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 2021-11-01 to 2025-11-01.)

Article	Citations
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	7546
Interpreting and comparing neural activity across systems by geometric deep learning	1371
Tamir Gonen	1001
More dimensions of the 3D genome	977
Exoskeleton empowers large-scale neural recordings in freely roaming mice	919
Modeling locomotion from environment to neurons	891
Analyzing submicron spatial transcriptomics data at their original resolution	761
Annotating unknown metabolites	751
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	607
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	595
BIONIC: biological network integration using convolutions	518
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE	490
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	442
Unlocking the power of spatial omics with AI	429
GWAS and eQTL disparity	373
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	369
Efficient targeted insertion of large DNA fragments without DNA donors	355
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	338
Maximum-likelihood model fitting for quantitative analysis of SMLM data	307
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	304
SNAP-tag2 improves live-cell imaging	285
How noncoding RNAs began to leave the junkyard	274
Line-scanning speeds up Brillouin microscopy	265
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	261
Chromoscope: interactive multiscale visualization for structural variation in human genomes	256

Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	247
Prediction of protein subcellular localization in single cells	247
Antibody stabilization for thermally accelerated deep immunostaining	246
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	246
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance	242
Fast and efficient template-mediated synthesis of genetic variants	241
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	239
Detecting and correcting false transients in calcium imaging	236
MRIcroGL: voxel-based visualization for neuroimaging	235
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	231
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	226
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	216
DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	216
Quest: my postdoc home	215
BATTLES: high-throughput screening of antigen recognition under force	207
Using machine learning to predict the structure of proteins that bind to DNA and RNA	205
Setting standards for stem cells	202
Non-invasive metabolic imaging of brown adipose tissue	201
Sensitive protein analysis with plexDIA	197
Tracking gene transfer using RNA tools	197
One cell, two cell, dead cell, true cell	187
The placozoan Trichoplax	175
Benchmarking genomic language models	174
Road trip home to start a lab	169
Bat organoids at bat	167
How developmental cell atlases inform stem cell embryo models	167
Author Correction: Learning single-cell perturbation responses using neural optimal transport	167
Trawling the ocean virome	165
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	165
ENTERing the world of immune cells	153
Peer review demystified: part 2	153
When labs welcome under-represented groups	152
Comparing classifier performance with baselines	147
Publisher Correction: Museum of spatial transcriptomics	145
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	145
Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution	145
The tidyomics ecosystem: enhancing omic data analyses	144
FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data	143
The crustacean Parhyale	142
Long-read sequencing in the era of epigenomics and epitranscriptomics	141
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	136
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	136
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	132
Tardigrades	131
From GWAS to single-cell MPRA	129
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	128
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	128
The Hodge Laplacian advances inference of single-cell trajectories	128
Nicheformer: a foundation model for single-cell and spatial omics	127
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	123

Detection of m6A from direct RNA sequencing using a multiple instance learning framework	123
InterPLM: discovering interpretable features in protein language models via sparse autoencoders	123
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	121
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	121
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	120
Indexing and searching petabase-scale nucleotide resources	118
StayGold variants for molecular fusion and membrane-targeting applications	118
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	117
A graph neural network that combines scRNA-seq and protein–protein interaction data	116
A method for quantitative and base-resolution sequencing of pseudouridine	116
The LGBTQ+ job hunt	114
Deciphering subcellular organization with multiplexed imaging and deep learning	113
Neural networks built with biomolecules	112
Combining compact human protein domains with CRISPR systems for robust gene activation	111
Science while parenting	111
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	110
CAD we share? Publishing reproducible microscope hardware	109
What makes a Nature Methods paper	109
Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells	109
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds	108
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	108
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function	108
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	107
Analyzing single-cell bisulfite sequencing data with MethSCAn	107
Inside the chase after those elusive proteoforms	106
Enabling global image data sharing in the life sciences	106
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	105
Mackenzie Weygandt Mathis	104
Building an automated three-dimensional flight agent for neural network reconstruction	103