Molecular Systems Biology

Article	Citations
State of the interactomes: an evaluation of molecular networks for generating biological insights	260
Dynamic human liver proteome atlas reveals functional insights into disease pathways	234
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	136
A split intein and split luciferase-coupled system for detecting protein-protein interactions	100
Development and validation of AI/ML derived splice-switching oligonucleotides	83
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	78
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	76
Systematic identification of 20S proteasome substrates	66
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	63
A transient mutational burst occurs during yeast colony development	60
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	59
Enhancing nutritional niche and host defenses by modifying the gut microbiome	57
Progress and new challenges in image-based profiling	56
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	53
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	52
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	50
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	47
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	46
A proximity proteomics pipeline with improved reproducibility and throughput	45
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	44
Predicting cellular responses to complex perturbations in high‐throughput screens	43
What we can learn from deep space communication for reproducible bioimaging and data analysis	39
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	37
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	37
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	37

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	35
Systematic identification of structure-specific protein–protein interactions	33
Deep learning for protein structure prediction and design—progress and applications	33
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	33
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	32
Predicting natural variation in the yeast phenotypic landscape with machine learning	32
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	32
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	32
Five dominant amino acid substitution signatures shape tumour immunity	30
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	28
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	28
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	27
Deep quantification of substrate turnover defines protease subsite cooperativity	27
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	26
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	25
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	24
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	24
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	23
Constraints on the optimization of gene product diversity	23
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
The molecular architecture of cell cycle arrest	21
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	20
The DNA dialect: a comprehensive guide to pretrained genomic language models	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	19
A scheduler for rhythmic gene expression	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
The solute carrier superfamily interactome	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	19
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
Who controls the tariffs of a human cell?	19
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	19
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	18
Real‐time genomics for One Health	18

Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	18
Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	18
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17
Proteome-wide AlphaFold pool party	17
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	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
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	16
The impact of genomic variation on protein phosphorylation states and regulatory networks	16
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	16
Updated benchmarking of variant effect predictors using deep mutational scanning	16
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL	14
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	14
Building and analyzing metacells in single-cell genomics data	14
Viro3D: a comprehensive database of virus protein structure predictions	14
Impact of drugs and environmental contaminants on amine production by gut bacteria	14
Oncogenic PIK3CA corrupts growth factor signaling specificity	14
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	14
Machine learning-guided deconvolution of plasma protein levels	14
Linking patient-specific basal MET phosphorylation levels to liver health	13
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	13
SLAM‐Drop ‐seq reveals mRNA kinetic rates throughout the cell cycle	13
Quantifying the phenotypic information in mRNA abundance	13
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	13
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	13
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	12
Single-cell analysis reveals critical toxin/antitoxin ratio triggering persister resuscitation	12
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	12
The population context is a driver of the heterogeneous response of epithelial cells to interferons	12
Compensatory evolution to DNA replication stress is robust to nutrient availability	12
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	12
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	12
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	12
Engineering mammalian cells for detection and treatment of cardiac injury	12
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	12
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	12
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	11
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	11
Protein complexes in cells by AI ‐assisted structural proteomics	11
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	11
The genetic interaction map of the human solute carrier superfamily	11
Growth‐mediated negative feedback shapes quantitative antibiotic response	11
CellNeighborEX : deciphering neighbor‐dependent gene expression from spatial transcriptomics data	11
A universal surface functionalization technique to chemically enhance live microbial cells	11
Synovial matrix turnover controls immune cell spatial patterning in inflammation resolution	11
Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis	10
Interrogation of RNA-protein interaction dynamics in bacterial growth	10
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	10
One‐shot 13 C 15 N	10
Cell cycle criticality as a mechanism for robust cell population control	10
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	10
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon	9
SyntheMol-RL: a flexible reinforcement learning framework for designing easily synthesizable antibiotics	9
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	9
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	9
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	9
Single‐cell biology: what does the future hold?	9
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	9
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	8
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	8
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	8
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	8
Dynamics of thyroid diseases and thyroid‐axis gland masses	8
Essentiality and dynamic expression of the human tRNA pool during viral infection	8
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map	7
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	7
Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs	6
Extensive folding variability between homologous chromosomes in mammalian cells	6
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	6
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	6
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	6
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response	6
Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	6

VEFill: accurate and generalizable deep mutational scanning score imputation across protein domains	6
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	6
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	6