OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 17. 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 2022-06-01 to 2026-06-01.)

Article	Citations
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	265
State of the interactomes: an evaluation of molecular networks for generating biological insights	245
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	139
Development and validation of AI/ML derived splice-switching oligonucleotides	104
Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms	87
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent	80
A split intein and split luciferase-coupled system for detecting protein-protein interactions	79
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	67
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	64
Systematic identification of 20S proteasome substrates	60
Toward trustworthy healthcare AI: designing academic research for translation readiness	58
Enhancing nutritional niche and host defenses by modifying the gut microbiome	57
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	55
Progress and new challenges in image-based profiling	53
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	53
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	50
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	48
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	48
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	45
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	44
A transient mutational burst occurs during yeast colony development	42
A proximity proteomics pipeline with improved reproducibility and throughput	39
Deep learning for protein structure prediction and design—progress and applications	37
Predicting cellular responses to complex perturbations in high‐throughput screens	37
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	37

Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	35
What we can learn from deep space communication for reproducible bioimaging and data analysis	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	34
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	34
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	34
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	30
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	29
Systematic identification of structure-specific protein–protein interactions	29
Five dominant amino acid substitution signatures shape tumour immunity	28
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	28
Predicting natural variation in the yeast phenotypic landscape with machine learning	28
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	27
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	27
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	27
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	25
Erratum To: Resuscitation dynamics reveal persister partitioning after antibiotic treatment	25
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	24
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	24
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	24
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	24
Deep quantification of substrate turnover defines protease subsite cooperativity	24
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
Constraints on the optimization of gene product diversity	22
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
Mutational biases favor complexity increases in protein interaction networks after gene duplication	22
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	21
The molecular architecture of cell cycle arrest	21
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	20
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	20
The solute carrier superfamily interactome	19
The DNA dialect: a comprehensive guide to pretrained genomic language models	19
Who controls the tariffs of a human cell?	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
Real‐time genomics for One Health	19
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	18
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	18
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	18

From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	17
Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	17
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	17
A scheduler for rhythmic gene expression	17