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 2021-08-01 to 2025-08-01.)

Article	Citations
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	251
Statistical modeling and analysis of cell counts from multiplexed imaging data	220
Approaching deconvolution with Fermi’s mindset	169
A framework for ultra-low-input spatial tissue proteomics	163
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	122
Pitfalls of genotyping microbial communities with rapidly growing genome collections	118
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	106
Engineering functional materials through bacteria-assisted living grafting	105
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	101
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	98
What are the current bottlenecks in developing and applying CRISPR technologies?	87
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	87
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	84
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	82
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	73
Evolutionary paths that link orthogonal pairs of binding proteins	71
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	69
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	68
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	67
What differentiates a stress response from responsiveness in general?	65
Homeostasis	65
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	65
The structure of the human cell cycle	64
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	63
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	61

How can concepts from ecology enable insights about cellular communities?	59
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	59
The geometry of cell fate	58
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	57
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	57
Modeling elucidates context dependence in adipose regulation	53
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	52
Mapping combinatorial expression perturbations to growth in Escherichia coli	51
The electrostatic landscape of MHC-peptide binding revealed using inception networks	50
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	48
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	48
The structure is the message: Preserving experimental context through tensor decomposition	45
The metallome and the biological periodic table: A metal atlas in cells	43
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	42
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	40
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	39
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	39
Coupled oscillator cooperativity as a control mechanism in chronobiology	37
Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science	36
Consequential drug combinations for tuberculosis treatments	35
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	33
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	33
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	32
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	32
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	32
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	31
A top variant identification pipeline for protein engineering	31
Environmental modulators of algae-bacteria interactions at scale	31
A complete allosteric map of a GTPase switch in its native cellular network	30
The structure of the human cell cycle	30
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	30
Identifying features of genome evolution to exploit cancer vulnerabilities	29
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	28
Evaluation of Williams et al.: On multiomics and mediation	28
A multi-scale map of protein assemblies in the DNA damage response	28
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	28
The substrate quality of CK2 target sites has a determinant role on their function and evolution	27
A convergent molecular network underlying autism and congenital heart disease	27
Multiomic profiling of the liver across diets and age in a diverse mouse population	26
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	26
Recent progress of gene circuit designs in immune cell therapies	26
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	25
Minding the gaps: The importance of navigating holes in protein fitness landscapes	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	25
Self-organization of plasticity and specialization in a primitively social insect	25
Noise distorts the epigenetic landscape and shapes cell-fate decisions	25
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	22

Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	22
Human plasma IgG1 repertoires are simple, unique, and dynamic	22
The need for speed: Migratory cells in tight spaces boost their molecular clock	22
Accurate top protein variant discovery via low-N pick-and-validate machine learning	22
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	22
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	22
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	22
The community-function landscape of microbial consortia	21
Cold and hot fibrosis define clinically distinct cardiac pathologies	21
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	21
Ligand-receptor promiscuity enables cellular addressing	20
Tissue Schematics: A framework to decipher tissue architecture and assembly	20
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	19
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	19
Unveiling the hidden network of STING’s subcellular regulation	18
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	18
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	18
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Single-cell colocalization analysis using a deep generative model	17
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	17
Widespread alteration of protein autoinhibition in human cancers	17
Functional attractors in microbial community assembly	17
Contrastive learning of T cell receptor representations	17
Studying stochastic systems biology of the cell with single-cell genomics data	17
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	16
Paving the path toward genomic privacy with secure imputation	16
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	16
What can recent methodological advances help us understand about protein and genome evolution?	16
A time-resolved proteomic and prognostic map of COVID-19	16
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	16