Molecular Systems Biology

Article	Citations
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	315
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	302
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	204
RNA velocity—current challenges and future perspectives	174
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	126
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	120
A single cell atlas of the human liver tumor microenvironment	112
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	105
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	96
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	95
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	90
Reproducibility in systems biology modelling	75
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	72
Protein complexes in cells by AI‐assisted structural proteomics	71
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	71
Predicting cellular responses to complex perturbations in high‐throughput screens	69
Evaluating the Arrhenius equation for developmental processes	67
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	67
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	61
A guidebook for DISCO tissue clearing	61
Joint cell segmentation and cell type annotation for spatial transcriptomics	59
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	53
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	52
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	51
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	46

Enabling high‐throughput biology with flexible open‐source automation	46
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	46
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	46
Updated benchmarking of variant effect predictors using deep mutational scanning	45
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	44
A genome‐scale yeast library with inducible expression of individual genes	44
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	44
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	43
The genotype‐phenotype landscape of an allosteric protein	41
The transcriptome dynamics of single cells during the cell cycle	41
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	38
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	37
Exploring amino acid functions in a deep mutational landscape	36
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	35
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	34
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	32
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	32
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	30
Single‐cell imaging of genome organization and dynamics	29
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	28
Dynamic human liver proteome atlas reveals functional insights into disease pathways	28
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	28
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	28
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks	27
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	27
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	27
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	27
Modeling glioblastoma heterogeneity as a dynamic network of cell states	26
Transcriptionally active enhancers in human cancer cells	26
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	26
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	25
The molecular architecture of cell cycle arrest	24
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	24
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback	24
Large‐scale survey and database of high affinity ligands for peptide recognition modules	23
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	23
Diauxic lags explain unexpected coexistence in multi‐resource environments	23
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	23
Using single‐plant‐omics in the field to link maize genes to functions and phenotypes	23
Behavioral fingerprints predict insecticide and anthelmintic mode of action	22
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators	22
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data	22
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	22
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis	21
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa	21
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape	21
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions	21
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	20
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	20
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids	20

An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	20
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	20
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	20
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration	20
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	20
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae	20
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	19
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	19
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	19
Deciphering the physiological response of Escherichia coli under high ATP demand	19
High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins	18
Automated assembly of molecular mechanisms at scale from text mining and curated databases	18
TATA and paused promoters active in differentiated tissues have distinct expression characteristics	18
Tensor‐structured decomposition improves systems serology analysis	18
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	17
A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast	17
Identifying modules of cooperating cancer drivers	17
Dynamics of thyroid diseases and thyroid‐axis gland masses	16
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	16
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	16
A spatial model of the plant circadian clock reveals design principles for coordinated timing	16
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	16
The impact of genomic variation on protein phosphorylation states and regulatory networks	16
Real‐time genomics for One Health	16
Genome‐scale metabolic modeling reveals key features of a minimal gene set	16
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	15
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	15
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	15
Growth‐dependent heterogeneity in the DNA damage response in Escherichia coli	15
Competitive dCas9 binding as a mechanism for transcriptional control	15
Levels of autonomy in synthetic biology engineering	15
CODEX, a neural network approach to explore signaling dynamics landscapes	15
Metabolic memory underlying minimal residual disease in breast cancer	15
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics	14
Computational estimation of quality and clinical relevance of cancer cell lines	14
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	14
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	14
A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord	14
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	14
Perspective: a stirring role for metabolism in cells	14
Natural variants suppress mutations in hundreds of essential genes	14
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	14
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	14
The Data Governance Act and the EU's move towards facilitating data sharing	13
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	13
From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration	12
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	12
Predictive evolution of metabolic phenotypes using model‐designed environments	12
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	12
Efficient plasmid transfer via natural competence in a microbial co‐culture	12
The circadian oscillator analysed at the single‐transcript level	12
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	12
Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion	12
A method for benchmarking genetic screens reveals a predominant mitochondrial bias	11
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit	11
Integrative characterization of the near‐minimal bacterium Mesoplasma florum	11
Systems‐level transcriptional regulation of Caenorhabditis elegans metabolism	11
Heterogeneity of the cancer cell line metabolic landscape	11
A human kinase yeast array for the identification of kinases modulating phosphorylation‐dependent protein–protein interactions	11
Multistability maintains redox homeostasis in human cells	11
The genotype‐phenotype landscape of an allosteric protein	11
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	11
Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype	10
One‐shot 13C15N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	10
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	10
Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria	10
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	10
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	10
Pooled genetic screens with image‐based profiling	10
Dormancy‐to‐death transition in yeast spores occurs due to gradual loss of gene‐expressing ability	10
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	10
Enablers and challenges of spatial omics, a melting pot of technologies	10
Genetic effects on molecular network states explain complex traits	9
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	9
Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli	9
The rise of proteome‐wide biophysics	9
A single‐cell RNA labeling strategy for measuring stress response upon tissue dissociation	9
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	9
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	9
A circuit for secretion‐coupled cellular autonomy in multicellular eukaryotic cells	9

Predictability of the community‐function landscape in wine yeast ecosystems	9
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	9
Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses	9
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	9
Single‐cell biology: what does the future hold?	9
Spurious regulatory connections dictate the expression‐fitness landscape of translation factors	9
Growth‐mediated negative feedback shapes quantitative antibiotic response	9