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 2022-05-01 to 2026-05-01.)

Article	Citations
State of the interactomes: an evaluation of molecular networks for generating biological insights	260
Dynamic human liver proteome atlas reveals functional insights into disease pathways	234
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	136
A split intein and split luciferase-coupled system for detecting protein-protein interactions	100
Development and validation of AI/ML derived splice-switching oligonucleotides	83
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	78
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	76
Systematic identification of 20S proteasome substrates	66
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	63
A transient mutational burst occurs during yeast colony development	60
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	59
Enhancing nutritional niche and host defenses by modifying the gut microbiome	57
Progress and new challenges in image-based profiling	56
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	53
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	52
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	50
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	47
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	46
A proximity proteomics pipeline with improved reproducibility and throughput	45
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	44
Predicting cellular responses to complex perturbations in high‐throughput screens	43
What we can learn from deep space communication for reproducible bioimaging and data analysis	39
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	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	37

A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	35
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Deep learning for protein structure prediction and design—progress and applications	33
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	33
Systematic identification of structure-specific protein–protein interactions	33
Predicting natural variation in the yeast phenotypic landscape with machine learning	32
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	32
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	32
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	32
Five dominant amino acid substitution signatures shape tumour immunity	30
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	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
Deep quantification of substrate turnover defines protease subsite cooperativity	27
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	27
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	26
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	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
Constraints on the optimization of gene product diversity	23
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Mutational biases favor complexity increases in protein interaction networks after gene duplication	23
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
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
The molecular architecture of cell cycle arrest	21
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	21
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	20
The DNA dialect: a comprehensive guide to pretrained genomic language models	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	19
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Who controls the tariffs of a human cell?	19
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	19
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	19
A scheduler for rhythmic gene expression	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
The solute carrier superfamily interactome	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Real‐time genomics for One Health	18
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	18

Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	18
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	18
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	17
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	17
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17
Proteome-wide AlphaFold pool party	17