OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 101. 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 2021-09-01 to 2025-09-01.)

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	7173
Tamir Gonen	1273
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	901
Modeling locomotion from environment to neurons	899
More dimensions of the 3D genome	831
Exoskeleton empowers large-scale neural recordings in freely roaming mice	824
Analyzing submicron spatial transcriptomics data at their original resolution	817
Annotating unknown metabolites	705
Chromoscope: interactive multiscale visualization for structural variation in human genomes	688
How noncoding RNAs began to leave the junkyard	629
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	614
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	562
Detecting and correcting false transients in calcium imaging	544
Line-scanning speeds up Brillouin microscopy	428
Fast and efficient template-mediated synthesis of genetic variants	421
GWAS and eQTL disparity	399
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	386
BIONIC: biological network integration using convolutions	348
Maximum-likelihood model fitting for quantitative analysis of SMLM data	348
MRIcroGL: voxel-based visualization for neuroimaging	319
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	314
Prediction of protein subcellular localization in single cells	285
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	276
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	263
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	259

MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	242
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	237
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	235
Antibody stabilization for thermally accelerated deep immunostaining	233
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	230
Unlocking the power of spatial omics with AI	228
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	228
Efficient targeted insertion of large DNA fragments without DNA donors	223
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	219
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	215
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	213
Using machine learning to predict the structure of proteins that bind to DNA and RNA	210
ENTERing the world of immune cells	210
BATTLES: high-throughput screening of antigen recognition under force	205
Quest: my postdoc home	196
Non-invasive metabolic imaging of brown adipose tissue	192
Setting standards for stem cells	189
Sensitive protein analysis with plexDIA	189
Trawling the ocean virome	189
From GWAS to single-cell MPRA	186
Bat organoids at bat	185
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	182
Indexing and searching petabase-scale nucleotide resources	179
Comparing classifier performance with baselines	179
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	179
When labs welcome under-represented groups	178
The crustacean Parhyale	173
Road trip home to start a lab	171
The tidyomics ecosystem: enhancing omic data analyses	167
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	167
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	163
The placozoan Trichoplax	162
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	161
Publisher Correction: Museum of spatial transcriptomics	160
Author Correction: Learning single-cell perturbation responses using neural optimal transport	159
One cell, two cell, dead cell, true cell	157
How developmental cell atlases inform stem cell embryo models	157
Peer review demystified: part 2	152
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	151
Tracking gene transfer using RNA tools	148
Tardigrades	147
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	146
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	144
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	137
Long-read sequencing in the era of epigenomics and epitranscriptomics	136
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	135
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	134
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	131
StayGold variants for molecular fusion and membrane-targeting applications	129
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	128

Detection of m6A from direct RNA sequencing using a multiple instance learning framework	125
The LGBTQ+ job hunt	123
Deciphering subcellular organization with multiplexed imaging and deep learning	122
A method for quantitative and base-resolution sequencing of pseudouridine	121
Neural networks built with biomolecules	121
The future of bioimage analysis: a dialog between mind and machine	120
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	120
A graph neural network that combines scRNA-seq and protein–protein interaction data	120
Inside the chase after those elusive proteoforms	118
Principles and challenges of modeling temporal and spatial omics data	118
Science while parenting	115
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	115
What makes a Nature Methods paper	114
Combining compact human protein domains with CRISPR systems for robust gene activation	113
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	112
Mackenzie Weygandt Mathis	111
Building an automated three-dimensional flight agent for neural network reconstruction	111
Genomics beyond complete genomes	110
Vector choices, vector surprises	107
Propensity score weighting	105
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	105
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	104
Image processing tools for petabyte-scale light sheet microscopy data	103
Enabling global image data sharing in the life sciences	103
Tackling tumor complexity with single-cell proteomics	103
Analyzing single-cell bisulfite sequencing data with MethSCAn	102
Comparison of transformations for single-cell RNA-seq data	101
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification	101