OOIR: Observatory of International Research

Papers

(The median citation count of Molecular Systems Biology is 9. 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 2021-01-01 to 2025-01-01.)

Article	Citations
SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle	315
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	302
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	204
ENDORSE: a prognostic model for endocrine therapy in estrogen‐receptor‐positive breast cancers	179
Dengue virus preferentially uses human and mosquito non-optimal codons	134
Stress‐sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis	132
The population context is a driver of the heterogeneous response of epithelial cells to interferons	105
Linking patient-specific basal MET phosphorylation levels to liver health	96
Quantifying the phenotypic information in mRNA abundance	95
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	90
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation	75
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors	72
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	71
A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism	71
Development and validation of AI/ML derived splice-switching oligonucleotides	69
Exploring the microbial savanna: predator-prey interactions in the soil	67
A new way of looking at transcription factor assays	67
A human kinase yeast array for the identification of kinases modulating phosphorylation‐dependent protein–protein interactions	61
Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival	61
The circadian oscillator analysed at the single‐transcript level	59
Systematic identification of 20S proteasome substrates	53
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd	52
Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor	51
Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels	48
High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein	46

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	46
Differentiation‐related epigenomic changes define clinically distinct keratinocyte cancer subclasses	46
TNF stimulation primarily modulates transcriptional burst size of NF‐κB‐regulated genes	45
A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X	44
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	44
Hotspot propensity across mutational processes	44
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies	43
Vesalius: high‐resolution in silico anatomization of spatial transcriptomic data using image analysis	41
Quantitative contributions of TNF receptor superfamily members to CD8 ⁺ T‐cell responses	38
Evolution of genome fragility enables microbial division of labor	37
Dynamic human liver proteome atlas reveals functional insights into disease pathways	36
Mapping single‐cell responses to population‐level dynamics during antibiotic treatment	35
Genetic effects on molecular network states explain complex traits	34
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	32
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	32
Genome‐scale metabolic modeling reveals key features of a minimal gene set	30
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system	29
Predictive evolution of metabolic phenotypes using model‐designed environments	28
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	28
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting	28
Translational efficiency across healthy and tumor tissues is proliferation‐related	28
Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)	27
A split intein and split luciferase-coupled system for detecting protein-protein interactions	27
Evolution and stability of complex microbial communities driven by trade-offs	27
State of the interactomes: an evaluation of molecular networks for generating biological insights	27
Transcription factor expression is the main determinant of variability in gene co‐activity	26
Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans	26
Multiplying insights from perturbation experiments: predicting new perturbation combinations	26
Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion	26
Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources	25
Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy	24
Monocyte‐crosstalk drives interferon‐mediated signaling following SARS‐CoV ‐2 exposure	24
Exploiting spatial dimensions to enable parallelized continuous directed evolution	24
Modeling unveils sex differences of signaling networks in mouse embryonic stem cells	23
Integrated systems biology approach identifies gene targets for endothelial dysfunction	23
Turning up the heat on essential E. coli genes	23
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	22
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	22
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	21
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	21
Basal MET phosphorylation is an indicator of hepatocyte dysregulation in liver disease	20
Predicting cellular responses to complex perturbations in high‐throughput screens	20
An engineered Mycoplasma pneumoniae to fight Staphylococcus aureus	20
Modeling glioblastoma heterogeneity as a dynamic network of cell states	20
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	20
Metabolic memory underlying minimal residual disease in breast cancer	20
Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses	19
A proximity proteomics pipeline with improved reproducibility and throughput	19
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	19
Efficient plasmid transfer via natural competence in a microbial co‐culture	19

Reproducibility in systems biology modelling	18
Enablers and challenges of spatial omics, a melting pot of technologies	18
A single‐cell RNA labeling strategy for measuring stress response upon tissue dissociation	18
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	18
A guidebook for DISCO tissue clearing	17
Suboptimal resource allocation in changing environments constrains response and growth in bacteria	17
A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks	17
Enhancing nutritional niche and host defenses by modifying the gut microbiome	16
Dimensionality reduction methods for extracting functional networks from large‐scaleCRISPRscreens	16
Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics	16
A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability	16
Competitive dCas9 binding as a mechanism for transcriptional control	16
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	16
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability	16
Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations	16
Deciphering the physiological response of Escherichia coli under high ATP demand	15
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms	15
Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions	15
Identification of covalent modifications regulating immune signaling complex composition and phenotype	15
Evaluating the Arrhenius equation for developmental processes	15
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium	15
Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach	15
What we can learn from deep space communication for reproducible bioimaging and data analysis	14
Unravelling metabolic cross‐feeding in a yeast–bacteria community using ¹³C‐based proteomics	14
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States	14
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	14
Tensor‐structured decomposition improves systems serology analysis	14
A multi‐layered network model identifies Akt1 as a common modulator of neurodegeneration	14
Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver	14
Molecular causality in the advent of foundation models	14
CRISPR memories in single cells	14
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	14
Multisite assessment of reproducibility in high‐content cell migration imaging data	13
Growth‐mediated negative feedback shapes quantitative antibiotic response	13
Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard‐to‐kill persister cells	13
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	12
CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing	12
A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord	12
Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants	12
Cell sorters see things more clearly now	12
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	12
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)	12
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition	12
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates	12
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community	12
Quantifying persistence in the T‐cell signaling network using an optically controllable antigen receptor	11
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	11
Real‐time genomics for One Health	11
CellNeighborEX: deciphering neighbor‐dependent gene expression from spatial transcriptomics data	11
Higher‐order modular regulation of the human proteome	11
Identification of type VI secretion system effector-immunity pairs using structural bioinformatics	11
Systematic identification of structure-specific protein–protein interactions	11
Single‐cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos	10
Bacterial live therapeutics for human diseases	10
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	10
Alternative proteoforms and proteoform-dependent assemblies in humans and plants	10
Deep learning for protein structure prediction and design—progress and applications	10
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases	10
Protein complexes in cells by AI‐assisted structural proteomics	10
Unique features of transcription termination and initiation at closely spaced tandem human genes	10
Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation	9
TATA and paused promoters active in differentiated tissues have distinct expression characteristics	9
Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies	9
Enabling high‐throughput biology with flexible open‐source automation	9
Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression	9
Heterogeneity of the cancer cell line metabolic landscape	9
Large‐scale analysis of Drosophila core promoter function using synthetic promoters	9
Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation	9
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	9
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis	9
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	9
CODEX, a neural network approach to explore signaling dynamics landscapes	9
The genotype‐phenotype landscape of an allosteric protein	9
Proteome-wide copy-number estimation from transcriptomics	9