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 2021-04-01 to 2025-04-01.)

Article	Citations
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	366
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	199
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response	148
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	115
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	107
Quantifying the phenotypic information in mRNA abundance	106
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	98
A human kinase yeast array for the identification of kinases modulating phosphorylation‐dependent protein–protein interactions	93
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	91
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	82
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	79
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	76
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	71
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	64
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	62
Dynamic human liver proteome atlas reveals functional insights into disease pathways	60
Systematic identification of 20S proteasome substrates	60
The population context is a driver of the heterogeneous response of epithelial cells to interferons	59
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	56
A split intein and split luciferase-coupled system for detecting protein-protein interactions	51
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	51
Development and validation of AI/ML derived splice-switching oligonucleotides	50
A new way of looking at transcription factor assays	50
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	49
A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X	47

Dengue virus preferentially uses human and mosquito non-optimal codons	46
Linking patient-specific basal MET phosphorylation levels to liver health	42
Hotspot propensity across mutational processes	40
Exploring the microbial savanna: predator-prey interactions in the soil	38
Genome‐scale metabolic modeling reveals key features of a minimal gene set	37
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	35
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	35
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	34
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	34
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	32
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	32
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	32
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	31
Evolution of genome fragility enables microbial division of labor	31
Predictive evolution of metabolic phenotypes using model‐designed environments	29
Genetic effects on molecular network states explain complex traits	28
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	28
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	28
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	27
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	27
State of the interactomes: an evaluation of molecular networks for generating biological insights	27
Modeling glioblastoma heterogeneity as a dynamic network of cell states	25
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	25
Enhancing nutritional niche and host defenses by modifying the gut microbiome	24
Metabolic memory underlying minimal residual disease in breast cancer	24
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	24
Integrated systems biology approach identifies gene targets for endothelial dysfunction	24
Multiplying insights from perturbation experiments: predicting new perturbation combinations	23
Exploiting spatial dimensions to enable parallelized continuous directed evolution	23
Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics	22
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	22
Competitive dCas9 binding as a mechanism for transcriptional control	22
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	22
Turning up the heat on essential E. coli genes	22
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	21
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	21
Enablers and challenges of spatial omics, a melting pot of technologies	21
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms	21
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	20
A single‐cell RNA labeling strategy for measuring stress response upon tissue dissociation	20
Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses	20
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	20
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	20
Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans	20
Abundant clock proteins point to missing molecular regulation in the plant circadian clock	20
An engineered Mycoplasma pneumoniae to fight Staphylococcus aureus	20
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	19
Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions	19