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 2021-09-01 to 2025-09-01.)

Article	Citations
Development and validation of AI/ML derived splice-switching oligonucleotides	410
A split intein and split luciferase-coupled system for detecting protein-protein interactions	172
Systematic identification of 20S proteasome substrates	143
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	109
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	94
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	93
State of the interactomes: an evaluation of molecular networks for generating biological insights	73
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	71
Dynamic human liver proteome atlas reveals functional insights into disease pathways	70
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	68
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	65
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	63
A transient mutational burst occurs during yeast colony development	58
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	54
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	51
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	50
Enhancing nutritional niche and host defenses by modifying the gut microbiome	49
A proximity proteomics pipeline with improved reproducibility and throughput	45
Predicting cellular responses to complex perturbations in high‐throughput screens	45
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	44
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	41
The genotype‐phenotype landscape of an allosteric protein	40
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	39
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	39
Tensor‐structured decomposition improves systems serology analysis	38

Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	37
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	35
What we can learn from deep space communication for reproducible bioimaging and data analysis	34
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
Systematic identification of structure-specific protein–protein interactions	33
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	32
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	31
Deep learning for protein structure prediction and design—progress and applications	31
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	29
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
Predicting natural variation in the yeast phenotypic landscape with machine learning	27
Deep quantification of substrate turnover defines protease subsite cooperativity	26
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	26
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	24
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	24
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	24
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	24
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
Constraints on the optimization of gene product diversity	24
Metabolomics paves the way for improved drug target identification	23
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
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
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	22
The molecular architecture of cell cycle arrest	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	21
Who controls the tariffs of a human cell?	21
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	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	19
The solute carrier superfamily interactome	19
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	18