OOIR: Observatory of International Research

Papers

(The H4-Index of Cell Systems is 36. 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 2022-05-01 to 2026-05-01.)

Article	Citations
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	370
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	184
Pitfalls of genotyping microbial communities with rapidly growing genome collections	117
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	108
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	107
A framework for ultra-low-input spatial tissue proteomics	103
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	102
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	92
Approaching deconvolution with Fermi’s mindset	87
Statistical modeling and analysis of cell counts from multiplexed imaging data	81
A combinatorial transcription factor screening platform for immune cell reprogramming	77
Engineering functional materials through bacteria-assisted living grafting	75
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	74
Evolutionary paths that link orthogonal pairs of binding proteins	69
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	61
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	58
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	57
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	56
Context-informed subgraph foundation models enable interpretable protein-function prediction	52
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	50
Identifying maximally informative signal-aware representations of single-cell data using the information bottleneck	49
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	49
From modality-specific to compositional foundation models for cell biology	45
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	44
Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling	43

Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	43
What are the current bottlenecks in developing and applying CRISPR technologies?	43
How can concepts from ecology enable insights about cellular communities?	42
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	42
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	42
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	41
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	40
Translation elongation as a rate-limiting step of protein production	38
The electrostatic landscape of MHC-peptide binding revealed using inception networks	37
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	37