OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 17. 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 2022-08-01 to 2026-08-01.)

Article	Citations
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	282
Development and validation of AI/ML derived splice-switching oligonucleotides	275
Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms	142
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	111
To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis	93
Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent	89
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	82
A split intein and split luciferase-coupled system for detecting protein-protein interactions	69
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	66
Systematic identification of 20S proteasome substrates	66
State of the interactomes: an evaluation of molecular networks for generating biological insights	62
Toward trustworthy healthcare AI: designing academic research for translation readiness	61
Enhancing nutritional niche and host defenses by modifying the gut microbiome	60
Molecular Systems Biology at 20: reflecting on the past, envisioning the future	58
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	58
Author Correction: Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets	57
Chromosome length is constrained by spindle scaling to ensure faithful mitosis in mammals	49
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species	49
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	44
A transient mutational burst occurs during yeast colony development	43
Dimensionality reduction methods for extracting functional networks from large‐scale CRISPR screens	41
A proximity proteomics pipeline with improved reproducibility and throughput	39
Progress and new challenges in image-based profiling	38
Predicting cellular responses to complex perturbations in high‐throughput screens	37
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	36

Systematic identification of structure-specific protein–protein interactions	36
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	36
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	36
What we can learn from deep space communication for reproducible bioimaging and data analysis	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind	33
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	31
Deep learning for protein structure prediction and design—progress and applications	30
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	29
Five dominant amino acid substitution signatures shape tumour immunity	28
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	28
CANTAO: guiding clustering and annotation in single-cell RNA sequencing using average overlap	28
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	28
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	27
Erratum To: Resuscitation dynamics reveal persister partitioning after antibiotic treatment	27
Predicting natural variation in the yeast phenotypic landscape with machine learning	27
Deep quantification of substrate turnover defines protease subsite cooperativity	26
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning	25
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	25
Mutational biases favor complexity increases in protein interaction networks after gene duplication	25
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	25
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Constraints on the optimization of gene product diversity	24
Automated assembly of molecular mechanisms at scale from text mining and curated databases	24
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	24
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	22
Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
The molecular architecture of cell cycle arrest	22
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	22
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
LaGrACE: estimating gene program dysregulation with latent regulatory network	21
Who controls the tariffs of a human cell?	21
Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	19
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	19
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	19
The solute carrier superfamily interactome	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19

Real‐time genomics for One Health	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
The DNA dialect: a comprehensive guide to pretrained genomic language models	19
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets	19
A scheduler for rhythmic gene expression	18
Fast analysis and engineering of protein function by microbe-independent deep assembly and screening	18
xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction	17
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
Proteome-wide AlphaFold pool party	17