Cell Systems

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
Engineering functional materials through bacteria-assisted living grafting	82
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	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
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	76
What are the current bottlenecks in developing and applying CRISPR technologies?	76
Evolutionary paths that link orthogonal pairs of binding proteins	72
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	71
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	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
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
The metallome and the biological periodic table: A metal atlas in cells	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
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	37
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	37
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
Consequential drug combinations for tuberculosis treatments	35
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	34
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
A top variant identification pipeline for protein engineering	33
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	32
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	31
The structure of the human cell cycle	30
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
Identifying features of genome evolution to exploit cancer vulnerabilities	29
Environmental modulators of algae-bacteria interactions at scale	29
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	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
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	27
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
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	26
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
A multi-scale map of protein assemblies in the DNA damage response	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	24
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	23
Human plasma IgG1 repertoires are simple, unique, and dynamic	23
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	23
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
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
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
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
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
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
Ligand-receptor promiscuity enables cellular addressing	19
The community-function landscape of microbial consortia	19
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
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	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
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
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
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
Entrainment and multi-stability of the p53 oscillator in human cells	15
TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples	15
Somatic XIST activation and features of X chromosome inactivation in male human cancers	15
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	15
Active learning of enhancers and silencers in the developing neural retina	15
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	14
Automated single-cell omics end-to-end framework with data-driven batch inference	14
Enhanced cellular longevity arising from environmental fluctuations	14
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	14
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	14
Privacy-preserving genotype imputation with fully homomorphic encryption	14
Assessing generative model coverage of protein structures with SHAPES	14
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	14
Emerging questions in transcriptional regulation	14
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	14
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	13
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models	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
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	13
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	13
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	13
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
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	12
What limits our ability to study the effects of microbial diversity on health and the environment?	12
Reproducibility metrics for context-specific CRISPR screens	12
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	11
Periodic spatial patterning with a single morphogen	11
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	11
Versatile system cores as a conceptual basis for generality in cell and developmental biology	10
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	10
A new age in protein design empowered by deep learning	10
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	10
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	10
The in silico lab: Improving academic code using lessons from biology	10
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
What do you most hope spatial molecular profiling will help us understand? Part 2	10
Integrase enables synthetic intercellular logic via bacterial conjugation	10
NAD+ flux is maintained in aged mice despite lower tissue concentrations	10
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	10
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	10
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	10
Evo-velocity: Protein language modeling accelerates the study of evolution	10

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
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	9
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	9
Biophysical metabolic modeling of complex bacterial colony morphology	9
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	9
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	9
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	9
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders	9
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	9
The time-resolved genomic impact of Wnt/β-catenin signaling	9
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	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
Control points for design of taxonomic composition in synthetic human gut communities	8
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	8
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
Information theory entering soils and tissues	8
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	8
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	8
Modes and motifs in multicellular communication	8
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	8
High-throughput functional characterization of combinations of transcriptional activators and repressors	8
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	8
The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community	8
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Evaluation of Ravindran et al.: Real-time detection of signaling pulses in vivo: making cells monitor themselves	7
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	7
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	7
Cracking the code of adaptive immunity: The role of computational tools	7
On knowing a gene: A distributional hypothesis of gene function	7
Benchmarking transcriptional host response signatures for infection diagnosis	7
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	7
Chemotherapy modulation by a cancer-associated microbiota metabolite	7
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	7
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	7
Systems genetics of metabolic health in the BXD mouse genetic reference population	7
How can Waddington-like landscapes facilitate insights beyond developmental biology?	7
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	7
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	7
Reframing the role of the objective function in its proper context for metabolic network modeling	7
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
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	6
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	6
Cell-free recombinase-integrated Boolean output system	6
Highly parallel production of designer organoids by mosaic patterning of progenitors	6
IgLM: Infilling language modeling for antibody sequence design	6
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	6
Multilevel relations among plankton stitched together with an eco-evolutionary needle	5
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	5
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	5
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	5
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	5
Convolutions are competitive with transformers for protein sequence pretraining	5
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	5
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	5
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle	5
The context-dependent, combinatorial logic of BMP signaling	5
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	5
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities	5
What is the key challenge in engineering microbiomes?	5
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	5
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	5
What is the current bottleneck in mapping molecular interaction networks?	5
How do you anticipate computational protein design will change biotechnology and therapeutic development?	5
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones	5
Data-driven batch detection enhances single-cell omics data analysis	5
DeST-OT: Alignment of spatiotemporal transcriptomics data	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