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 2021-10-01 to 2025-10-01.)

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	7366
Interpreting and comparing neural activity across systems by geometric deep learning	1329
Tamir Gonen	955
BIONIC: biological network integration using convolutions	935
Maximum-likelihood model fitting for quantitative analysis of SMLM data	873
More dimensions of the 3D genome	865
Exoskeleton empowers large-scale neural recordings in freely roaming mice	854
Modeling locomotion from environment to neurons	735
Analyzing submicron spatial transcriptomics data at their original resolution	720
GWAS and eQTL disparity	690
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	633
Fast and efficient template-mediated synthesis of genetic variants	577
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	570
SNAP-tag2 improves live-cell imaging	465
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	457
Prediction of protein subcellular localization in single cells	418
How noncoding RNAs began to leave the junkyard	417
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	366
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	357
Line-scanning speeds up Brillouin microscopy	338
Detecting and correcting false transients in calcium imaging	326
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	294
MRIcroGL: voxel-based visualization for neuroimaging	293
Antibody stabilization for thermally accelerated deep immunostaining	270
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	263

Unlocking the power of spatial omics with AI	259
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	250
Annotating unknown metabolites	247
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	239
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	238
Chromoscope: interactive multiscale visualization for structural variation in human genomes	238
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	238
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	234
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	229
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	228
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	226
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	223
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	211
Efficient targeted insertion of large DNA fragments without DNA donors	210
Quest: my postdoc home	207
BATTLES: high-throughput screening of antigen recognition under force	202
Using machine learning to predict the structure of proteins that bind to DNA and RNA	200
Setting standards for stem cells	196
Non-invasive metabolic imaging of brown adipose tissue	194
Sensitive protein analysis with plexDIA	193
Tardigrades	192
Tracking gene transfer using RNA tools	190
One cell, two cell, dead cell, true cell	188
The placozoan Trichoplax	186
Benchmarking genomic language models	181
Road trip home to start a lab	179
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	165
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	165
Author Correction: Learning single-cell perturbation responses using neural optimal transport	163
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	163
How developmental cell atlases inform stem cell embryo models	162
The crustacean Parhyale	161
Bat organoids at bat	159
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	156
From GWAS to single-cell MPRA	156
Trawling the ocean virome	151
ENTERing the world of immune cells	147
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	145
Peer review demystified: part 2	144
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	140
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	140
When labs welcome under-represented groups	137
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	136
Publisher Correction: Museum of spatial transcriptomics	132
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	132
StayGold variants for molecular fusion and membrane-targeting applications	132
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	131
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	131
The tidyomics ecosystem: enhancing omic data analyses	127
Comparing classifier performance with baselines	126

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	124
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	124
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	124
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	123
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	120
Long-read sequencing in the era of epigenomics and epitranscriptomics	118
Indexing and searching petabase-scale nucleotide resources	116
A graph neural network that combines scRNA-seq and protein–protein interaction data	115
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	115
The future of bioimage analysis: a dialog between mind and machine	115
A method for quantitative and base-resolution sequencing of pseudouridine	114
Deciphering subcellular organization with multiplexed imaging and deep learning	113
The LGBTQ+ job hunt	113
Neural networks built with biomolecules	111
Tackling tumor complexity with single-cell proteomics	110
Science while parenting	110
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	109
Combining compact human protein domains with CRISPR systems for robust gene activation	108
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	108
What makes a Nature Methods paper	107
Method of the Year: protein structure prediction	106
Propensity score weighting	106
Building an automated three-dimensional flight agent for neural network reconstruction	105
Mackenzie Weygandt Mathis	105
CAD we share? Publishing reproducible microscope hardware	105
Genomics beyond complete genomes	103
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	103