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 2021-06-01 to 2025-06-01.)

Article	Citations
Development and validation of AI/ML derived splice-switching oligonucleotides	386
A split intein and split luciferase-coupled system for detecting protein-protein interactions	209
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	152
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	121
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	102
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	99
State of the interactomes: an evaluation of molecular networks for generating biological insights	86
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	85
Dynamic human liver proteome atlas reveals functional insights into disease pathways	81
Systematic identification of 20S proteasome substrates	67
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	67
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	65
Enhancing nutritional niche and host defenses by modifying the gut microbiome	63
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	63
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	61
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	59
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	57
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	53
A proximity proteomics pipeline with improved reproducibility and throughput	53
Predicting cellular responses to complex perturbations in high‐throughput screens	49
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	47
Evaluating the Arrhenius equation for developmental processes	47
Systematic identification of structure-specific protein–protein interactions	45
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	41
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	40

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	38
What we can learn from deep space communication for reproducible bioimaging and data analysis	38
The genotype‐phenotype landscape of an allosteric protein	38
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	37
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	37
Tensor‐structured decomposition improves systems serology analysis	37
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	35
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	34
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	32
Deep learning for protein structure prediction and design—progress and applications	32
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	32
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	31
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	31
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	30
Deep quantification of substrate turnover defines protease subsite cooperativity	30
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	29
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	28
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit	27
Model‐guided development of an evolutionarily stable yeast chassis	27
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	27
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	27
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	26
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	26
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	24
Constraints on the optimization of gene product diversity	24
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	24
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	23
Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration	23
The molecular architecture of cell cycle arrest	23
Metabolomics paves the way for improved drug target identification	23
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	22
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	22
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	21
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	21
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
The solute carrier superfamily interactome	20
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	20
Who controls the tariffs of a human cell?	19
Integrated systems biology approach identifies gene targets for endothelial dysfunction	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	19
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	18
Real‐time genomics for One Health	18

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