Molecular Systems Biology

Article	Citations
The protein expression profile of ACE2 in human tissues	705
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	252
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	213
SBML Level 3: an extensible format for the exchange and reuse of biological models	175
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	154
Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease	153
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation	127
RNA velocity—current challenges and future perspectives	127
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome	126
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations	119
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder	93
A single cell atlas of the human liver tumor microenvironment	91
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	89
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	87
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	84
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	81
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference	80
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	76
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	74
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks	72
Reproducibility in systems biology modelling	66
Predicting antigen specificity of single T cells based on TCR CDR 3 regions	65
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	64
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate	61
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens	60

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics	58
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	57
Evaluating the Arrhenius equation for developmental processes	55
Programmable CRISPR‐Cas transcriptional activation in bacteria	55
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	54
A guidebook for DISCO tissue clearing	52
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation	49
Joint cell segmentation and cell type annotation for spatial transcriptomics	48
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	48
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	48
In vitro and in vivo identification of clinically approved drugs that modify ACE 2	47
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	46
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads	45
Enhancing scientific discoveries in molecular biology with deep generative models	45
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity	45
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	44
Protein complexes in cells by AI‐assisted structural proteomics	44
Systematic analysis of bypass suppression of essential genes	44
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch	43
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	43
Enabling high‐throughput biology with flexible open‐source automation	42
Predictive features of gene expression variation reveal mechanistic link with differential expression	41
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction	41
Proteomic patterns associated with response to breast cancer neoadjuvant treatment	40
Predicting cellular responses to complex perturbations in high‐throughput screens	39
A genome‐scale yeast library with inducible expression of individual genes	37
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non‐alcoholic fatty liver disease	37
Multiplexing cell‐cell communication	37
STAT 3 ‐dependent analysis reveals PDK 4 as	37
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	36
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	36
Protease‐resistant streptavidin for interaction proteomics	36
Community standards to facilitate development and address challenges in metabolic modeling	36
The genotype‐phenotype landscape of an allosteric protein	35
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	35
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	35
The transcriptome dynamics of single cells during the cell cycle	34
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	33
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	33
A substrate‐based ontology for human solute carriers	32
Exploring the virulence gene interactome withCRISPR/dCas9 in the human malaria parasite	32
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	32
Exploring amino acid functions in a deep mutational landscape	31
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	31
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation	30
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	29
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
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	27
Aggregation and disaggregation features of the human proteome	26

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance	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
Building biosecurity for synthetic biology	24
Transcriptionally active enhancers in human cancer cells	24
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver	24
Impact of C‐terminal amino acid composition on protein expression in bacteria	24
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	23
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	23
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	23
Dynamic human liver proteome atlas reveals functional insights into disease pathways	23
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	22
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	22
Large‐scale survey and database of high affinity ligands for peptide recognition modules	22
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	22
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	22
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	22
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
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	21
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	21
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback	21
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	20
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	20
DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks	20
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration	19
Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states	19
Updated benchmarking of variant effect predictors using deep mutational scanning	19
Modeling glioblastoma heterogeneity as a dynamic network of cell states	19
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa	19
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks	18
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape	18
Behavioral fingerprints predict insecticide and anthelmintic mode of action	18
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions	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
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data	17
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	17
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators	17
Diauxic lags explain unexpected coexistence in multi‐resource environments	17
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids	17
TATA and paused promoters active in differentiated tissues have distinct expression characteristics	16
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	16
The molecular architecture of cell cycle arrest	16
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	16
High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins	16
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	16
Genome‐scale metabolic modeling reveals key features of a minimal gene set	15
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	15
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	15
CODEX, a neural network approach to explore signaling dynamics landscapes	14
The Cancer Dependency Map enables drug mechanism‐of‐action investigations	14
Metabolic memory underlying minimal residual disease in breast cancer	14
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	14
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function	14
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	14
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	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	13
Identifying modules of cooperating cancer drivers	13
Natural variants suppress mutations in hundreds of essential genes	13
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	13
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	13
Dynamics of thyroid diseases and thyroid‐axis gland masses	13
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	13
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	13
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	13
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	13
CEN ‐tools: an integrative platform to identify the contexts of essential genes	13
Levels of autonomy in synthetic biology engineering	13
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	12
Tensor‐structured decomposition improves systems serology analysis	12
Competitive dCas9 binding as a mechanism for transcriptional control	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
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	12
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics	12
Computational estimation of quality and clinical relevance of cancer cell lines	12
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	12

A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	12
The genotype‐phenotype landscape of an allosteric protein	11
Integrative characterization of the near‐minimal bacterium Mesoplasma florum	11
Bayesian modeling reveals metabolite‐dependent ultrasensitivity in the cyanobacterial circadian clock	11
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	11
A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord	11
Efficient plasmid transfer via natural competence in a microbial co‐culture	11