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 2021-09-01 to 2025-09-01.)

Article	Citations
Development and validation of AI/ML derived splice-switching oligonucleotides	410
A split intein and split luciferase-coupled system for detecting protein-protein interactions	172
Systematic identification of 20S proteasome substrates	143
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	109
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	94
Exogenous prion-like proteins and their potential to trigger cognitive dysfunction	93
State of the interactomes: an evaluation of molecular networks for generating biological insights	73
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	71
Dynamic human liver proteome atlas reveals functional insights into disease pathways	70
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	68
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	65
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	63
A transient mutational burst occurs during yeast colony development	58
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	54
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	51
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	50
Enhancing nutritional niche and host defenses by modifying the gut microbiome	49
Predicting cellular responses to complex perturbations in high‐throughput screens	45
A proximity proteomics pipeline with improved reproducibility and throughput	45
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	44
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	41
The genotype‐phenotype landscape of an allosteric protein	40
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	39
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	39
Tensor‐structured decomposition improves systems serology analysis	38

Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	37
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	35
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	34
What we can learn from deep space communication for reproducible bioimaging and data analysis	34
Systematic identification of structure-specific protein–protein interactions	33
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	32
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	31
Deep learning for protein structure prediction and design—progress and applications	31
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	29
Author Correction: Predictive evolution of metabolic phenotypes using model-designed environments	29
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival	29
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions	28
Predicting natural variation in the yeast phenotypic landscape with machine learning	27
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes	27
Resuscitation dynamics reveal persister partitioning after antibiotic treatment	26
Deep quantification of substrate turnover defines protease subsite cooperativity	26
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	26
Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine	25
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	25
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II	24
Constraints on the optimization of gene product diversity	24
Mutational biases favor complexity increases in protein interaction networks after gene duplication	24
Paralog dispensability shapes homozygous deletion patterns in tumor genomes	24
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis	24
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages	24
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation	24
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota	23
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	23
System‐wide optimization of an orthogonal translation system with enhanced biological tolerance	23
Metabolomics paves the way for improved drug target identification	23
The molecular architecture of cell cycle arrest	22
Automated assembly of molecular mechanisms at scale from text mining and curated databases	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	22
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	22
Who controls the tariffs of a human cell?	21
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	21
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	21
PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations	21
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	21
Transcription factor expression is the main determinant of variability in gene co‐activity	20
Integrated systems biology approach identifies gene targets for endothelial dysfunction	20
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	20
LaGrACE: estimating gene program dysregulation with latent regulatory network	20
The solute carrier superfamily interactome	19
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	19
From microbes to molecules: unveiling host-microbe interactions with spatial metabolomics	18
Proteomic compensation by paralogs preserves protein interaction networks after gene loss in cancer	18
Real‐time genomics for One Health	17
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	17

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	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	17
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	17
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	17
Unique features of transcription termination and initiation at closely spaced tandem human genes	17
An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways	16
Updated benchmarking of variant effect predictors using deep mutational scanning	16
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics	16
Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate	16
PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data	15
Building and analyzing metacells in single-cell genomics data	15
The impact of genomic variation on protein phosphorylation states and regulatory networks	15
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections	15
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups inCLL	15
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	15
Impact of drugs and environmental contaminants on amine production by gut bacteria	15
Keep calm and transcribe on: chromatin changes with age, but transcription can learn to live with it	15
Spatial entropy drives the maintenance and dissemination of transferable plasmids	15
Oncogenic PIK3CA corrupts growth factor signaling specificity	14
Perspective: a stirring role for metabolism in cells	14
Linking patient-specific basal MET phosphorylation levels to liver health	14
Quantifying the phenotypic information in mRNA abundance	13
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	13
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	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	12
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	12
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	12
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	12
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	11
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	11
Compensatory evolution to DNA replication stress is robust to nutrient availability	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 metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	11
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	11
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	11
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	10
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	10
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression	10
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Protein complexes in cells by AI‐assisted structural proteomics	10
Deciphering the physiological response of Escherichia coli under high ATP demand	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
Growth‐mediated negative feedback shapes quantitative antibiotic response	10
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
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	9
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion	9
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations	9
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	9
One‐shot ¹³C¹⁵N‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux	9
Dynamics of thyroid diseases and thyroid‐axis gland masses	9
Probing cell identity hierarchies by fate titration and collision during direct reprogramming	9
Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions	9
Interrogation of RNA-protein interaction dynamics in bacterial growth	9
Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors	9
Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter	9
Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells	9
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	8
Single‐cell biology: what does the future hold?	8
A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli	8
A functional analysis of 180 cancer cell lines reveals conserved intrinsic metabolic programs	8
Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria	8
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map	8
High order expression dependencies finely resolve cryptic states and subtypes in single cell data	8
Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC	8
Distinct transcription kinetics of pluripotent cell states	8
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	7
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	7
Extensive folding variability between homologous chromosomes in mammalian cells	7
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	7
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	7
Predictive evolution of metabolic phenotypes using model‐designed environments	7
Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	7
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	7
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	7
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements	7
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	7