Molecular Systems Biology

(The median citation count of Molecular Systems Biology is 11. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
The protein expression profile of ACE2 in human tissues718
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation258
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models221
SBML Level 3: an extensible format for the exchange and reuse of biological models180
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis158
Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease154
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation136
RNA velocity—current challenges and future perspectives133
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome129
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations120
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder100
A single cell atlas of the human liver tumor microenvironment98
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery95
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases93
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions86
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies84
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference80
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses77
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut77
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks76
Predicting antigen specificity of single T cells based on TCR CDR 3 regions68
Reproducibility in systems biology modelling68
Towards a mechanistic understanding of reciprocal drug–microbiome interactions65
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens62
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate62
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial61
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics59
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery57
A guidebook for DISCO tissue clearing56
Programmable CRISPR‐Cas transcriptional activation in bacteria56
Evaluating the Arrhenius equation for developmental processes55
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans54
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation50
Joint cell segmentation and cell type annotation for spatial transcriptomics49
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms48
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity48
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing48
In vitro and in vivo identification of clinically approved drugs that modify ACE 2 47
Enhancing scientific discoveries in molecular biology with deep generative models46
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads46
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin45
Predictive features of gene expression variation reveal mechanistic link with differential expression45
Predicting cellular responses to complex perturbations in high‐throughput screens44
Protein complexes in cells by AI‐assisted structural proteomics44
Systematic analysis of bypass suppression of essential genes44
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments44
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch43
Enabling high‐throughput biology with flexible open‐source automation42
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction41
Protease‐resistant streptavidin for interaction proteomics40
Proteomic patterns associated with response to breast cancer neoadjuvant treatment40
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost40
The genotype‐phenotype landscape of an allosteric protein38
Multiplexing cell‐cell communication37
Suboptimal resource allocation in changing environments constrains response and growth in bacteria37
A genome‐scale yeast library with inducible expression of individual genes37
Community standards to facilitate development and address challenges in metabolic modeling37
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls36
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes36
The transcriptome dynamics of single cells during the cell cycle36
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome36
Exploring the virulence gene interactome withCRISPR/dCas9 in the human malaria parasite35
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence34
A substrate‐based ontology for human solute carriers34
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation33
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels33
Exploring amino acid functions in a deep mutational landscape32
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics32
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation30
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities30
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway29
Can ACE 2 expression explain SARS ‐CoV‐2 infection of the respiratory epithelia in COVID ‐19?27
Building biosecurity for synthetic biology26
Dynamic human liver proteome atlas reveals functional insights into disease pathways26
Aggregation and disaggregation features of the human proteome26
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks25
Impact of C‐terminal amino acid composition on protein expression in bacteria25
Single‐cell imaging of genome organization and dynamics25
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies25
Transcriptionally active enhancers in human cancer cells25
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma24
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection24
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations24
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver24
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion24
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo23
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback23
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients23
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing22
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis22
Behavioral fingerprints predict insecticide and anthelmintic mode of action22
Large‐scale survey and database of high affinity ligands for peptide recognition modules22
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection22
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets22
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms21
DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks21
Updated benchmarking of variant effect predictors using deep mutational scanning21
Modeling glioblastoma heterogeneity as a dynamic network of cell states21
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis21
Using single‐plant‐omics in the field to link maize genes to functions and phenotypes21
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions21
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa19
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks19
Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states19
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration19
The molecular architecture of cell cycle arrest18
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis18
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape18
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids18
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release18
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators18
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data17
Diauxic lags explain unexpected coexistence in multi‐resource environments17
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq17
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae17
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria17
TATA and paused promoters active in differentiated tissues have distinct expression characteristics17
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism17
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection16
Genome‐scale metabolic modeling reveals key features of a minimal gene set16
High‐throughput metabolomics predicts drug–target relationships for eukaryotic proteins16
The Cancer Dependency Map enables drug mechanism‐of‐action investigations15
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress15
Metabolic memory underlying minimal residual disease in breast cancer15
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system15
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations15
CEN ‐tools: an integrative platform to identify the contexts of essential genes14
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots14
Levels of autonomy in synthetic biology engineering14
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness14
Large‐scale analysis of Drosophila core promoter function using synthetic promoters14
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing14
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel14
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein14
Identifying modules of cooperating cancer drivers14
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver14
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function14
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 genes14
Perspective: a stirring role for metabolism in cells14
CODEX, a neural network approach to explore signaling dynamics landscapes14
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance13
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor13
Dynamics of thyroid diseases and thyroid‐axis gland masses13
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies13
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans13
Natural variants suppress mutations in hundreds of essential genes13
The impact of genomic variation on protein phosphorylation states and regulatory networks12
Probing cell identity hierarchies by fate titration and collision during direct reprogramming12
Tensor‐structured decomposition improves systems serology analysis12
Automated assembly of molecular mechanisms at scale from text mining and curated databases12
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs12
Computational estimation of quality and clinical relevance of cancer cell lines12
Competitive dCas9 binding as a mechanism for transcriptional control12
Non‐canonical metabolic pathways in the malaria parasite detected by isotope‐tracing metabolomics12
The Data Governance Act and the EU's move towards facilitating data sharing12
The protein architecture of the endocytic coat analyzed by FRET microscopy12
Bayesian modeling reveals metabolite‐dependent ultrasensitivity in the cyanobacterial circadian clock11
Deciphering the physiological response of Escherichia coli under high ATP demand11
The circadian oscillator analysed at the single‐transcript level11
Real‐time genomics for One Health11
Integrative characterization of the near‐minimal bacterium Mesoplasma florum11
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation11
The genotype‐phenotype landscape of an allosteric protein11
Efficient plasmid transfer via natural competence in a microbial co‐culture11