OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 105. 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 2021-05-01 to 2025-05-01.)

Article	Citations
Chromoscope: interactive multiscale visualization for structural variation in human genomes	6287
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	1091
Interpreting and comparing neural activity across systems by geometric deep learning	786
Tamir Gonen	727
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	716
Modeling locomotion from environment to neurons	696
More dimensions of the 3D genome	678
How noncoding RNAs began to leave the junkyard	675
Exoskeleton empowers large-scale neural recordings in freely roaming mice	607
Analyzing submicron spatial transcriptomics data at their original resolution	603
GWAS and eQTL disparity	535
Maximum-likelihood model fitting for quantitative analysis of SMLM data	503
Annotating unknown metabolites	439
Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer	423
MARBLE: interpretable representations of neural population dynamics using geometric deep learning	417
Line-scanning speeds up Brillouin microscopy	328
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics	322
Detecting and correcting false transients in calcium imaging	306
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	300
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models	287
Antibody stabilization for thermally accelerated deep immunostaining	282
Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag	264
SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction	259
Fast and efficient template-mediated synthesis of genetic variants	259
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts	248

DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction	246
Unlocking the power of spatial omics with AI	244
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references	241
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	236
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells	231
Mass spectrometry imaging: the rise of spatially resolved single-cell omics	222
Understanding the invisible hands of sample preparation for cryo-EM	220
Efficient targeted insertion of large DNA fragments without DNA donors	220
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	217
BIONIC: biological network integration using convolutions	216
Best practices and tools for reporting reproducible fluorescence microscopy methods	209
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	204
When labs welcome under-represented groups	198
Using machine learning to predict the structure of proteins that bind to DNA and RNA	198
BATTLES: high-throughput screening of antigen recognition under force	196
ENTERing the world of immune cells	196
Quest: my postdoc home	187
Setting standards for stem cells	186
Sensitive protein analysis with plexDIA	186
Non-invasive metabolic imaging of brown adipose tissue	186
From GWAS to single-cell MPRA	184
Publisher Correction: Museum of spatial transcriptomics	183
Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells	175
wwPDB biocuration: on the front line of structural biology	172
Tardigrades	169
Trawling the ocean virome	165
Long-read sequencing in the era of epigenomics and epitranscriptomics	162
De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	161
Comparing classifier performance with baselines	159
The placozoan Trichoplax	158
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging	158
Peer review demystified: part 2	158
Author Correction: Learning single-cell perturbation responses using neural optimal transport	157
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps	156
How developmental cell atlases inform stem cell embryo models	156
One cell, two cell, dead cell, true cell	155
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures	155
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing	154
Indexing and searching petabase-scale nucleotide resources	152
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity	152
The crustacean Parhyale	150
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation	148
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data	148
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology	146
LIVECell—A large-scale dataset for label-free live cell segmentation	144
Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells	143
Detection of m6A from direct RNA sequencing using a multiple instance learning framework	143
The tidyomics ecosystem: enhancing omic data analyses	142
StayGold variants for molecular fusion and membrane-targeting applications	141
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting	139

The LGBTQ+ job hunt	136
Deciphering subcellular organization with multiplexed imaging and deep learning	135
Neural networks built with biomolecules	132
A method for quantitative and base-resolution sequencing of pseudouridine	130
A graph neural network that combines scRNA-seq and protein–protein interaction data	129
Image processing tools for petabyte-scale light sheet microscopy data	126
Enabling global image data sharing in the life sciences	126
Inside the chase after those elusive proteoforms	123
Analyzing single-cell bisulfite sequencing data with MethSCAn	122
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence	122
Tackling tumor complexity with single-cell proteomics	122
DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps	122
The future of bioimage analysis: a dialog between mind and machine	120
Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing	119
Method of the Year 2024: spatial proteomics	119
Propensity score weighting	118
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing	117
SODB facilitates comprehensive exploration of spatial omics data	117
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq	115
Comparison of transformations for single-cell RNA-seq data	114
Combining compact human protein domains with CRISPR systems for robust gene activation	113
What makes a Nature Methods paper	113
Science while parenting	113
Multimodal large language models for bioimage analysis	110
Publisher Correction: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study	109
Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution	109
CAD we share? Publishing reproducible microscope hardware	108
Building an automated three-dimensional flight agent for neural network reconstruction	107
Mackenzie Weygandt Mathis	105
Method of the Year: protein structure prediction	105