OOIR: Observatory of International Research

Papers

(The H4-Index of Nature Methods is 98. 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 2021-02-01 to 2025-02-01.)

Article	Citations
Combined sequencing of genomes and epigenomes	5315
Super-resolution 3D live cell imaging	2661
A celebration of structural biology	2068
Human tonsils in a dish	896
Jie Xiao	781
Genome-wide analysis of structural variation	628
Expanding views of the transcriptome	577
iSCAT gets a signal boost	569
Mapping human hematopoiesis	542
Methods lead the way	519
New happenings at Nature Methods	511
Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision	486
Author Correction: Arkitekt: streaming analysis and real-time workflows for microscopy	481
Capture of membrane proteins in their native membrane milieu	431
Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity	412
A multimodal whole-body atlas	366
Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering	366
Seeking more nucleases	346
When peace arrives	336
Inferring biological age from the transcriptome with RAPToR	319
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques	278
How’s your health, forests?	265
Deep learning method for the prediction of glycan structures from mass spectrometry data	264
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data	253
BIONIC: biological network integration using convolutions	240

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments	237
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics	237
Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain	232
Nonnegative spatial factorization applied to spatial genomics	229
Local shape descriptors for neuron segmentation	227
Cell type-specific inference of differential expression in spatial transcriptomics	210
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set	208
FlyWire: online community for whole-brain connectomics	206
SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment	201
SCITO-seq: single-cell combinatorial indexed cytometry sequencing	196
MSNovelist: de novo structure generation from mass spectra	195
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia	188
Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library	185
Best practices for reporting throughput in biomedical research	182
Chroma is a generative model for protein design	182
Artificial intelligence gives neuron reconstruction a performance boost	178
The long and winding road of development: a coordinated song of transcription factors	177
Line-scanning speeds up Brillouin microscopy	174
Fluorophores’ talk turns them dark	171
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice	164
Doubling the resolution of light-sheet fluorescence microscopy	164
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput	163
ReX: an integrative tool for quantifying and optimizing measurement reliability for the study of individual differences	162
Neural networks learn the motions of molecular machines	161
A general method for chemogenetic control of peptide function	152
GWAS and eQTL disparity	148
Phasor plots and the future of spectral and lifetime imaging	147
Long-term monosynaptic tracing	147
DART.2: bidirectional synaptic pharmacology with thousandfold cellular specificity	146
Assembling organs in vitro	144
Dissecting subcellular architecture of whole cells	143
Light-Seq: from microscopy to transcriptomics and back	142
Deep-learning language models help to improve protein sequence alignment	140
Ultra-long-working-distance multiphoton objective unlocks new possibilities for imaging	137
Computation and biology: a partnership	136
Breaking barriers for intravital imaging	136
Vascular subtypes on a dish	135
Diving deeper in the 3D genome	133
Deep brain imaging on the move	131
LocMoFit quantifies cellular structures in super-resolution data	131
Targeted illumination confocal microscopy enables in vivo voltage imaging in thick tissue	130
LiMCA: Hi-C gets an RNA twist	129
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals	128
Integrating one’s LGBTQ+ identity into one’s science	128
Reconstruction of dynamic mammary mini gland in vitro for normal physiology and oncogenesis	127
Spatially resolved multiomics	123
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry	122
Better detection for localization microscopy	120
Chromoscope: interactive multiscale visualization for structural variation in human genomes	119
Accessible computing platforms democratize neuroimaging data analysis	119

Synthetic tissue environments	119
SynNotch tuned for tension	118
Navigating two-body challenges	118
Soil researchers dig deeper into dirt’s complexity	117
Modeling condensate formation in silico	116
Deep learning identifies A-to-I RNA edits using nanopore sequencing data	116
Tamir Gonen	115
Editing naive CD4+ T cells	113
A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding	113
Ex utero synthetic embryos	112
Nanopores distinguish RNA modifications	112
How regulatory sequences learn cell representations	108
The chemistry of microbiome–host togetherness	106
Reporting T cell proliferation	106
Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling	105
Fast and robust metagenomic sequence comparison through sparse chaining with skani	105
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ	104
Synthetic condensates probe chromatin viscoelasticity	104
Adventures in AI	100
Ringside seats to a pandemic	100
Analyzing submicron spatial transcriptomics data at their original resolution	99
Disentangling parallel processes with BEYOND	98
A decade of neuroscience	98