OOIR: Observatory of International Research

Papers

(The TQCC of Molecular Systems Biology is 20. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation	315
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models	302
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis	204
RNA velocity—current challenges and future perspectives	174
Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery	126
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases	120
A single cell atlas of the human liver tumor microenvironment	112
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies	105
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses	96
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions	95
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	90
Reproducibility in systems biology modelling	75
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial	72
Towards a mechanistic understanding of reciprocal drug–microbiome interactions	71
Protein complexes in cells by AI‐assisted structural proteomics	71
Predicting cellular responses to complex perturbations in high‐throughput screens	69
SARS‐CoV‐2–host proteome interactions for antiviral drug discovery	67
Evaluating the Arrhenius equation for developmental processes	67
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing	61
A guidebook for DISCO tissue clearing	61
Joint cell segmentation and cell type annotation for spatial transcriptomics	59
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms	53
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin	52
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome	51
Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost	46

Suboptimal resource allocation in changing environments constrains response and growth in bacteria	46
Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments	46
Enabling high‐throughput biology with flexible open‐source automation	46
Updated benchmarking of variant effect predictors using deep mutational scanning	45
HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence	44
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes	44
A genome‐scale yeast library with inducible expression of individual genes	44
DOMINO: a network‐based active module identification algorithm with reduced rate of false calls	43
The transcriptome dynamics of single cells during the cell cycle	41
The genotype‐phenotype landscape of an allosteric protein	41
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation	38
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations	37
Exploring amino acid functions in a deep mutational landscape	36
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks	35
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics	34
Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing	32
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities	32
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel	30
Single‐cell imaging of genome organization and dynamics	29
Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion	28
CellRegMap : a statistical framework for mapping context‐specific regulatory variants using scRNA ‐seq	28
Dynamic human liver proteome atlas reveals functional insights into disease pathways	28
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma	28
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients	27
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks	27
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	27
A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection	27
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets	26
Modeling glioblastoma heterogeneity as a dynamic network of cell states	26
Transcriptionally active enhancers in human cancer cells	26
Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo	25
MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback	24
The molecular architecture of cell cycle arrest	24
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness	24
SARS‐CoV‐2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms	23
Using single‐plant‐omics in the field to link maize genes to functions and phenotypes	23
Large‐scale survey and database of high affinity ligands for peptide recognition modules	23
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis	23
Diauxic lags explain unexpected coexistence in multi‐resource environments	23
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection	22
Behavioral fingerprints predict insecticide and anthelmintic mode of action	22
CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators	22
spliceJAC : transition genes and state‐specific gene regulation from single‐cell transcriptome data	22
SARS‐CoV‐2 infection remodels the host protein thermal stability landscape	21
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF‐induced necroptosis decisions	21
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis	21
Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa	21
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration	20
Machine learning identifies molecular regulators and therapeutics for targeting SARS‐CoV2‐induced cytokine release	20
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae	20

Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance	20
Genetic regulation of liver lipids in a mouse model of insulin resistance and hepatic steatosis	20
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids	20
An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria	20
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots	20
Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress	20