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 2022-08-01 to 2026-08-01.)

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	425
Statistical modeling and analysis of cell counts from multiplexed imaging data	210
Engineering functional materials through bacteria-assisted living grafting	132
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	128
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	117
A combinatorial transcription factor screening platform for immune cell reprogramming	116
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	112
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	99
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	91
A data-driven modeling framework for mapping genotypes to synthetic microbial community functions	88
Pitfalls of genotyping microbial communities with rapidly growing genome collections	67
A framework for ultra-low-input spatial tissue proteomics	61
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	60
Context-informed subgraph foundation models enable interpretable protein-function prediction	57
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	55
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	53
What are the current bottlenecks in developing and applying CRISPR technologies?	53
Evolutionary paths that link orthogonal pairs of binding proteins	51
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	49
Identifying maximally informative signal-aware representations of single-cell data using the information bottleneck	49
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	48
Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling	46
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	45
From modality-specific to compositional foundation models for cell biology	45
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	44

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	43
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	43
Quantifying protein unfolding kinetics with a high-throughput microfluidic platform	43
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	40
How can concepts from ecology enable insights about cellular communities?	39
The electrostatic landscape of MHC-peptide binding revealed using inception networks	37
Modeling elucidates context dependence in adipose regulation	36
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	36
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	36
Translation elongation as a rate-limiting step of protein production	35
Mapping combinatorial expression perturbations to growth in Escherichia coli	34
The metallome and the biological periodic table: A metal atlas in cells	32
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	32
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	32
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	31
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	31
NOT-gated chimeric antigen receptor circuits in T and NK cells	31
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	31
The structure is the message: Preserving experimental context through tensor decomposition	31
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	30
A top variant identification pipeline for protein engineering	30
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	30
Environmental modulators of algae-bacteria interactions at scale	30
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	29
DynamicGT: A dynamic-aware geometric transformer model to predict protein-binding interfaces in flexible and disordered regions	29
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	28
High-throughput machine learning-aided antibody discovery for cell surface antigens	28
A complete allosteric map of a GTPase switch in its native cellular network	28
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	28
Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities	27
Identifying microbial protease allergens through protein language model-guided homology	27
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	26
Coupled oscillator cooperativity as a control mechanism in chronobiology	26
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	25
Recent progress of gene circuit designs in immune cell therapies	25
A multi-scale map of protein assemblies in the DNA damage response	24
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	24
The molecular landscape of cellular metal ion biology	24
The substrate quality of CK2 target sites has a determinant role on their function and evolution	24
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	24
Pooled combinatorial screening identifies transcription factor sets that drive hematopoietic progenitor-like cell fate	24
Capturing the dynamics of STAT6 macrophage polarization using bioluminescence temporal signatures	23
Learning antibody sequence constraints from allelic inclusion	23
Self-organization of plasticity and specialization in a primitively social insect	23
Ectopic expression to synthetic design: Deriving engineering principles of lncRNA-mediated epigenetic regulation	23
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	23
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	23
Harnessing heterogeneity for the rational design of cell manufacturing	23
Transcriptional competition biases the effects of second messengers in Escherichia coli	23
Observations and implication of thermal tolerance in the Arabidopsis proteome	23

Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	22
Recurrent neural chemical reaction networks that approximate arbitrary dynamics	22
Programmable regenerative tissues: Converging mammalian synthetic biology and tissue engineering	22
Discovering what is possible: How synthetic biology illuminates development	22
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	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
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	22
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	22
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	22
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning	21
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	21
Cold and hot fibrosis define clinically distinct cardiac pathologies	21
Resource competition shapes CRISPR-mediated gene activation	21
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	21
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	20
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	20
The community-function landscape of microbial consortia	20
Widespread alteration of protein autoinhibition in human cancers	20
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	20
Accurate top protein variant discovery via low-N pick-and-validate machine learning	20
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	20
Unveiling the hidden network of STING’s subcellular regulation	19
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	19
Dango: Predicting higher-order genetic interactions	19
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	19
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	18
Disobind: A sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Morphology and gene expression profiling provide complementary information for mapping cell state	18
Single-cell colocalization analysis using a deep generative model	18
Studying stochastic systems biology of the cell with single-cell genomics data	18
Glycoform engineering of a mammalian platform to sculpt a humanized recombinant bioscavenger	18
Entrainment and multi-stability of the p53 oscillator in human cells	17
Foundation model reveals the shared organization of transcription and topologically associating domains	17
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	17
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	17
Contrastive learning of T cell receptor representations	17
The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering	17
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	17
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states	17
Modeling chimeric antigen receptor response at the single-cell level with conditional optimal transport	17
Automated single-cell omics end-to-end framework with data-driven batch inference	16
How well do contextual protein encodings learn structure, function, and evolutionary context?	16
Somatic XIST activation and features of X chromosome inactivation in male human cancers	16
What can recent methodological advances help us understand about protein and genome evolution?	16