Molecular Systems Biology

Article	Citations
The protein expression profile of ACE2 in human tissues	733
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	285
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	251
SBML Level 3: an extensible format for the exchange and reuse of biological models	185
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	169
RNA velocity—current challenges and future perspectives	148
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations	125
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder	108
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	106
A single cell atlas of the human liver tumor microenvironment	104
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	102
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	93
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	88
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	84
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks	78
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	78
Reproducibility in systems biology modelling	72
Predicting antigen specificity of single T cells based on TCR CDR 3 regions	71
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	68
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	67
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	62
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens	62
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	60
Programmable CRISPR‐Cas transcriptional activation in bacteria	60
Evaluating the Arrhenius equation for developmental processes	59

Predicting cellular responses to complex perturbations in high‐throughput screens	56
A guidebook for DISCO tissue clearing	56
Protein complexes in cells by AI‐assisted structural proteomics	53
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	52
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation	51
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	51
Joint cell segmentation and cell type annotation for spatial transcriptomics	51
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads	50
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	50
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	47
Predictive features of gene expression variation reveal mechanistic link with differential expression	46
Systematic analysis of bypass suppression of essential genes	45
Enabling high‐throughput biology with flexible open‐source automation	44
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	44
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	42
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	42
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	42
Proteomic patterns associated with response to breast cancer neoadjuvant treatment	41
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction	41
A genome‐scale yeast library with inducible expression of individual genes	40
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	40
The genotype‐phenotype landscape of an allosteric protein	40
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	39
Community standards to facilitate development and address challenges in metabolic modeling	38
Multiplexing cell‐cell communication	38
The transcriptome dynamics of single cells during the cell cycle	38
Exploring the virulence gene interactome withCRISPR/dCas9 in the human malaria parasite	37
A substrate‐based ontology for human solute carriers	37
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	35
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	35
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	34
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	34
Exploring amino acid functions in a deep mutational landscape	33
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway	33
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	31
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	30
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	29
Updated benchmarking of variant effect predictors using deep mutational scanning	28
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	28
Single‐cell imaging of genome organization and dynamics	28
Dynamic human liver proteome atlas reveals functional insights into disease pathways	27
Can ACE 2 expression explain SARS ‐CoV‐2 infection of the respiratory epithelia in COVID ‐19?	27
Building biosecurity for synthetic biology	26
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	26
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	26
Modeling glioblastoma heterogeneity as a dynamic network of cell states	26
Transcriptionally active enhancers in human cancer cells	26
Aggregation and disaggregation features of the human proteome	26
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	25

Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	25
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	25
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback	24
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	24
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	24
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	23
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	23
Large‐scale survey and database of high affinity ligands for peptide recognition modules	22
Behavioral fingerprints predict insecticide and anthelmintic mode of action	22
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	22
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	22
DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks	22
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
The molecular architecture of cell cycle arrest	21
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis	21
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks	21
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	20
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	20
Diauxic lags explain unexpected coexistence in multi‐resource environments	20
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators	20
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration	20
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	20
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids	19
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape	19
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae	19
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa	19
TATA and paused promoters active in differentiated tissues have distinct expression characteristics	18
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	18
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	18
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data	18
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	18
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	17
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	17
Identifying modules of cooperating cancer drivers	16
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	16
High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins	16
The Cancer Dependency Map enables drug mechanism‐of‐action investigations	16
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	16
Genome‐scale metabolic modeling reveals key features of a minimal gene set	16
CEN ‐tools: an integrative platform to identify the contexts of essential genes	15
Levels of autonomy in synthetic biology engineering	15
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	15
CODEX, a neural network approach to explore signaling dynamics landscapes	15
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	15
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	15
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	15
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function	15
Metabolic memory underlying minimal residual disease in breast cancer	15
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	15
The impact of genomic variation on protein phosphorylation states and regulatory networks	15
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics	14
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	14
Computational estimation of quality and clinical relevance of cancer cell lines	14
LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN 2 as a regulator	14
Automated assembly of molecular mechanisms at scale from text mining and curated databases	14
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	14
Growth‐dependent heterogeneity in the DNA damage response in Escherichia coli	14
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	14
Perspective: a stirring role for metabolism in cells	14
Dynamics of thyroid diseases and thyroid‐axis gland masses	14
Real‐time genomics for One Health	14
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	14
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	13
Tensor‐structured decomposition improves systems serology analysis	13
Natural variants suppress mutations in hundreds of essential genes	13
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	13
A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord	13
Competitive dCas9 binding as a mechanism for transcriptional control	13
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	12
A spatial model of the plant circadian clock reveals design principles for coordinated timing	12
Deciphering the physiological response of Escherichia coli under high ATP demand	12
The Data Governance Act and the EU's move towards facilitating data sharing	12
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	12
The genotype‐phenotype landscape of an allosteric protein	11
The circadian oscillator analysed at the single‐transcript level	11
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	11
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	11
Integrative characterization of the near‐minimal bacterium Mesoplasma florum	11
From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration	11

Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	11
Efficient plasmid transfer via natural competence in a microbial co‐culture	11
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	11