Cell Systems

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	236
Statistical modeling and analysis of cell counts from multiplexed imaging data	173
Approaching deconvolution with Fermi’s mindset	126
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	123
Engineering functional materials through bacteria-assisted living grafting	115
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	106
A framework for ultra-low-input spatial tissue proteomics	103
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	101
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	89
What are the current bottlenecks in developing and applying CRISPR technologies?	87
Pitfalls of genotyping microbial communities with rapidly growing genome collections	87
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	85
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	76
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	74
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	73
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	73
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	70
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	69
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	68
Evolutionary paths that link orthogonal pairs of binding proteins	67
Homeostasis	67
What differentiates a stress response from responsiveness in general?	64
The structure of the human cell cycle	63
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	62
How can concepts from ecology enable insights about cellular communities?	60

Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	59
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	58
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	54
The geometry of cell fate	52
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	51
Modeling elucidates context dependence in adipose regulation	49
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	48
The electrostatic landscape of MHC-peptide binding revealed using inception networks	46
The metallome and the biological periodic table: A metal atlas in cells	43
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	43
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	41
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	40
Mapping combinatorial expression perturbations to growth in Escherichia coli	40
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	38
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	37
The structure is the message: Preserving experimental context through tensor decomposition	37
Coupled oscillator cooperativity as a control mechanism in chronobiology	34
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	34
Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science	33
Consequential drug combinations for tuberculosis treatments	33
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	32
Environmental modulators of algae-bacteria interactions at scale	32
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	32
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	32
The structure of the human cell cycle	31
A complete allosteric map of a GTPase switch in its native cellular network	31
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	30
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	30
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	30
A top variant identification pipeline for protein engineering	29
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	28
Identifying features of genome evolution to exploit cancer vulnerabilities	28
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	28
Noise distorts the epigenetic landscape and shapes cell-fate decisions	27
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	27
Evaluation of Williams et al.: On multiomics and mediation	27
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	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	26
Multiomic profiling of the liver across diets and age in a diverse mouse population	25
Recent progress of gene circuit designs in immune cell therapies	25
A convergent molecular network underlying autism and congenital heart disease	25
The substrate quality of CK2 target sites has a determinant role on their function and evolution	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	24
Minding the gaps: The importance of navigating holes in protein fitness landscapes	23
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	22
Learning antibody sequence constraints from allelic inclusion	22
Human plasma IgG1 repertoires are simple, unique, and dynamic	22
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22

Self-organization of plasticity and specialization in a primitively social insect	22
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	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	21
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	21
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	21
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	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
The need for speed: Migratory cells in tight spaces boost their molecular clock	21
Accurate top protein variant discovery via low-N pick-and-validate machine learning	20
Ligand-receptor promiscuity enables cellular addressing	19
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	19
The community-function landscape of microbial consortia	19
Cold and hot fibrosis define clinically distinct cardiac pathologies	19
Unveiling the hidden network of STING’s subcellular regulation	18
Tissue Schematics: A framework to decipher tissue architecture and assembly	18
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	18
Single-cell colocalization analysis using a deep generative model	17
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	17
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	17
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	17
Studying stochastic systems biology of the cell with single-cell genomics data	17
Widespread alteration of protein autoinhibition in human cancers	17
Contrastive learning of T cell receptor representations	16
Functional attractors in microbial community assembly	16
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	16
Paving the path toward genomic privacy with secure imputation	15
What can recent methodological advances help us understand about protein and genome evolution?	14
How well do contextual protein encodings learn structure, function, and evolutionary context?	14
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	14
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	14
Privacy-preserving genotype imputation with fully homomorphic encryption	14
Entrainment and multi-stability of the p53 oscillator in human cells	14
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	14
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	14
Automated single-cell omics end-to-end framework with data-driven batch inference	14
Somatic XIST activation and features of X chromosome inactivation in male human cancers	14
Active learning of enhancers and silencers in the developing neural retina	14
A molecular clock controls periodically driven cell migration in confined spaces	13
Enhanced cellular longevity arising from environmental fluctuations	13
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	13
Assessing generative model coverage of protein structures with SHAPES	13
Emerging questions in transcriptional regulation	13
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	13
BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences	13
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	13
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	13
What limits our ability to study the effects of microbial diversity on health and the environment?	12
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	12
Reproducibility metrics for context-specific CRISPR screens	12
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	12
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	12
Efficient retroelement-mediated DNA writing in bacteria	12
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	12
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals	12
Periodic spatial patterning with a single morphogen	11
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	11
Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons	11
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	11
NAD+ flux is maintained in aged mice despite lower tissue concentrations	11
The in silico lab: Improving academic code using lessons from biology	11
Versatile system cores as a conceptual basis for generality in cell and developmental biology	10
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	10
What do you most hope spatial molecular profiling will help us understand? Part 2	10
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	10
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	10
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	10
Parallel engineering and activity profiling of a base editor system	10
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	10
A new age in protein design empowered by deep learning	10
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	9
Biophysical metabolic modeling of complex bacterial colony morphology	9
Truncated protein isoforms generate diversity of protein localization and function in yeast	9
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	9
Evo-velocity: Protein language modeling accelerates the study of evolution	9
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	9

Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	9
Integrase enables synthetic intercellular logic via bacterial conjugation	9
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders	9
The time-resolved genomic impact of Wnt/β-catenin signaling	9
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	9
Evaluation of Lee et al.: Clarity and interpretation of mutual information in promoter transfer functions	8
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods	8
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	8
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	8
Information theory entering soils and tissues	8
High-throughput functional characterization of combinations of transcriptional activators and repressors	8
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	8
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	8
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	8
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	8
Control points for design of taxonomic composition in synthetic human gut communities	8
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	8
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	8
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	8
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	8
Evaluation of Ravindran et al.: Real-time detection of signaling pulses in vivo: making cells monitor themselves	7
Privacy-preserving genotype imputation in a trusted execution environment	7
How can Waddington-like landscapes facilitate insights beyond developmental biology?	7
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	7
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	7
Benchmarking transcriptional host response signatures for infection diagnosis	7
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	7
Systems genetics of metabolic health in the BXD mouse genetic reference population	7
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	7
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	7
Modes and motifs in multicellular communication	7
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	6
IgLM: Infilling language modeling for antibody sequence design	6
What is the key challenge in engineering microbiomes?	6
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	6
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	6
Cracking the code of adaptive immunity: The role of computational tools	6
Modeling non-genetic adaptation in tumor cells	6
On knowing a gene: A distributional hypothesis of gene function	6
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	6
Reframing the role of the objective function in its proper context for metabolic network modeling	6
Data-driven batch detection enhances single-cell omics data analysis	6
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	5
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	5
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	5
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	5
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	5
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	5
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	5
DeST-OT: Alignment of spatiotemporal transcriptomics data	5
Convolutions are competitive with transformers for protein sequence pretraining	5
Highly parallel production of designer organoids by mosaic patterning of progenitors	5
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	5
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	5
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities	5
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	5