Molecular Systems Biology

(The TQCC of Molecular Systems Biology is 25. 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
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments44
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
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
Transcriptionally active enhancers in human cancer cells25
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