OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 18. 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 2021-08-01 to 2025-08-01.)

Article	Citations
A split intein and split luciferase-coupled system for detecting protein-protein interactions	401
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	219
Development and validation of AI/ML derived splice-switching oligonucleotides	163
State of the interactomes: an evaluation of molecular networks for generating biological insights	137
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	108
Systematic identification of 20S proteasome substrates	107
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	93
Dynamic human liver proteome atlas reveals functional insights into disease pathways	93
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	88
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	71
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	70
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	67
A transient mutational burst occurs during yeast colony development	66
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	63
Evaluating the Arrhenius equation for developmental processes	61
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	56
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	52
Enhancing nutritional niche and host defenses by modifying the gut microbiome	49
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	48
A proximity proteomics pipeline with improved reproducibility and throughput	48
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	43
Predicting cellular responses to complex perturbations in high‐throughput screens	43
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	42
Systematic identification of structure-specific protein–protein interactions	41
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	40

What we can learn from deep space communication for reproducible bioimaging and data analysis	40
The genotype‐phenotype landscape of an allosteric protein	39
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	39
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	35
Deep learning for protein structure prediction and design—progress and applications	35
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	34
Tensor‐structured decomposition improves systems serology analysis	33
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	33
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	32
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	31
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	30
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Deep quantification of substrate turnover defines protease subsite cooperativity	28
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	27
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	27
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Constraints on the optimization of gene product diversity	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Metabolomics paves the way for improved drug target identification	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	22
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
The molecular architecture of cell cycle arrest	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	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
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	20
Who controls the tariffs of a human cell?	20
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	20
The solute carrier superfamily interactome	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	18
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18

Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	18
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	18