OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 24. 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 2020-04-01 to 2024-04-01.)

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
RNA velocity—current challenges and future perspectives	127
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation	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
Programmable CRISPR‐Cas transcriptional activation in bacteria	55
Evaluating the Arrhenius equation for developmental processes	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
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
Joint cell segmentation and cell type annotation for spatial transcriptomics	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
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity	45
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
Systematic analysis of bypass suppression of essential genes	44
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	44
Protein complexes in cells by AI‐assisted structural proteomics	44
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	43
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch	43
Enabling high‐throughput biology with flexible open‐source automation	42
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction	41
Predictive features of gene expression variation reveal mechanistic link with differential expression	41
Proteomic patterns associated with response to breast cancer neoadjuvant treatment	40
Predicting cellular responses to complex perturbations in high‐throughput screens	39
Multiplexing cell‐cell communication	37
STAT 3 ‐dependent analysis reveals PDK 4 as	37
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
Protease‐resistant streptavidin for interaction proteomics	36
Community standards to facilitate development and address challenges in metabolic modeling	36
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
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 genotype‐phenotype landscape of an allosteric protein	35
The transcriptome dynamics of single cells during the cell cycle	34
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	33
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	33
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
A substrate‐based ontology for human solute carriers	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
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway	29
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	29
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	27
Can ACE 2 expression explain SARS ‐CoV‐2 infection of the respiratory epithelia in COVID ‐19?	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
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies	25
Single‐cell imaging of genome organization and dynamics	25
Impact of C‐terminal amino acid composition on protein expression in bacteria	24
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