OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 15. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	428
Dynamic human liver proteome atlas reveals functional insights into disease pathways	208
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	168
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	115
Systematic identification of 20S proteasome substrates	79
Development and validation of AI/ML derived splice-switching oligonucleotides	76
A split intein and split luciferase-coupled system for detecting protein-protein interactions	73
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	65
State of the interactomes: an evaluation of molecular networks for generating biological insights	65
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	57
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	56
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	55
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	53
Enhancing nutritional niche and host defenses by modifying the gut microbiome	52
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	46
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	45
A transient mutational burst occurs during yeast colony development	43
A proximity proteomics pipeline with improved reproducibility and throughput	43
Predicting cellular responses to complex perturbations in high‐throughput screens	40
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	40
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	37
What we can learn from deep space communication for reproducible bioimaging and data analysis	36
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	33
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	32

Systematic identification of structure-specific protein–protein interactions	31
The genotype‐phenotype landscape of an allosteric protein	31
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	30
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	30
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	29
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Predicting natural variation in the yeast phenotypic landscape with machine learning	29
Deep learning for protein structure prediction and design—progress and applications	29
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Deep quantification of substrate turnover defines protease subsite cooperativity	26
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	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
Constraints on the optimization of gene product diversity	24
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	24
The molecular architecture of cell cycle arrest	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Metabolomics paves the way for improved drug target identification	23
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
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	21
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	19
Who controls the tariffs of a human cell?	19
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	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
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	17
A scheduler for rhythmic gene expression	17
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	17
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	17
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	16
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	16
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Updated benchmarking of variant effect predictors using deep mutational scanning	15

Unique features of transcription termination and initiation at closely spaced tandem human genes	15
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	15
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	15
Real‐time genomics for One Health	15
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	15
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	15
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	15