OOIR: Observatory of International Research

Papers

(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.)

Article	Citations
The protein expression profile of ACE2 in human tissues	575
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	172
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	137
SBML Level 3: an extensible format for the exchange and reuse of biological models	124
Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease	114
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	113
Thermal proteome profiling for interrogating protein interactions	108
Automated sample preparation with SP 3 for low‐input clinical proteomics	94
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome	91
Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation	91
An integrated workflow for crosslinking mass spectrometry	88
Mammalian gene expression variability is explained by underlying cell state	86
RNA velocity—current challenges and future perspectives	86
R2‐P2 rapid‐robotic phosphoproteomics enables multidimensional cell signaling studies	81
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations	77
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	66
A single cell atlas of the human liver tumor microenvironment	62
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder	60
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	57
Reproducibility in systems biology modelling	57
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	56
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference	56
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	54
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	53
Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens	50

A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks	50
Predicting antigen specificity of single T cells based on TCR CDR 3 regions	49
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics	47
Combinatorial prediction of marker panels from single‐cell transcriptomic data	47
Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate	46
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	45
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	45
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	43
Evaluating the Arrhenius equation for developmental processes	42
In vitro and in vivo identification of clinically approved drugs that modify ACE 2	41
Programmable CRISPR‐Cas transcriptional activation in bacteria	41
Programming Escherichia coli to function as a digital display	41
Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation	40
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch	39
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity	38
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae	37
Joint cell segmentation and cell type annotation for spatial transcriptomics	36
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans	36
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	34
A guidebook for DISCO tissue clearing	33
Predictive features of gene expression variation reveal mechanistic link with differential expression	33
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	32
Multiplexing cell‐cell communication	32
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	31
Learning causal networks using inducible transcription factors and transcriptome‐wide time series	31
The genotype‐phenotype landscape of an allosteric protein	31
Proteomic patterns associated with response to breast cancer neoadjuvant treatment	31
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	31
Paralog dependency indirectly affects the robustness of human cells	31
STAT 3 ‐dependent analysis reveals PDK 4 as	31
Translational efficiency across healthy and tumor tissues is proliferation‐related	30
Protease‐resistant streptavidin for interaction proteomics	30
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	30
Endogenous fluctuations of OCT 4 and SOX 2 bias pluripotent cell fate decisions	29
Co‐catabolism of arginine and succinate drives symbiotic nitrogen fixation	29
Personalized signaling models for personalized treatments	29
Systematic analysis of bypass suppression of essential genes	29
Exploring the virulence gene interactome with CRISPR / dC as9 in the human malaria parasite	28
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads	28
A genome‐scale yeast library with inducible expression of individual genes	28
Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor	28
Disentangling molecular mechanisms regulating sensitization of interferon alpha signal transduction	28
Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module	28
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	28
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies	27
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	27
Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels	27
The transcriptome dynamics of single cells during the cell cycle	27
Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability	26
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non‐alcoholic fatty liver disease	26

Suboptimal resource allocation in changing environments constrains response and growth in bacteria	26
Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling	25
Enabling high‐throughput biology with flexible open‐source automation	25
Community standards to facilitate development and address challenges in metabolic modeling	25