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 2021-10-01 to 2025-10-01.)

Article	Citations
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	420
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	182
State of the interactomes: an evaluation of molecular networks for generating biological insights	160
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	113
Systematic identification of 20S proteasome substrates	96
Dynamic human liver proteome atlas reveals functional insights into disease pathways	96
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	78
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	74
Development and validation of AI/ML derived splice-switching oligonucleotides	71
A split intein and split luciferase-coupled system for detecting protein-protein interactions	69
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	64
A transient mutational burst occurs during yeast colony development	56
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	54
A proximity proteomics pipeline with improved reproducibility and throughput	51
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	51
Enhancing nutritional niche and host defenses by modifying the gut microbiome	50
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	45
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	45
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	43
Predicting cellular responses to complex perturbations in high‐throughput screens	42
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	40
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	40
What we can learn from deep space communication for reproducible bioimaging and data analysis	38
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	37

Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	37
Deep learning for protein structure prediction and design—progress and applications	36
Systematic identification of structure-specific protein–protein interactions	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
The genotype‐phenotype landscape of an allosteric protein	32
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	32
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	30
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	30
Predicting natural variation in the yeast phenotypic landscape with machine learning	29
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	28
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	27
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
Deep quantification of substrate turnover defines protease subsite cooperativity	27
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	27
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	26
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Constraints on the optimization of gene product diversity	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Automated assembly of molecular mechanisms at scale from text mining and curated databases	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	23
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Metabolomics paves the way for improved drug target identification	23
The molecular architecture of cell cycle arrest	22
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	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
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	18
The solute carrier superfamily interactome	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	18
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	17
Real‐time genomics for One Health	17
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	17

Unique features of transcription termination and initiation at closely spaced tandem human genes	17
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	17
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	16
Updated benchmarking of variant effect predictors using deep mutational scanning	16
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	16
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	16
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	15
The impact of genomic variation on protein phosphorylation states and regulatory networks	15
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	15
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections	15
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	15
Viro3D: a comprehensive database of virus protein structure predictions	15
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Oncogenic PIK3CA corrupts growth factor signaling specificity	14
Building and analyzing metacells in single-cell genomics data	14
Perspective: a stirring role for metabolism in cells	14
Impact of drugs and environmental contaminants on amine production by gut bacteria	13
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	13
Linking patient-specific basal MET phosphorylation levels to liver health	13
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	13
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	12
The population context is a driver of the heterogeneous response of epithelial cells to interferons	12
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	12
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	12
Quantifying the phenotypic information in mRNA abundance	12
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	11
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	11
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	11
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	11
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	11
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	11
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	11
The genetic interaction map of the human solute carrier superfamily	11
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	11
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	11
Compensatory evolution to DNA replication stress is robust to nutrient availability	11
Protein complexes in cells by AI‐assisted structural proteomics	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	10
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	10
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	10
Deciphering the physiological response of Escherichia coli under high ATP demand	9
Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis	9
Interrogation of RNA-protein interaction dynamics in bacterial growth	9
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	9
Synovial matrix turnover controls immune cell spatial patterning in inflammation resolution	9
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	9
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	9
One‐shot ¹³C¹⁵N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	9
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	9
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	9
Growth‐mediated negative feedback shapes quantitative antibiotic response	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	9
Distinct transcription kinetics of pluripotent cell states	8
Single‐cell biology: what does the future hold?	8
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	8
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	8
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	8
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	8
Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon	8
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map	8
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	8
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	8
Dynamics of thyroid diseases and thyroid‐axis gland masses	8
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	8
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	7
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	7
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	7
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	7
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	7
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	7
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	7
Extensive folding variability between homologous chromosomes in mammalian cells	7