Genomics beyond complete genomes	113
Vector choices, vector surprises	112
CAD we share? Publishing reproducible microscope hardware	111
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	110
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	110
A guide to the optogenetic regulation of endogenous molecules	109
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	105
Comparison of transformations for single-cell RNA-seq data	103
Tackling tumor complexity with single-cell proteomics	103
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	103