OOIR: Observatory of International Research

Papers

(The H4-Index of Cell Systems is 35. 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 2022-06-01 to 2026-06-01.)

Article	Citations
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	384
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	194
Statistical modeling and analysis of cell counts from multiplexed imaging data	119
Engineering functional materials through bacteria-assisted living grafting	113
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	110
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	107
A combinatorial transcription factor screening platform for immune cell reprogramming	104
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	92
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	86
A framework for ultra-low-input spatial tissue proteomics	81
Pitfalls of genotyping microbial communities with rapidly growing genome collections	70
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	62
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	60
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	58
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	58
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	56
Context-informed subgraph foundation models enable interpretable protein-function prediction	54
Identifying maximally informative signal-aware representations of single-cell data using the information bottleneck	52
Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling	50
What are the current bottlenecks in developing and applying CRISPR technologies?	47
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	46
Evolutionary paths that link orthogonal pairs of binding proteins	45
From modality-specific to compositional foundation models for cell biology	44
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	44
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	44

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	43
How can concepts from ecology enable insights about cellular communities?	42
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	42
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	41
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	38
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	37
The metallome and the biological periodic table: A metal atlas in cells	36
The electrostatic landscape of MHC-peptide binding revealed using inception networks	36
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	35
Modeling elucidates context dependence in adipose regulation	35