OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 19. 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 2021-01-01 to 2025-01-01.)

Article	Citations
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	315
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	302
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	204
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	179
Dengue virus preferentially uses human and mosquito non-optimal codons	134
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	132
The population context is a driver of the heterogeneous response of epithelial cells to interferons	105
Linking patient-specific basal MET phosphorylation levels to liver health	96
Quantifying the phenotypic information in mRNA abundance	95
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	90
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	75
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	72
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	71
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	71
Development and validation of AI/ML derived splice-switching oligonucleotides	69
Exploring the microbial savanna: predator-prey interactions in the soil	67
A new way of looking at transcription factor assays	67
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	61
A human kinase yeast array for the identification of kinases modulating phosphorylation‐dependent protein–protein interactions	61
The circadian oscillator analysed at the single‐transcript level	59
Systematic identification of 20S proteasome substrates	53
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	52
Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor	51
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	48
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	46

Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	46
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	46
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	45
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	44
Hotspot propensity across mutational processes	44
A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X	44
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	43
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	41
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	38
Evolution of genome fragility enables microbial division of labor	37
Dynamic human liver proteome atlas reveals functional insights into disease pathways	36
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	35
Genetic effects on molecular network states explain complex traits	34
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	32
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	32
Genome‐scale metabolic modeling reveals key features of a minimal gene set	30
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	29
Predictive evolution of metabolic phenotypes using model‐designed environments	28
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	28
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	28
Translational efficiency across healthy and tumor tissues is proliferation‐related	28
A split intein and split luciferase-coupled system for detecting protein-protein interactions	27
Evolution and stability of complex microbial communities driven by trade-offs	27
State of the interactomes: an evaluation of molecular networks for generating biological insights	27
Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)	27
Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans	26
Multiplying insights from perturbation experiments: predicting new perturbation combinations	26
Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion	26
Transcription factor expression is the main determinant of variability in gene co‐activity	26
Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources	25
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	24
Exploiting spatial dimensions to enable parallelized continuous directed evolution	24
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	24
Integrated systems biology approach identifies gene targets for endothelial dysfunction	23
Turning up the heat on essential E. coli genes	23
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	23
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	22
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	22
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	21
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	21
Basal MET phosphorylation is an indicator of hepatocyte dysregulation in liver disease	20
Predicting cellular responses to complex perturbations in high‐throughput screens	20
An engineered Mycoplasma pneumoniae to fight Staphylococcus aureus	20
Modeling glioblastoma heterogeneity as a dynamic network of cell states	20
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	20
Metabolic memory underlying minimal residual disease in breast cancer	20
Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses	19
A proximity proteomics pipeline with improved reproducibility and throughput	19
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	19
Efficient plasmid transfer via natural competence in a microbial co‐culture	19