OOIR: Observatory of International Research

Papers

(The median citation count of Molecular Systems Biology is 8. 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 2021-05-01 to 2025-05-01.)

Article	Citations
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	379
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	206
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	150
A split intein and split luciferase-coupled system for detecting protein-protein interactions	116
Systematic identification of 20S proteasome substrates	116
Dynamic human liver proteome atlas reveals functional insights into disease pathways	113
State of the interactomes: an evaluation of molecular networks for generating biological insights	100
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	95
Development and validation of AI/ML derived splice-switching oligonucleotides	83
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	80
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	77
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	73
Enhancing nutritional niche and host defenses by modifying the gut microbiome	65
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	64
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	64
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	62
A proximity proteomics pipeline with improved reproducibility and throughput	61
Evaluating the Arrhenius equation for developmental processes	57
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	56
Predicting cellular responses to complex perturbations in high‐throughput screens	55
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	53
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	52
Deep learning for protein structure prediction and design—progress and applications	48
The genotype‐phenotype landscape of an allosteric protein	47
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	47

Systematic identification of structure-specific protein–protein interactions	46
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	43
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	40
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	39
What we can learn from deep space communication for reproducible bioimaging and data analysis	37
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	35
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	35
Tensor‐structured decomposition improves systems serology analysis	35
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	35
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	33
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	32
Deep quantification of substrate turnover defines protease subsite cooperativity	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	31
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	31
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	30
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	29
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	29
Model‐guided development of an evolutionarily stable yeast chassis	28
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	27
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	27
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit	27
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	27
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	27
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
Mutational biases favor complexity increases in protein interaction networks after gene duplication	25
Metabolomics paves the way for improved drug target identification	25
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	24
Constraints on the optimization of gene product diversity	24
Automated assembly of molecular mechanisms at scale from text mining and curated databases	24
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	23
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	22
The molecular architecture of cell cycle arrest	22
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	21
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	20
Real‐time genomics for One Health	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	20
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Transcription factor expression is the main determinant of variability in gene co‐activity	20
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	20
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	19
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	19

Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	18
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	18
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	18
Unique features of transcription termination and initiation at closely spaced tandem human genes	18
Updated benchmarking of variant effect predictors using deep mutational scanning	18
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	18
The impact of genomic variation on protein phosphorylation states and regulatory networks	17
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections	17
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	17
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	16
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	16
Spatial entropy drives the maintenance and dissemination of transferable plasmids	16
Oncogenic PIK3CA corrupts growth factor signaling specificity	15
Perspective: a stirring role for metabolism in cells	15
Building and analyzing metacells in single-cell genomics data	15
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	15
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	15
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	15
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	14
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	14
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	14
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	14
Genome‐scale metabolic modeling reveals key features of a minimal gene set	14
Quantifying the phenotypic information in mRNA abundance	14
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	14
The population context is a driver of the heterogeneous response of epithelial cells to interferons	14
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	14
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	14
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	14
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	14
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	14
Linking patient-specific basal MET phosphorylation levels to liver health	14
Growth‐mediated negative feedback shapes quantitative antibiotic response	13
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	13
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	13
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	13
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	13
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	12
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	12
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	12
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	12
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	11
Deciphering the physiological response of Escherichia coli under high ATP demand	11
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	11
The rise of proteome‐wide biophysics	11
Protein complexes in cells by AI‐assisted structural proteomics	11
Interrogation of RNA-protein interaction dynamics in bacterial growth	10
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	10
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	10
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	10
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	10
One‐shot ¹³C¹⁵N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	10
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	10
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	9
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	9
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	9
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	9
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	9
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	9
Dynamics of thyroid diseases and thyroid‐axis gland masses	9
Single‐cell biology: what does the future hold?	9
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	9
Distinct transcription kinetics of pluripotent cell states	9
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	9
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	8
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	8
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	8
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	8
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	8
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	8
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	8
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response	8
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	8
Predictive evolution of metabolic phenotypes using model‐designed environments	8
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	8