OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 16. 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 2021-12-01 to 2025-12-01.)

Article	Citations
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	435
Systematic identification of 20S proteasome substrates	219
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	180
Development and validation of AI/ML derived splice-switching oligonucleotides	121
A split intein and split luciferase-coupled system for detecting protein-protein interactions	82
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	78
Dynamic human liver proteome atlas reveals functional insights into disease pathways	77
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	68
State of the interactomes: an evaluation of molecular networks for generating biological insights	65
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	60
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	59
Enhancing nutritional niche and host defenses by modifying the gut microbiome	57
A transient mutational burst occurs during yeast colony development	53
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	53
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	50
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	47
A proximity proteomics pipeline with improved reproducibility and throughput	46
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	43
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	42
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	42
Predicting cellular responses to complex perturbations in high‐throughput screens	42
What we can learn from deep space communication for reproducible bioimaging and data analysis	38
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	37
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	35
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	33

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	33
Systematic identification of structure-specific protein–protein interactions	32
The genotype‐phenotype landscape of an allosteric protein	32
Deep learning for protein structure prediction and design—progress and applications	32
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	32
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	31
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	30
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	29
Predicting natural variation in the yeast phenotypic landscape with machine learning	29
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	27
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Deep quantification of substrate turnover defines protease subsite cooperativity	26
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	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
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	24
Metabolomics paves the way for improved drug target identification	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	23
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	22
The molecular architecture of cell cycle arrest	22
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	21
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	21
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
Automated assembly of molecular mechanisms at scale from text mining and curated databases	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	20
Who controls the tariffs of a human cell?	19
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	19
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	19
LaGrACE: estimating gene program dysregulation with latent regulatory network	18
Transcription factor expression is the main determinant of variability in gene co‐activity	18
The solute carrier superfamily interactome	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	17
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	17
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	17
Real‐time genomics for One Health	16
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	16
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	16
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	16
Unique features of transcription termination and initiation at closely spaced tandem human genes	16

Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	16
A scheduler for rhythmic gene expression	16
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	16