OOIR: Observatory of International Research

Papers

(The median citation count of Molecular Systems Biology is 7. 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 2022-01-01 to 2026-01-01.)

Article	Citations
Systematic identification of 20S proteasome substrates	444
Development and validation of AI/ML derived splice-switching oligonucleotides	224
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	188
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	124
A split intein and split luciferase-coupled system for detecting protein-protein interactions	84
State of the interactomes: an evaluation of molecular networks for generating biological insights	79
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	78
Dynamic human liver proteome atlas reveals functional insights into disease pathways	69
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	62
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	61
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	58
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	56
A transient mutational burst occurs during yeast colony development	55
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	50
Enhancing nutritional niche and host defenses by modifying the gut microbiome	50
A proximity proteomics pipeline with improved reproducibility and throughput	46
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	45
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	44
Predicting cellular responses to complex perturbations in high‐throughput screens	43
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	42
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	39
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	38
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	38
What we can learn from deep space communication for reproducible bioimaging and data analysis	36
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	33
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	33
Systematic identification of structure-specific protein–protein interactions	33
Deep learning for protein structure prediction and design—progress and applications	31
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	31
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	30
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	30
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	29
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	29
Predicting natural variation in the yeast phenotypic landscape with machine learning	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	27
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	27
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	26
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Deep quantification of substrate turnover defines protease subsite cooperativity	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
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	25
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Constraints on the optimization of gene product diversity	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	22
Metabolomics paves the way for improved drug target identification	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	21
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	21
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	21
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
Mutational biases favor complexity increases in protein interaction networks after gene duplication	21
The molecular architecture of cell cycle arrest	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	19
Who controls the tariffs of a human cell?	19
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	19
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	18
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	17
A scheduler for rhythmic gene expression	17
The solute carrier superfamily interactome	17
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	17
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	17
Real‐time genomics for One Health	17
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	17
Integrated systems biology approach identifies gene targets for endothelial dysfunction	17
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	16
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	16

Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Updated benchmarking of variant effect predictors using deep mutational scanning	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
Unique features of transcription termination and initiation at closely spaced tandem human genes	15
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	15
The impact of genomic variation on protein phosphorylation states and regulatory networks	14
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	14
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	14
Perspective: a stirring role for metabolism in cells	14
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	14
Viro3D: a comprehensive database of virus protein structure predictions	14
Machine learning-guided deconvolution of plasma protein levels	14
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	14
Oncogenic PIK3CA corrupts growth factor signaling specificity	13
Building and analyzing metacells in single-cell genomics data	13
The population context is a driver of the heterogeneous response of epithelial cells to interferons	13
Impact of drugs and environmental contaminants on amine production by gut bacteria	13
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL	13
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	13
Quantifying the phenotypic information in mRNA abundance	12
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	12
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	12
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	12
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	12
Linking patient-specific basal MET phosphorylation levels to liver health	12
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	12
SLAM‐Drop ‐seq reveals mRNA kinetic rates throughout the cell cycle	12
Compensatory evolution to DNA replication stress is robust to nutrient availability	11
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	11
The genetic interaction map of the human solute carrier superfamily	11
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	11
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	11
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	11
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	11
Engineering mammalian cells for detection and treatment of cardiac injury	11
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	11
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	11
Growth‐mediated negative feedback shapes quantitative antibiotic response	11
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	10
Interrogation of RNA-protein interaction dynamics in bacterial growth	10
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	10
Synovial matrix turnover controls immune cell spatial patterning in inflammation resolution	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	10
Protein complexes in cells by AI ‐assisted structural proteomics	10
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	10
CellNeighborEX : deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	10
Cell cycle criticality as a mechanism for robust cell population control	10
One‐shot ¹³ C ¹⁵ N	10
Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon	9
Dynamics of thyroid diseases and thyroid‐axis gland masses	9
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	9
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis	9
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	9
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map	8
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	8
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	8
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	8
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	8
Single‐cell biology: what does the future hold?	8
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	8
Distinct transcription kinetics of pluripotent cell states	7
Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	7
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	7
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	7
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	7
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	7
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	7
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	7
Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs	7