OOIR: Observatory of International Research

Papers

(The TQCC of Cell Systems is 17. 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 2021-05-01 to 2025-05-01.)

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	343
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	221
Approaching deconvolution with Fermi’s mindset	176
Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads	159
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	155
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	154
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	110
A framework for ultra-low-input spatial tissue proteomics	96
Engineering functional materials through bacteria-assisted living grafting	95
Pitfalls of genotyping microbial communities with rapidly growing genome collections	95
Which image-based phenotypes are most promising for using AI to understand cellular functions and why?	94
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	93
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	93
What are the current bottlenecks in developing and applying CRISPR technologies?	83
Evolutionary paths that link orthogonal pairs of binding proteins	83
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	82
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	80
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	77
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	69
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	66
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	66
Homeostasis	64
What differentiates a stress response from responsiveness in general?	62
The structure of the human cell cycle	62
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	59

Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	58
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	57
A forecast for large-scale, predictive biology: Lessons from meteorology	57
How can concepts from ecology enable insights about cellular communities?	57
Mapping the multiscale structure of biological systems	56
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	56
The geometry of cell fate	56
Schrödinger’s What Is Life? at 75	55
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	54
Modeling elucidates context dependence in adipose regulation	54
Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions	53
The structure is the message: Preserving experimental context through tensor decomposition	53
Mapping combinatorial expression perturbations to growth in Escherichia coli	51
The electrostatic landscape of MHC-peptide binding revealed using inception networks	51
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	49
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	47
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	47
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	44
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	43
Machine learning for perturbational single-cell omics	42
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	40
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	39
Coupled oscillator cooperativity as a control mechanism in chronobiology	39
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	39
Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science	38
Consequential drug combinations for tuberculosis treatments	37
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	35
Environmental modulators of algae-bacteria interactions at scale	35
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	34
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	34
A top variant identification pipeline for protein engineering	32
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	32
A complete allosteric map of a GTPase switch in its native cellular network	32
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	31
The structure of the human cell cycle	31
The substrate quality of CK2 target sites has a determinant role on their function and evolution	30
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	30
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	30
Identifying features of genome evolution to exploit cancer vulnerabilities	30
Evaluation of Williams et al.: On multiomics and mediation	29
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	29
A convergent molecular network underlying autism and congenital heart disease	28
Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition	28
Recent progress of gene circuit designs in immune cell therapies	28
Database-independent de novo metaproteomics of complex microbial communities	26
Multiomic profiling of the liver across diets and age in a diverse mouse population	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
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	25

A multi-scale map of protein assemblies in the DNA damage response	25
Minding the gaps: The importance of navigating holes in protein fitness landscapes	25
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	25
Hotspot identifies informative gene modules across modalities of single-cell genomics	25
Human plasma IgG1 repertoires are simple, unique, and dynamic	25
Self-organization of plasticity and specialization in a primitively social insect	25
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	24
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	24
The need for speed: Migratory cells in tight spaces boost their molecular clock	24
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	24
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	24
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	23
Accurate top protein variant discovery via low-N pick-and-validate machine learning	23
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	22
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain	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
Ligand-receptor promiscuity enables cellular addressing	21
Tissue Schematics: A framework to decipher tissue architecture and assembly	20
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	20
Cold and hot fibrosis define clinically distinct cardiac pathologies	20
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	19
Unveiling the hidden network of STING’s subcellular regulation	19
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	19
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	19
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria	18
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	18
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	18
Widespread alteration of protein autoinhibition in human cancers	18
Functional attractors in microbial community assembly	17
Studying stochastic systems biology of the cell with single-cell genomics data	17