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 2021-04-01 to 2025-04-01.)

Article	Citations
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	366
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data	199
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response	148
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	115
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	107
Quantifying the phenotypic information in mRNA abundance	106
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	98
A human kinase yeast array for the identification of kinases modulating phosphorylation‐dependent protein–protein interactions	93
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	91
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	82
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	79
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	76
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	71
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	64
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	62
Systematic identification of 20S proteasome substrates	60
Dynamic human liver proteome atlas reveals functional insights into disease pathways	60
The population context is a driver of the heterogeneous response of epithelial cells to interferons	59
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	56
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	51
A split intein and split luciferase-coupled system for detecting protein-protein interactions	51
Development and validation of AI/ML derived splice-switching oligonucleotides	50
A new way of looking at transcription factor assays	50
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	49
A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X	47

Dengue virus preferentially uses human and mosquito non-optimal codons	46
Linking patient-specific basal MET phosphorylation levels to liver health	42
Hotspot propensity across mutational processes	40
Exploring the microbial savanna: predator-prey interactions in the soil	38
Genome‐scale metabolic modeling reveals key features of a minimal gene set	37
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	35
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	35
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	34
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	34
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	32
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	32
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	32
Evolution of genome fragility enables microbial division of labor	31
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	31
Predictive evolution of metabolic phenotypes using model‐designed environments	29
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	28
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	28
Genetic effects on molecular network states explain complex traits	28
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	27
State of the interactomes: an evaluation of molecular networks for generating biological insights	27
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	27
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	25
Modeling glioblastoma heterogeneity as a dynamic network of cell states	25
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	24
Integrated systems biology approach identifies gene targets for endothelial dysfunction	24
Enhancing nutritional niche and host defenses by modifying the gut microbiome	24
Metabolic memory underlying minimal residual disease in breast cancer	24
Exploiting spatial dimensions to enable parallelized continuous directed evolution	23
Multiplying insights from perturbation experiments: predicting new perturbation combinations	23
Competitive dCas9 binding as a mechanism for transcriptional control	22
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	22
Turning up the heat on essential E. coli genes	22
Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics	22
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	22
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	21
Enablers and challenges of spatial omics, a melting pot of technologies	21
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms	21
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	21
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs	20
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	20
Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans	20
Abundant clock proteins point to missing molecular regulation in the plant circadian clock	20
An engineered Mycoplasma pneumoniae to fight Staphylococcus aureus	20
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	20
A single‐cell RNA labeling strategy for measuring stress response upon tissue dissociation	20
Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses	20
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	19
Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions	19
Basal MET phosphorylation is an indicator of hepatocyte dysregulation in liver disease	18
Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources	18

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)	18
Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach	18
Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics	17
A proximity proteomics pipeline with improved reproducibility and throughput	17
Evolution and stability of complex microbial communities driven by trade-offs	17
Evaluating the Arrhenius equation for developmental processes	16
Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion	16
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	16
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	16
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	16
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	15
Predicting cellular responses to complex perturbations in high‐throughput screens	15
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	15
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	15
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	15
Transcription factor expression is the main determinant of variability in gene co‐activity	15
Efficient plasmid transfer via natural competence in a microbial co‐culture	15
A multiplex method for rapidly identifying viral protease inhibitors	14
Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants	14
Unravelling metabolic cross‐feeding in a yeast–bacteria community using ¹³C‐based proteomics	14
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	14
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	14
Multisite assessment of reproducibility in high‐content cell migration imaging data	14
CRISPR memories in single cells	14
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	14
Tensor‐structured decomposition improves systems serology analysis	14
A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord	13
Higher‐order modular regulation of the human proteome	13
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux	12
Identification of covalent modifications regulating immune signaling complex composition and phenotype	12
Cell sorters see things more clearly now	12
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	12
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	12
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	12
What we can learn from deep space communication for reproducible bioimaging and data analysis	11
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	11
Alternative proteoforms and proteoform-dependent assemblies in humans and plants	11
Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies	11
Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard‐to‐kill persister cells	11
Bacterial live therapeutics for human diseases	11
Proteome-wide copy-number estimation from transcriptomics	11
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	10
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	10
The genotype‐phenotype landscape of an allosteric protein	10
Growth‐mediated negative feedback shapes quantitative antibiotic response	10
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	10
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	10
Unique features of transcription termination and initiation at closely spaced tandem human genes	10
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	10
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	10
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	10
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	10
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	9
Deciphering the physiological response of Escherichia coli under high ATP demand	9
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	9
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks	9
Deep learning for protein structure prediction and design—progress and applications	9
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	9
Protein complexes in cells by AI‐assisted structural proteomics	9
Real‐time genomics for One Health	9
Systematic identification of structure-specific protein–protein interactions	9
Identification of type VI secretion system effector-immunity pairs using structural bioinformatics	9
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	9
Molecular causality in the advent of foundation models	9
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	9
Growth‐dependent heterogeneity in the DNA damage response in Escherichia coli	8
Computational estimation of quality and clinical relevance of cancer cell lines	8
From genes to modules, from cells to ecosystems	8
Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility	8
Spurious regulatory connections dictate the expression‐fitness landscape of translation factors	8
The rise of proteome‐wide biophysics	8
Single‐cell imaging of genome organization and dynamics	8
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	8
A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes	8