OOIR: Observatory of International Research

Papers

(The TQCC of Cell Systems is 16. 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 2021-12-01 to 2025-12-01.)

Article	Citations
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	286
Statistical modeling and analysis of cell counts from multiplexed imaging data	151
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	130
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	113
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	110
Pitfalls of genotyping microbial communities with rapidly growing genome collections	108
Approaching deconvolution with Fermi’s mindset	100
Evaluation of Peterson et al.: MAPK cascades don’t work in silos: MAP3K cross-activation of MAPKs and the effect of crosstalk on cellular responses	92
Engineering functional materials through bacteria-assisted living grafting	89
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	84
A framework for ultra-low-input spatial tissue proteomics	84
What are the current bottlenecks in developing and applying CRISPR technologies?	81
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	79
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	79
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	78
Evolutionary paths that link orthogonal pairs of binding proteins	76
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	75
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	72
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	68
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	67
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	67
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	66
The structure of the human cell cycle	63
What differentiates a stress response from responsiveness in general?	57
The geometry of cell fate	53

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	52
Homeostasis	51
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	50
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	49
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	48
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	45
How can concepts from ecology enable insights about cellular communities?	42
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	41
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	41
Mapping combinatorial expression perturbations to growth in Escherichia coli	40
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	39
The electrostatic landscape of MHC-peptide binding revealed using inception networks	38
The metallome and the biological periodic table: A metal atlas in cells	38
The structure is the message: Preserving experimental context through tensor decomposition	38
Modeling elucidates context dependence in adipose regulation	36
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	36
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	36
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	36
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	35
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	34
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	34
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	33
A top variant identification pipeline for protein engineering	33
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	32
Coupled oscillator cooperativity as a control mechanism in chronobiology	31
A complete allosteric map of a GTPase switch in its native cellular network	31
Environmental modulators of algae-bacteria interactions at scale	30
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	30
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	30
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	30
The structure of the human cell cycle	29
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	29
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	28
Noise distorts the epigenetic landscape and shapes cell-fate decisions	27
Multiomic profiling of the liver across diets and age in a diverse mouse population	27
A multi-scale map of protein assemblies in the DNA damage response	27
Evaluation of Williams et al.: On multiomics and mediation	26
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	26
Recent progress of gene circuit designs in immune cell therapies	26
Identifying features of genome evolution to exploit cancer vulnerabilities	26
The substrate quality of CK2 target sites has a determinant role on their function and evolution	26
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	24
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	24
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	23
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	23
Self-organization of plasticity and specialization in a primitively social insect	23
Learning antibody sequence constraints from allelic inclusion	23
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	23
Observations and implication of thermal tolerance in the Arabidopsis proteome	23
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	23

Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	23
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	22
Human plasma IgG1 repertoires are simple, unique, and dynamic	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	22
Cold and hot fibrosis define clinically distinct cardiac pathologies	21
The need for speed: Migratory cells in tight spaces boost their molecular clock	21
Accurate top protein variant discovery via low-N pick-and-validate machine learning	21
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	20
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	20
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	19
The community-function landscape of microbial consortia	19
Ligand-receptor promiscuity enables cellular addressing	19
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	18
Contrastive learning of T cell receptor representations	18
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning	18
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	18
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	18
Tissue Schematics: A framework to decipher tissue architecture and assembly	18
Widespread alteration of protein autoinhibition in human cancers	18
Unveiling the hidden network of STING’s subcellular regulation	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	17
Single-cell colocalization analysis using a deep generative model	17
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	17
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	17
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	17
Active learning of enhancers and silencers in the developing neural retina	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Functional attractors in microbial community assembly	16
How well do contextual protein encodings learn structure, function, and evolutionary context?	16
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	16
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	16
Privacy-preserving genotype imputation with fully homomorphic encryption	16
Studying stochastic systems biology of the cell with single-cell genomics data	16