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 2020-07-01 to 2024-07-01.)

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
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	78
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks	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
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens	62
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	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
Joint cell segmentation and cell type annotation for spatial transcriptomics	51
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
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
The genotype‐phenotype landscape of an allosteric protein	40
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
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	39
The transcriptome dynamics of single cells during the cell cycle	38
Community standards to facilitate development and address challenges in metabolic modeling	38
Multiplexing cell‐cell communication	38
A substrate‐based ontology for human solute carriers	37
Exploring the virulence gene interactome withCRISPR/dCas9 in the human malaria parasite	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
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	34
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	34
Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway	33
Exploring amino acid functions in a deep mutational landscape	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
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	24
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