Molecular Systems Biology

Article	Citations
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	282
Development and validation of AI/ML derived splice-switching oligonucleotides	275
Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms	142
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	111
To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis	93
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent	89
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	82
A split intein and split luciferase-coupled system for detecting protein-protein interactions	69
Systematic identification of 20S proteasome substrates	66
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	66
State of the interactomes: an evaluation of molecular networks for generating biological insights	62
Toward trustworthy healthcare AI: designing academic research for translation readiness	61
Enhancing nutritional niche and host defenses by modifying the gut microbiome	60
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	58
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	58
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	57
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	49
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	49
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	44
A transient mutational burst occurs during yeast colony development	43
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	41
A proximity proteomics pipeline with improved reproducibility and throughput	39
Progress and new challenges in image-based profiling	38
Predicting cellular responses to complex perturbations in high‐throughput screens	37
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	36

Systematic identification of structure-specific protein–protein interactions	36
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	36
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	36
What we can learn from deep space communication for reproducible bioimaging and data analysis	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	33
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	31
Deep learning for protein structure prediction and design—progress and applications	30
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	29
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
Five dominant amino acid substitution signatures shape tumour immunity	28
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	28
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	28
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	28
Erratum To: Resuscitation dynamics reveal persister partitioning after antibiotic treatment	27
Predicting natural variation in the yeast phenotypic landscape with machine learning	27
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	27
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
Deep quantification of substrate turnover defines protease subsite cooperativity	26
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	25
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	25
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Mutational biases favor complexity increases in protein interaction networks after gene duplication	25
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Constraints on the optimization of gene product diversity	24
Automated assembly of molecular mechanisms at scale from text mining and curated databases	24
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	22
Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
The molecular architecture of cell cycle arrest	22
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	22
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
LaGrACE: estimating gene program dysregulation with latent regulatory network	21
Who controls the tariffs of a human cell?	21
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Transcription factor expression is the main determinant of variability in gene co‐activity	19
The DNA dialect: a comprehensive guide to pretrained genomic language models	19
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	19
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	19
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	19

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	19
The solute carrier superfamily interactome	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
Real‐time genomics for One Health	19
Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	18
A scheduler for rhythmic gene expression	18
Proteome-wide AlphaFold pool party	17
xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction	17
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	16
qMAP decodes RNA fragmentation dynamics in development and disease	16
Updated benchmarking of variant effect predictors using deep mutational scanning	16
CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq	16
Viro3D: a comprehensive database of virus protein structure predictions	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	15
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	15
Immunoglobulin sub-class levels define inter-donor plasma variability: a longitudinal dual-lab study	15
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	15
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	14
Multiscale learning of gene network-driven phenotypic dynamics of single cells	14
E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients	14
Impact of drugs and environmental contaminants on amine production by gut bacteria	14
Decoding and steering spatially resolved cellular dynamics	14
Machine learning-guided deconvolution of plasma protein levels	13
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL	13
Linking patient-specific basal MET phosphorylation levels to liver health	13
Oncogenic PIK3CA corrupts growth factor signaling specificity	13
The population context is a driver of the heterogeneous response of epithelial cells to interferons	13
Building and analyzing metacells in single-cell genomics data	13
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	12
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	12
Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses	12
Quantifying the phenotypic information in mRNA abundance	12
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	12
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	12
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	12
SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle	12
Compensatory evolution to DNA replication stress is robust to nutrient availability	12
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	11
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	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
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV‐2 exposure	11
Engineering mammalian cells for detection and treatment of cardiac injury	11
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	11
Single-cell analysis reveals critical toxin/antitoxin ratio triggering persister resuscitation	11
Protein complexes in cells by AI‐assisted structural proteomics	10
The genetic interaction map of the human solute carrier superfamily	10
Bacterial expression of a designed single‐chain IL‐10 prevents severe lung inflammation	10
Growth‐mediated negative feedback shapes quantitative antibiotic response	10
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	10
A universal surface functionalization technique to chemically enhance live microbial cells	10
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	10
Cell cycle criticality as a mechanism for robust cell population control	9
Interrogation of RNA-protein interaction dynamics in bacterial growth	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
One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	9
Synovial matrix turnover controls immune cell spatial patterning in inflammation resolution	9
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	9
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	9
Single‐cell biology: what does the future hold?	8
SyntheMol-RL: a flexible reinforcement learning framework for designing easily synthesizable antibiotics	8
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	8
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	8
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	8
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	7
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
Dynamics of thyroid diseases and thyroid‐axis gland masses	7
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	7
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	7
Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon	7
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	7
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	7
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	7
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	7

VEFill: accurate and generalizable deep mutational scanning score imputation across protein domains	6
Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	6
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response	6
Essentiality and dynamic expression of the human tRNA pool during viral infection	6
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	6
Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery	6
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	6
Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs	6