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 2022-07-01 to 2026-07-01.)

Article	Citations
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	269
Development and validation of AI/ML derived splice-switching oligonucleotides	263
Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms	142
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	107
To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis	87
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	83
Systematic identification of 20S proteasome substrates	82
A split intein and split luciferase-coupled system for detecting protein-protein interactions	69
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	67
State of the interactomes: an evaluation of molecular networks for generating biological insights	63
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	62
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent	62
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	57
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	57
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	56
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	55
Enhancing nutritional niche and host defenses by modifying the gut microbiome	54
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	49
A transient mutational burst occurs during yeast colony development	47
Toward trustworthy healthcare AI: designing academic research for translation readiness	43
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	41
Progress and new challenges in image-based profiling	38
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	37
A proximity proteomics pipeline with improved reproducibility and throughput	37
Predicting cellular responses to complex perturbations in high‐throughput screens	37

Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	36
What we can learn from deep space communication for reproducible bioimaging and data analysis	36
Deep learning for protein structure prediction and design—progress and applications	35
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	34
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	32
Systematic identification of structure-specific protein–protein interactions	30
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	30
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	30
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	30
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	28
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	28
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	28
Five dominant amino acid substitution signatures shape tumour immunity	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Predicting natural variation in the yeast phenotypic landscape with machine learning	27
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	26
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	26
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	26
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	25
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	25
Deep quantification of substrate turnover defines protease subsite cooperativity	25
Erratum To: Resuscitation dynamics reveal persister partitioning after antibiotic treatment	25
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	25
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Constraints on the optimization of gene product diversity	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	24
The molecular architecture of cell cycle arrest	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	22
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
Transcription factor expression is the main determinant of variability in gene co‐activity	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
The DNA dialect: a comprehensive guide to pretrained genomic language models	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
The solute carrier superfamily interactome	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	20
Who controls the tariffs of a human cell?	20
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
Real‐time genomics for One Health	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	19

A scheduler for rhythmic gene expression	18
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	18
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	18
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
Updated benchmarking of variant effect predictors using deep mutational scanning	17
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	17
Proteome-wide AlphaFold pool party	17
CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq	17