OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 20. 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 2021-05-01 to 2025-05-01.)

Article	Citations
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	379
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	206
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	150
A split intein and split luciferase-coupled system for detecting protein-protein interactions	116
Systematic identification of 20S proteasome substrates	116
Dynamic human liver proteome atlas reveals functional insights into disease pathways	113
State of the interactomes: an evaluation of molecular networks for generating biological insights	100
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	95
Development and validation of AI/ML derived splice-switching oligonucleotides	83
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	80
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	77
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	73
Enhancing nutritional niche and host defenses by modifying the gut microbiome	65
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	64
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	64
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	62
A proximity proteomics pipeline with improved reproducibility and throughput	61
Evaluating the Arrhenius equation for developmental processes	57
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	56
Predicting cellular responses to complex perturbations in high‐throughput screens	55
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	53
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	52
Deep learning for protein structure prediction and design—progress and applications	48
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	47
The genotype‐phenotype landscape of an allosteric protein	47

Systematic identification of structure-specific protein–protein interactions	46
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	43
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	40
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	39
What we can learn from deep space communication for reproducible bioimaging and data analysis	37
Tensor‐structured decomposition improves systems serology analysis	35
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	35
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	35
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	35
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	33
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	32
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	31
Deep quantification of substrate turnover defines protease subsite cooperativity	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	31
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	30
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	29
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	29
Model‐guided development of an evolutionarily stable yeast chassis	28
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	27
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	27
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	27
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit	27
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	27
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Metabolomics paves the way for improved drug target identification	25
Mutational biases favor complexity increases in protein interaction networks after gene duplication	25
Automated assembly of molecular mechanisms at scale from text mining and curated databases	24
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	24
Constraints on the optimization of gene product diversity	24
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	23
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	22
The molecular architecture of cell cycle arrest	22
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	21
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Transcription factor expression is the main determinant of variability in gene co‐activity	20
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	20
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	20
Real‐time genomics for One Health	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	20