OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 102. 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 2021-08-01 to 2025-08-01.)

Article	Citations
Interpreting and comparing neural activity across systems by geometric deep learning	6972
Tamir Gonen	1240
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	884
Modeling locomotion from environment to neurons	864
More dimensions of the 3D genome	801
Exoskeleton empowers large-scale neural recordings in freely roaming mice	797
Analyzing submicron spatial transcriptomics data at their original resolution	775
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	684
GWAS and eQTL disparity	670
Annotating unknown metabolites	590
Chromoscope: interactive multiscale visualization for structural variation in human genomes	575
How noncoding RNAs began to leave the junkyard	548
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	518
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	464
Unlocking the power of spatial omics with AI	407
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	385
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	381
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	360
Line-scanning speeds up Brillouin microscopy	337
Detecting and correcting false transients in calcium imaging	337
Fast and efficient template-mediated synthesis of genetic variants	309
Maximum-likelihood model fitting for quantitative analysis of SMLM data	293
Prediction of protein subcellular localization in single cells	277
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	261
Antibody stabilization for thermally accelerated deep immunostaining	257

MRIcroGL: voxel-based visualization for neuroimaging	257
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	255
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	237
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	231
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	225
BIONIC: biological network integration using convolutions	222
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	221
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	219
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	216
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	214
Efficient targeted insertion of large DNA fragments without DNA donors	210
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	205
Using machine learning to predict the structure of proteins that bind to DNA and RNA	205
ENTERing the world of immune cells	204
BATTLES: high-throughput screening of antigen recognition under force	203
Quest: my postdoc home	200
Non-invasive metabolic imaging of brown adipose tissue	192
Sensitive protein analysis with plexDIA	191
Setting standards for stem cells	186
Trawling the ocean virome	183
The crustacean Parhyale	182
From GWAS to single-cell MPRA	180
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	175
Comparing classifier performance with baselines	175
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	172
Bat organoids at bat	172
Indexing and searching petabase-scale nucleotide resources	171
Long-read sequencing in the era of epigenomics and epitranscriptomics	171
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	169
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	166
The tidyomics ecosystem: enhancing omic data analyses	164
How developmental cell atlases inform stem cell embryo models	162
Author Correction: Learning single-cell perturbation responses using neural optimal transport	162
One cell, two cell, dead cell, true cell	162
Peer review demystified: part 2	158
Tardigrades	157
Tracking gene transfer using RNA tools	155
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	154
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	153
Publisher Correction: Museum of spatial transcriptomics	149
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	147
When labs welcome under-represented groups	147
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	146
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	145
The placozoan Trichoplax	144
StayGold variants for molecular fusion and membrane-targeting applications	143
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	141
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	140
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	132
LIVECell—A large-scale dataset for label-free live cell segmentation	131

The LGBTQ+ job hunt	130
Neural networks built with biomolecules	130
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	130
Deciphering subcellular organization with multiplexed imaging and deep learning	130
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	130
A method for quantitative and base-resolution sequencing of pseudouridine	127
A graph neural network that combines scRNA-seq and protein–protein interaction data	122
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	122
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	121
Science while parenting	120
The future of bioimage analysis: a dialog between mind and machine	120
What makes a Nature Methods paper	119
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	114
Combining compact human protein domains with CRISPR systems for robust gene activation	114
Genomics beyond complete genomes	111
Mackenzie Weygandt Mathis	111
Building an automated three-dimensional flight agent for neural network reconstruction	111
Multimodal large language models for bioimage analysis	110
Vector choices, vector surprises	110
Method of the Year: protein structure prediction	109
Propensity score weighting	109
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	107
CAD we share? Publishing reproducible microscope hardware	106
Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data	105
Tackling tumor complexity with single-cell proteomics	104
Enabling global image data sharing in the life sciences	103
Image processing tools for petabyte-scale light sheet microscopy data	102
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	102