Cell Systems

Article	Citations
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	299
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	156
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	132
Pitfalls of genotyping microbial communities with rapidly growing genome collections	118
Approaching deconvolution with Fermi’s mindset	111
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	109
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	104
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	93
Engineering functional materials through bacteria-assisted living grafting	88
Statistical modeling and analysis of cell counts from multiplexed imaging data	87
A framework for ultra-low-input spatial tissue proteomics	84
What are the current bottlenecks in developing and applying CRISPR technologies?	83
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	81
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	79
Evolutionary paths that link orthogonal pairs of binding proteins	76
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	69
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	69
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	68
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	67
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	59
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	54
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	54
What differentiates a stress response from responsiveness in general?	53
The structure of the human cell cycle	53
The geometry of cell fate	52

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	52
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	46
How can concepts from ecology enable insights about cellular communities?	43
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	42
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	42
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	41
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	41
The electrostatic landscape of MHC-peptide binding revealed using inception networks	40
Modeling elucidates context dependence in adipose regulation	39
The metallome and the biological periodic table: A metal atlas in cells	39
The structure is the message: Preserving experimental context through tensor decomposition	37
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	37
Mapping combinatorial expression perturbations to growth in Escherichia coli	37
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	36
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	36
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	36
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	36
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	36
A top variant identification pipeline for protein engineering	35
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	33
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	32
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	32
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	31
Coupled oscillator cooperativity as a control mechanism in chronobiology	31
Environmental modulators of algae-bacteria interactions at scale	30
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	30
The structure of the human cell cycle	30
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	30
DynamicGT: A dynamic-aware geometric transformer model to predict protein-binding interfaces in flexible and disordered regions	30
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	29
Evaluation of Williams et al.: On multiomics and mediation	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
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	28
The substrate quality of CK2 target sites has a determinant role on their function and evolution	27
Recent progress of gene circuit designs in immune cell therapies	26
Ectopic expression to synthetic design: Deriving engineering principles of lncRNA-mediated epigenetic regulation	26
Noise distorts the epigenetic landscape and shapes cell-fate decisions	26
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	26
A multi-scale map of protein assemblies in the DNA damage response	25
Multiomic profiling of the liver across diets and age in a diverse mouse population	25
Self-organization of plasticity and specialization in a primitively social insect	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	24
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	24
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	23
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	23
Learning antibody sequence constraints from allelic inclusion	23
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

Harnessing heterogeneity for the rational design of cell manufacturing	23
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
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
The need for speed: Migratory cells in tight spaces boost their molecular clock	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	20
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	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
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	19
Widespread alteration of protein autoinhibition in human cancers	19
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	19
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
Tissue Schematics: A framework to decipher tissue architecture and assembly	18
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	18
Single-cell colocalization analysis using a deep generative model	18
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	18
Studying stochastic systems biology of the cell with single-cell genomics data	18
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	18
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	17
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	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
How well do contextual protein encodings learn structure, function, and evolutionary context?	16
Functional attractors in microbial community assembly	16
Entrainment and multi-stability of the p53 oscillator in human cells	16
Automated single-cell omics end-to-end framework with data-driven batch inference	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	16
Somatic XIST activation and features of X chromosome inactivation in male human cancers	16
Active learning of enhancers and silencers in the developing neural retina	16
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	16
What can recent methodological advances help us understand about protein and genome evolution?	16
Emerging questions in transcriptional regulation	15
Privacy-preserving genotype imputation with fully homomorphic encryption	15
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models	15
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	15
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	15
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	15
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	15
TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples	15
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	14
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	14
A molecular clock controls periodically driven cell migration in confined spaces	14
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	14
Enhanced cellular longevity arising from environmental fluctuations	14
Assessing generative model coverage of protein structures with SHAPES	14
BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences	13
What limits our ability to study the effects of microbial diversity on health and the environment?	13
High-throughput mapping of modular regulatory domains in human RNA-binding proteins	13
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	13
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	13
Reproducibility metrics for context-specific CRISPR screens	12
Periodic spatial patterning with a single morphogen	12
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	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
The in silico lab: Improving academic code using lessons from biology	11
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	11
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	11
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	11
Versatile system cores as a conceptual basis for generality in cell and developmental biology	11
Parallel engineering and activity profiling of a base editor system	11
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	11
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	11
A new age in protein design empowered by deep learning	10
Integrase enables synthetic intercellular logic via bacterial conjugation	10
The time-resolved genomic impact of Wnt/β-catenin signaling	10
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	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
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	10
What do you most hope we will achieve with mammalian synthetic biology within the next decade?	10
Evo-velocity: Protein language modeling accelerates the study of evolution	10
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	10
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	10

Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	10
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	10
Information theory entering soils and tissues	9
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	9
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	9
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	9
Control points for design of taxonomic composition in synthetic human gut communities	9
The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community	9
Biophysical metabolic modeling of complex bacterial colony morphology	9
What do you most hope spatial molecular profiling will help us understand? Part 2	9
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	9
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	9
High-throughput functional characterization of combinations of transcriptional activators and repressors	9
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	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
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	9
Lighting up hidden microbial enzyme diversity and functional opportunities from fermented foods	9
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
How can Waddington-like landscapes facilitate insights beyond developmental biology?	8
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	8
Modes and motifs in multicellular communication	8
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods	8
Benchmarking transcriptional host response signatures for infection diagnosis	8
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	8
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	8
Evaluation of Ravindran et al.: Real-time detection of signaling pulses in vivo: making cells monitor themselves	8
Systems genetics of metabolic health in the BXD mouse genetic reference population	8
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	8
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	7
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	7
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	7
Cell-free recombinase-integrated Boolean output system	7
Reframing the role of the objective function in its proper context for metabolic network modeling	7
Chemotherapy modulation by a cancer-associated microbiota metabolite	7
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	7
IgLM: Infilling language modeling for antibody sequence design	7
Data-driven batch detection enhances single-cell omics data analysis	7
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	7
Cracking the code of adaptive immunity: The role of computational tools	7
On knowing a gene: A distributional hypothesis of gene function	7
Modeling non-genetic adaptation in tumor cells	7
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	7
DeST-OT: Alignment of spatiotemporal transcriptomics data	6
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	6
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	6
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	6
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	6
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	6
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	6
What is the key challenge in engineering microbiomes?	6
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities	6
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	6
Highly parallel production of designer organoids by mosaic patterning of progenitors	6
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	6
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	6
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	5
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle	5
Protein surface chemistry encodes an adaptive tolerance to desiccation	5
Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems	5
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	5
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	5
Multilevel relations among plankton stitched together with an eco-evolutionary needle	5
How do you anticipate computational protein design will change biotechnology and therapeutic development?	5
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	5
Molecular armor: Simple rules to keep proteins (re)soluble	5
An adversarial scheme for integrating multi-modal data on protein function	5
Convolutions are competitive with transformers for protein sequence pretraining	5
What is the current bottleneck in mapping molecular interaction networks?	5
The context-dependent, combinatorial logic of BMP signaling	5
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones	5
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	5
Vascular scaling: A careful balancing act between proliferation and extrusion	5