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	251
Statistical modeling and analysis of cell counts from multiplexed imaging data	220
Approaching deconvolution with Fermi’s mindset	169
A framework for ultra-low-input spatial tissue proteomics	163
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	122
Pitfalls of genotyping microbial communities with rapidly growing genome collections	118
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	106
Engineering functional materials through bacteria-assisted living grafting	105
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	101
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	98
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	87
What are the current bottlenecks in developing and applying CRISPR technologies?	87
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	84
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	82
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	73
Evolutionary paths that link orthogonal pairs of binding proteins	71
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	69
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	68
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	67
Homeostasis	65
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	65
What differentiates a stress response from responsiveness in general?	65
The structure of the human cell cycle	64
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	63
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	61

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	59
How can concepts from ecology enable insights about cellular communities?	59
The geometry of cell fate	58
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	57
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	57
Modeling elucidates context dependence in adipose regulation	53
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	52
Mapping combinatorial expression perturbations to growth in Escherichia coli	51
The electrostatic landscape of MHC-peptide binding revealed using inception networks	50
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	48
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	48
The structure is the message: Preserving experimental context through tensor decomposition	45
The metallome and the biological periodic table: A metal atlas in cells	43
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	42
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	40
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	39
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	39
Coupled oscillator cooperativity as a control mechanism in chronobiology	37
Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science	36
Consequential drug combinations for tuberculosis treatments	35
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	33
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	33
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	32
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	32
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	32
A top variant identification pipeline for protein engineering	31
Environmental modulators of algae-bacteria interactions at scale	31
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	31
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	30
A complete allosteric map of a GTPase switch in its native cellular network	30
The structure of the human cell cycle	30
Identifying features of genome evolution to exploit cancer vulnerabilities	29
A multi-scale map of protein assemblies in the DNA damage response	28
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	28
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	28
Evaluation of Williams et al.: On multiomics and mediation	28
The substrate quality of CK2 target sites has a determinant role on their function and evolution	27
A convergent molecular network underlying autism and congenital heart disease	27
Recent progress of gene circuit designs in immune cell therapies	26
Multiomic profiling of the liver across diets and age in a diverse mouse population	26
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	26
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	25
Self-organization of plasticity and specialization in a primitively social insect	25
Noise distorts the epigenetic landscape and shapes cell-fate decisions	25
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	25
Minding the gaps: The importance of navigating holes in protein fitness landscapes	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	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

Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	22
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	22
Human plasma IgG1 repertoires are simple, unique, and dynamic	22
The need for speed: Migratory cells in tight spaces boost their molecular clock	22
Accurate top protein variant discovery via low-N pick-and-validate machine learning	22
Cold and hot fibrosis define clinically distinct cardiac pathologies	21
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	21
The community-function landscape of microbial consortia	21
Tissue Schematics: A framework to decipher tissue architecture and assembly	20
Ligand-receptor promiscuity enables cellular addressing	20
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	19
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	19
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Unveiling the hidden network of STING’s subcellular regulation	18
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	18
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	18
Contrastive learning of T cell receptor representations	17
Studying stochastic systems biology of the cell with single-cell genomics data	17
Single-cell colocalization analysis using a deep generative model	17
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	17
Widespread alteration of protein autoinhibition in human cancers	17
Functional attractors in microbial community assembly	17
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	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	16
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	16
What can recent methodological advances help us understand about protein and genome evolution?	16
A time-resolved proteomic and prognostic map of COVID-19	16
Automated single-cell omics end-to-end framework with data-driven batch inference	15
Privacy-preserving genotype imputation with fully homomorphic encryption	15
How well do contextual protein encodings learn structure, function, and evolutionary context?	15
Entrainment and multi-stability of the p53 oscillator in human cells	14
Emerging questions in transcriptional regulation	14
Somatic XIST activation and features of X chromosome inactivation in male human cancers	14
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	14
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	14
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	14
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	14
Artificial intelligence for proteomics and biomarker discovery	14
Active learning of enhancers and silencers in the developing neural retina	14
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	13
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	13
Enhanced cellular longevity arising from environmental fluctuations	13
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	13
Assessing generative model coverage of protein structures with SHAPES	13
BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences	13
A molecular clock controls periodically driven cell migration in confined spaces	13
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	13
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	12
Reproducibility metrics for context-specific CRISPR screens	12
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	12
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	12
NAD+ flux is maintained in aged mice despite lower tissue concentrations	12
Periodic spatial patterning with a single morphogen	12
Efficient retroelement-mediated DNA writing in bacteria	12
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals	12
Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons	12
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	12
What limits our ability to study the effects of microbial diversity on health and the environment?	12
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	11
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	11
The in silico lab: Improving academic code using lessons from biology	11
Parallel engineering and activity profiling of a base editor system	10
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	10
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders	10
What do you most hope spatial molecular profiling will help us understand? Part 2	10
Versatile system cores as a conceptual basis for generality in cell and developmental biology	10
A new age in protein design empowered by deep learning	10
Integrase enables synthetic intercellular logic via bacterial conjugation	10
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	10
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	10
Evo-velocity: Protein language modeling accelerates the study of evolution	10
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	10
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	9
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	9

Truncated protein isoforms generate diversity of protein localization and function in yeast	9
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	9
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	9
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	9
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	9
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
Evaluation of Ravindran et al.: Real-time detection of signaling pulses in vivo: making cells monitor themselves	8
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	8
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	8
The time-resolved genomic impact of Wnt/β-catenin signaling	8
Information theory entering soils and tissues	8
High-throughput functional characterization of combinations of transcriptional activators and repressors	8
Degradation of host translational machinery drives tRNA acquisition in viruses	8
Modes and motifs in multicellular communication	8
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	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
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods	8
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	8
Systems genetics of metabolic health in the BXD mouse genetic reference population	8
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	8
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	8
Evaluation of Lee et al.: Clarity and interpretation of mutual information in promoter transfer functions	8
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	8
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	7
Benchmarking transcriptional host response signatures for infection diagnosis	7
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	7
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Privacy-preserving genotype imputation in a trusted execution environment	7
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	7
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	7
How can Waddington-like landscapes facilitate insights beyond developmental biology?	7
On knowing a gene: A distributional hypothesis of gene function	6
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	6
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	6
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	6
Reframing the role of the objective function in its proper context for metabolic network modeling	6
IgLM: Infilling language modeling for antibody sequence design	6
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	6
Modeling non-genetic adaptation in tumor cells	6
Cracking the code of adaptive immunity: The role of computational tools	6
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	6
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	6
What is the key challenge in engineering microbiomes?	6
What does the success of mRNA vaccines tell us about the future of biological therapeutics?	6
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	5
Highly parallel production of designer organoids by mosaic patterning of progenitors	5
DeST-OT: Alignment of spatiotemporal transcriptomics data	5
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	5
Data-driven batch detection enhances single-cell omics data analysis	5
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	5
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	5
Convolutions are competitive with transformers for protein sequence pretraining	5
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	5
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	5
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	5