OOIR: Observatory of International Research

Papers

(The median citation count of Molecular Systems Biology is 7. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	428
Dynamic human liver proteome atlas reveals functional insights into disease pathways	208
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	168
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	115
Systematic identification of 20S proteasome substrates	79
Development and validation of AI/ML derived splice-switching oligonucleotides	76
A split intein and split luciferase-coupled system for detecting protein-protein interactions	73
State of the interactomes: an evaluation of molecular networks for generating biological insights	65
Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities	65
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	57
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	56
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	55
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	53
Enhancing nutritional niche and host defenses by modifying the gut microbiome	52
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	46
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	45
A proximity proteomics pipeline with improved reproducibility and throughput	43
A transient mutational burst occurs during yeast colony development	43
Predicting cellular responses to complex perturbations in high‐throughput screens	40
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci	40
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	37
What we can learn from deep space communication for reproducible bioimaging and data analysis	36
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	33
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	32

Systematic identification of structure-specific protein–protein interactions	31
The genotype‐phenotype landscape of an allosteric protein	31
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	30
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	30
Predicting natural variation in the yeast phenotypic landscape with machine learning	29
Deep learning for protein structure prediction and design—progress and applications	29
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	29
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	28
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Deep quantification of substrate turnover defines protease subsite cooperativity	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	25
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	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	24
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	24
Constraints on the optimization of gene product diversity	24
Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline	24
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
Metabolomics paves the way for improved drug target identification	23
The molecular architecture of cell cycle arrest	23
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	22
Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures	22
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
Automated assembly of molecular mechanisms at scale from text mining and curated databases	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	20
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	19
Who controls the tariffs of a human cell?	19
Transcription factor expression is the main determinant of variability in gene co‐activity	18
The solute carrier superfamily interactome	18
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	18
LaGrACE: estimating gene program dysregulation with latent regulatory network	18
A scheduler for rhythmic gene expression	17
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	17
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	17
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	17
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	16
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	16
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	15
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	15

Real‐time genomics for One Health	15
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	15
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	15
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Updated benchmarking of variant effect predictors using deep mutational scanning	15
Unique features of transcription termination and initiation at closely spaced tandem human genes	15
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	14
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections	14
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	14
The impact of genomic variation on protein phosphorylation states and regulatory networks	13
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	13
Viro3D: a comprehensive database of virus protein structure predictions	13
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	13
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	12
Oncogenic PIK3CA corrupts growth factor signaling specificity	12
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	12
Impact of drugs and environmental contaminants on amine production by gut bacteria	12
Building and analyzing metacells in single-cell genomics data	12
Machine learning-guided deconvolution of plasma protein levels	12
Perspective: a stirring role for metabolism in cells	12
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	11
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	11
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	11
The population context is a driver of the heterogeneous response of epithelial cells to interferons	11
Linking patient-specific basal MET phosphorylation levels to liver health	11
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	11
Quantifying the phenotypic information in mRNA abundance	11
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	11
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	11
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	10
Compensatory evolution to DNA replication stress is robust to nutrient availability	10
Growth‐mediated negative feedback shapes quantitative antibiotic response	10
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	10
The genetic interaction map of the human solute carrier superfamily	10
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	10
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	10
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
Engineering mammalian cells for detection and treatment of cardiac injury	10
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	10
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	10
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	10
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	10
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	9
Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis	9
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	9
Interrogation of RNA-protein interaction dynamics in bacterial growth	9
Deciphering the physiological response of Escherichia coli under high ATP demand	9
Synovial matrix turnover controls immune cell spatial patterning in inflammation resolution	9
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
Protein complexes in cells by AI‐assisted structural proteomics	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	9
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Dynamics of thyroid diseases and thyroid‐axis gland masses	8
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	8
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	8
Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon	8
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	8
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	8
One‐shot ¹³C¹⁵N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	8
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	8
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	8
Single‐cell biology: what does the future hold?	7
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	7
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	7
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	7
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	7
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	7
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	7
Distinct transcription kinetics of pluripotent cell states	7
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	7
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map	7