OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 19. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Development and validation of AI/ML derived splice-switching oligonucleotides	386
A split intein and split luciferase-coupled system for detecting protein-protein interactions	209
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	152
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	121
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	102
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	99
State of the interactomes: an evaluation of molecular networks for generating biological insights	86
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	85
Dynamic human liver proteome atlas reveals functional insights into disease pathways	81
Systematic identification of 20S proteasome substrates	67
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	67
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	65
Enhancing nutritional niche and host defenses by modifying the gut microbiome	63
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	63
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	61
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	59
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	57
A proximity proteomics pipeline with improved reproducibility and throughput	53
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	53
Predicting cellular responses to complex perturbations in high‐throughput screens	49
Evaluating the Arrhenius equation for developmental processes	47
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	47
Systematic identification of structure-specific protein–protein interactions	45
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	41
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	40

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	38
What we can learn from deep space communication for reproducible bioimaging and data analysis	38
The genotype‐phenotype landscape of an allosteric protein	38
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	37
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	37
Tensor‐structured decomposition improves systems serology analysis	37
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	35
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	34
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	32
Deep learning for protein structure prediction and design—progress and applications	32
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	32
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	31
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	31
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	30
Deep quantification of substrate turnover defines protease subsite cooperativity	30
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	29
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	28
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit	27
Model‐guided development of an evolutionarily stable yeast chassis	27
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	27
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	26
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	26
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Constraints on the optimization of gene product diversity	24
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
The molecular architecture of cell cycle arrest	23
Metabolomics paves the way for improved drug target identification	23
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	23
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	22
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	22
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	21
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	21
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
The solute carrier superfamily interactome	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
Who controls the tariffs of a human cell?	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	19