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 2021-11-01 to 2025-11-01.)

Article	Citations
Approaching deconvolution with Fermi’s mindset	274
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	183
Statistical modeling and analysis of cell counts from multiplexed imaging data	143
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	124
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	111
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	107
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	106
A framework for ultra-low-input spatial tissue proteomics	94
Pitfalls of genotyping microbial communities with rapidly growing genome collections	91
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	83
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	82
Engineering functional materials through bacteria-assisted living grafting	82
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	78
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	77
What are the current bottlenecks in developing and applying CRISPR technologies?	76
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	76
Evolutionary paths that link orthogonal pairs of binding proteins	72
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	71
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	71
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	65
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	65
Homeostasis	64
What differentiates a stress response from responsiveness in general?	63
The structure of the human cell cycle	62
The geometry of cell fate	61

Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	56
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	54
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	53
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	52
How can concepts from ecology enable insights about cellular communities?	50
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	49
Modeling elucidates context dependence in adipose regulation	48
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	47
The structure is the message: Preserving experimental context through tensor decomposition	43
The metallome and the biological periodic table: A metal atlas in cells	41
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
The electrostatic landscape of MHC-peptide binding revealed using inception networks	40
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	39
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	38
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	37
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	37
Consequential drug combinations for tuberculosis treatments	35
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	35
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	35
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	35
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	34
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	34
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	34
A top variant identification pipeline for protein engineering	33
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	32
A complete allosteric map of a GTPase switch in its native cellular network	32
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	32
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	31
Coupled oscillator cooperativity as a control mechanism in chronobiology	30
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	30
The structure of the human cell cycle	30
Environmental modulators of algae-bacteria interactions at scale	29
Identifying features of genome evolution to exploit cancer vulnerabilities	29
Evaluation of Williams et al.: On multiomics and mediation	28
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	28
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	27
The substrate quality of CK2 target sites has a determinant role on their function and evolution	27
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	26
A convergent molecular network underlying autism and congenital heart disease	26
Noise distorts the epigenetic landscape and shapes cell-fate decisions	26
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	26
A multi-scale map of protein assemblies in the DNA damage response	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
Recent progress of gene circuit designs in immune cell therapies	25
Multiomic profiling of the liver across diets and age in a diverse mouse population	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	24
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	23
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	23
Human plasma IgG1 repertoires are simple, unique, and dynamic	23
Learning antibody sequence constraints from allelic inclusion	22

Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	22
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
Minding the gaps: The importance of navigating holes in protein fitness landscapes	22
The need for speed: Migratory cells in tight spaces boost their molecular clock	21
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	21
Accurate top protein variant discovery via low-N pick-and-validate machine learning	21
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	21
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	21
Self-organization of plasticity and specialization in a primitively social insect	21
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	21
Cold and hot fibrosis define clinically distinct cardiac pathologies	20
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning	20
Ligand-receptor promiscuity enables cellular addressing	19
The community-function landscape of microbial consortia	19
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	19
Tissue Schematics: A framework to decipher tissue architecture and assembly	19
Unveiling the hidden network of STING’s subcellular regulation	18
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
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	18
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	17
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	17
Functional attractors in microbial community assembly	17
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	17
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	17
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	17
Studying stochastic systems biology of the cell with single-cell genomics data	16
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	16
How well do contextual protein encodings learn structure, function, and evolutionary context?	16
Single-cell colocalization analysis using a deep generative model	16
What can recent methodological advances help us understand about protein and genome evolution?	16
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	16
Widespread alteration of protein autoinhibition in human cancers	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16