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. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-09-01 to 2023-09-01.)
The protein expression profile of ACE2 in human tissues575
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation172
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models137
SBML Level 3: an extensible format for the exchange and reuse of biological models124
Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease114
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis113
Thermal proteome profiling for interrogating protein interactions108
Automated sample preparation with SP 3 for low‐input clinical proteomics94
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome91
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation91
An integrated workflow for crosslinking mass spectrometry88
Mammalian gene expression variability is explained by underlying cell state86
RNA velocity—current challenges and future perspectives86
R2‐P2 rapid‐robotic phosphoproteomics enables multidimensional cell signaling studies81
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations77
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases66
A single cell atlas of the human liver tumor microenvironment62
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder60
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions57
Reproducibility in systems biology modelling57
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies56
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference56
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses54
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut53
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens50
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks50
Predicting antigen specificity of single T cells based on TCR CDR 3 regions49
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics47
Combinatorial prediction of marker panels from single‐cell transcriptomic data47
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate46
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial45
Towards a mechanistic understanding of reciprocal drug–microbiome interactions45
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery43
Evaluating the Arrhenius equation for developmental processes42
In vitro and in vivo identification of clinically approved drugs that modify ACE 2 41
Programmable CRISPR‐Cas transcriptional activation in bacteria41
Programming Escherichia coli to function as a digital display41
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation40
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch39
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity38
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae37
Joint cell segmentation and cell type annotation for spatial transcriptomics36
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans36
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments34
A guidebook for DISCO tissue clearing33
Predictive features of gene expression variation reveal mechanistic link with differential expression33
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing32
Multiplexing cell‐cell communication32
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms31
Learning causal networks using inducible transcription factors and transcriptome‐wide time series31
The genotype‐phenotype landscape of an allosteric protein31
Proteomic patterns associated with response to breast cancer neoadjuvant treatment31
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery31
Paralog dependency indirectly affects the robustness of human cells31
STAT 3 ‐dependent analysis reveals PDK 4 as 31
Translational efficiency across healthy and tumor tissues is proliferation‐related30
Protease‐resistant streptavidin for interaction proteomics30
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin30
Endogenous fluctuations of OCT 4 and SOX 2 bias pluripotent cell fate decisions29
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation29
Personalized signaling models for personalized treatments29
Systematic analysis of bypass suppression of essential genes29
Exploring the virulence gene interactome with CRISPR / dC as9 in the human malaria parasite28
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads28
A genome‐scale yeast library with inducible expression of individual genes28
Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor28
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction28
Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module28
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls28
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies27
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost27
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels27
The transcriptome dynamics of single cells during the cell cycle27
Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability26
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non‐alcoholic fatty liver disease26
Suboptimal resource allocation in changing environments constrains response and growth in bacteria26
Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling25
Enabling high‐throughput biology with flexible open‐source automation25
Community standards to facilitate development and address challenges in metabolic modeling25