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 2021-08-01 to 2025-08-01.)

Article	Citations
A split intein and split luciferase-coupled system for detecting protein-protein interactions	401
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	219
Development and validation of AI/ML derived splice-switching oligonucleotides	163
State of the interactomes: an evaluation of molecular networks for generating biological insights	137
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	108
Systematic identification of 20S proteasome substrates	107
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	93
Dynamic human liver proteome atlas reveals functional insights into disease pathways	93
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	88
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	71
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	70
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	67
A transient mutational burst occurs during yeast colony development	66
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	63
Evaluating the Arrhenius equation for developmental processes	61
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	56
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	52
Enhancing nutritional niche and host defenses by modifying the gut microbiome	49
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	48
A proximity proteomics pipeline with improved reproducibility and throughput	48
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	43
Predicting cellular responses to complex perturbations in high‐throughput screens	43
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	42
Systematic identification of structure-specific protein–protein interactions	41
What we can learn from deep space communication for reproducible bioimaging and data analysis	40

Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	40
The genotype‐phenotype landscape of an allosteric protein	39
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	39
Deep learning for protein structure prediction and design—progress and applications	35
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
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	33
Tensor‐structured decomposition improves systems serology analysis	33
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	32
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	31
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	30
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Deep quantification of substrate turnover defines protease subsite cooperativity	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
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	27
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	26
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	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
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Metabolomics paves the way for improved drug target identification	23
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	23
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
Automated assembly of molecular mechanisms at scale from text mining and curated databases	22
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	22
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	22
Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation	21
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
The molecular architecture of cell cycle arrest	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
Who controls the tariffs of a human cell?	20
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	20
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	19
The solute carrier superfamily interactome	19
Transcription factor expression is the main determinant of variability in gene co‐activity	19
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	18
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	18
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	18

Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18
Real‐time genomics for One Health	17
Unique features of transcription termination and initiation at closely spaced tandem human genes	17
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	17
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer	17
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	16
Updated benchmarking of variant effect predictors using deep mutational scanning	16
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	16
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	16
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	16
Impact of drugs and environmental contaminants on amine production by gut bacteria	15
Building and analyzing metacells in single-cell genomics data	15
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	15
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	15
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections	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
Spatial entropy drives the maintenance and dissemination of transferable plasmids	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	14
Oncogenic PIK3CA corrupts growth factor signaling specificity	14
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	14
Linking patient-specific basal MET phosphorylation levels to liver health	13
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	13
The population context is a driver of the heterogeneous response of epithelial cells to interferons	13
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	13
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	13
Perspective: a stirring role for metabolism in cells	13
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	13
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	12
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	12
Quantifying the phenotypic information in mRNA abundance	12
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	11
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	11
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	11
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	11
Compensatory evolution to DNA replication stress is robust to nutrient availability	11
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	11
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	11
The genetic interaction map of the human solute carrier superfamily	10
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	10
Protein complexes in cells by AI‐assisted structural proteomics	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	10
Growth‐mediated negative feedback shapes quantitative antibiotic response	9
Interrogation of RNA-protein interaction dynamics in bacterial growth	9
One‐shot ¹³C¹⁵N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	9
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	9
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	9
Deciphering the physiological response of Escherichia coli under high ATP demand	9
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	9
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	9
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	9
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	9
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	8
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	8
Single‐cell biology: what does the future hold?	8
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	8
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	8
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	8
Dynamics of thyroid diseases and thyroid‐axis gland masses	8
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	8
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	8