Molecular Systems Biology

Article	Citations
The protein expression profile of ACE2 in human tissues	718
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	258
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	221
SBML Level 3: an extensible format for the exchange and reuse of biological models	180
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	158
Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease	154
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation	136
RNA velocity—current challenges and future perspectives	133
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome	129
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations	120
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder	100
A single cell atlas of the human liver tumor microenvironment	98
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	95
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	93
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	86
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	84
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference	80
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	77
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	77
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks	76
Predicting antigen specificity of single T cells based on TCR CDR 3 regions	68
Reproducibility in systems biology modelling	68
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	65
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens	62
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate	62

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	61
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics	59
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	57
Programmable CRISPR‐Cas transcriptional activation in bacteria	56
A guidebook for DISCO tissue clearing	56
Evaluating the Arrhenius equation for developmental processes	55
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	54
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation	50
Joint cell segmentation and cell type annotation for spatial transcriptomics	49
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	48
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	48
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity	48
In vitro and in vivo identification of clinically approved drugs that modify ACE 2	47
Enhancing scientific discoveries in molecular biology with deep generative models	46
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads	46
Predictive features of gene expression variation reveal mechanistic link with differential expression	45
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	45
Systematic analysis of bypass suppression of essential genes	44
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	44
Predicting cellular responses to complex perturbations in high‐throughput screens	44
Protein complexes in cells by AI‐assisted structural proteomics	44
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch	43
Enabling high‐throughput biology with flexible open‐source automation	42
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction	41
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	40
Protease‐resistant streptavidin for interaction proteomics	40
Proteomic patterns associated with response to breast cancer neoadjuvant treatment	40
The genotype‐phenotype landscape of an allosteric protein	38
Community standards to facilitate development and address challenges in metabolic modeling	37
Multiplexing cell‐cell communication	37
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	37
A genome‐scale yeast library with inducible expression of individual genes	37
The transcriptome dynamics of single cells during the cell cycle	36
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	36
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	36
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	36
Exploring the virulence gene interactome withCRISPR/dCas9 in the human malaria parasite	35
A substrate‐based ontology for human solute carriers	34
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	34
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	33
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	33
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	32
Exploring amino acid functions in a deep mutational landscape	32
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	30
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation	30
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway	29
Can ACE 2 expression explain SARS ‐CoV‐2 infection of the respiratory epithelia in COVID ‐19?	27
Aggregation and disaggregation features of the human proteome	26
Building biosecurity for synthetic biology	26
Dynamic human liver proteome atlas reveals functional insights into disease pathways	26

Single‐cell imaging of genome organization and dynamics	25
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies	25
Transcriptionally active enhancers in human cancer cells	25
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	25
Impact of C‐terminal amino acid composition on protein expression in bacteria	25
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver	24
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	24
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	24
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	24
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	24
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	23
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	23
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback	23
Behavioral fingerprints predict insecticide and anthelmintic mode of action	22
Large‐scale survey and database of high affinity ligands for peptide recognition modules	22
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	22
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	22
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	22
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	22
Updated benchmarking of variant effect predictors using deep mutational scanning	21
Modeling glioblastoma heterogeneity as a dynamic network of cell states	21
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis	21
Using single‐plant‐omics in the field to link maize genes to functions and phenotypes	21
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions	21
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	21
DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks	21
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks	19
Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states	19
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration	19
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa	19
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape	18
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids	18
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	18
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators	18
The molecular architecture of cell cycle arrest	18
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	18
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	17
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae	17
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	17
TATA and paused promoters active in differentiated tissues have distinct expression characteristics	17
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	17
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data	17
Diauxic lags explain unexpected coexistence in multi‐resource environments	17
Genome‐scale metabolic modeling reveals key features of a minimal gene set	16
High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins	16
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	16
Metabolic memory underlying minimal residual disease in breast cancer	15
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	15
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	15
The Cancer Dependency Map enables drug mechanism‐of‐action investigations	15
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	15
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	14
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	14
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	14
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	14
Identifying modules of cooperating cancer drivers	14
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	14
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function	14
LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN 2 as a regulator	14
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	14
Perspective: a stirring role for metabolism in cells	14
CODEX, a neural network approach to explore signaling dynamics landscapes	14
CEN ‐tools: an integrative platform to identify the contexts of essential genes	14
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	14
Levels of autonomy in synthetic biology engineering	14
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	14
Dynamics of thyroid diseases and thyroid‐axis gland masses	13
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	13
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	13
Natural variants suppress mutations in hundreds of essential genes	13
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	13
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	13
Automated assembly of molecular mechanisms at scale from text mining and curated databases	12
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	12
Computational estimation of quality and clinical relevance of cancer cell lines	12
Competitive dCas9 binding as a mechanism for transcriptional control	12
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics	12
The Data Governance Act and the EU's move towards facilitating data sharing	12
The protein architecture of the endocytic coat analyzed by FRET microscopy	12
The impact of genomic variation on protein phosphorylation states and regulatory networks	12

Probing cell identity hierarchies by fate titration and collision during direct reprogramming	12
Tensor‐structured decomposition improves systems serology analysis	12
Real‐time genomics for One Health	11
Integrative characterization of the near‐minimal bacterium Mesoplasma florum	11
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	11
The genotype‐phenotype landscape of an allosteric protein	11
Efficient plasmid transfer via natural competence in a microbial co‐culture	11
Bayesian modeling reveals metabolite‐dependent ultrasensitivity in the cyanobacterial circadian clock	11
Deciphering the physiological response of Escherichia coli under high ATP demand	11
The circadian oscillator analysed at the single‐transcript level	11