Cell Systems

Article	Citations
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	370
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	184
Pitfalls of genotyping microbial communities with rapidly growing genome collections	117
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	108
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	107
A framework for ultra-low-input spatial tissue proteomics	103
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	102
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	92
Approaching deconvolution with Fermi’s mindset	87
Statistical modeling and analysis of cell counts from multiplexed imaging data	81
A combinatorial transcription factor screening platform for immune cell reprogramming	77
Engineering functional materials through bacteria-assisted living grafting	75
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	74
Evolutionary paths that link orthogonal pairs of binding proteins	69
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	61
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	58
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	57
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	56
Context-informed subgraph foundation models enable interpretable protein-function prediction	52
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	50
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	49
Identifying maximally informative signal-aware representations of single-cell data using the information bottleneck	49
From modality-specific to compositional foundation models for cell biology	45
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	44
What are the current bottlenecks in developing and applying CRISPR technologies?	43

Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling	43
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	43
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	42
How can concepts from ecology enable insights about cellular communities?	42
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	42
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	41
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	40
Translation elongation as a rate-limiting step of protein production	38
The electrostatic landscape of MHC-peptide binding revealed using inception networks	37
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	37
The metallome and the biological periodic table: A metal atlas in cells	35
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	34
The structure is the message: Preserving experimental context through tensor decomposition	33
Modeling elucidates context dependence in adipose regulation	33
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	33
NOT-gated chimeric antigen receptor circuits in T and NK cells	32
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	30
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	30
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	30
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	29
DynamicGT: A dynamic-aware geometric transformer model to predict protein-binding interfaces in flexible and disordered regions	29
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	29
A top variant identification pipeline for protein engineering	28
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	28
A complete allosteric map of a GTPase switch in its native cellular network	28
Coupled oscillator cooperativity as a control mechanism in chronobiology	28
Identifying microbial protease allergens through protein language model-guided homology	28
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	27
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	27
Environmental modulators of algae-bacteria interactions at scale	26
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	26
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	26
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	26
The substrate quality of CK2 target sites has a determinant role on their function and evolution	25
Ectopic expression to synthetic design: Deriving engineering principles of lncRNA-mediated epigenetic regulation	24
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	23
Recent progress of gene circuit designs in immune cell therapies	23
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	23
A multi-scale map of protein assemblies in the DNA damage response	23
Observations and implication of thermal tolerance in the Arabidopsis proteome	23
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	23
Learning antibody sequence constraints from allelic inclusion	22
Self-organization of plasticity and specialization in a primitively social insect	22
Harnessing heterogeneity for the rational design of cell manufacturing	22
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	22
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	21
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	21
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	21
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	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
Recurrent neural chemical reaction networks that approximate arbitrary dynamics	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
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning	20
Ligand-receptor promiscuity enables cellular addressing	20
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	20
Cold and hot fibrosis define clinically distinct cardiac pathologies	20
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	20
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	19
The community-function landscape of microbial consortia	19
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	19
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	19
Resource competition shapes CRISPR-mediated gene activation	19
Disobind: A sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions	18
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	18
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	18
Unveiling the hidden network of STING’s subcellular regulation	18
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	18
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states	17
Modeling chimeric antigen receptor response at the single-cell level with conditional optimal transport	17
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	17
Studying stochastic systems biology of the cell with single-cell genomics data	17
Dango: Predicting higher-order genetic interactions	17
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	17
Single-cell colocalization analysis using a deep generative model	17
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	17
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Widespread alteration of protein autoinhibition in human cancers	16
What can recent methodological advances help us understand about protein and genome evolution?	16
Contrastive learning of T cell receptor representations	16
Entrainment and multi-stability of the p53 oscillator in human cells	15
Somatic XIST activation and features of X chromosome inactivation in male human cancers	15
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	15
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	15
Automated single-cell omics end-to-end framework with data-driven batch inference	15
Active learning of enhancers and silencers in the developing neural retina	15
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	15
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	15
How well do contextual protein encodings learn structure, function, and evolutionary context?	15
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	15
The impact of package selection and versioning on single-cell RNA-seq analysis	15
TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples	15
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	14
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	14
Enhanced cellular longevity arising from environmental fluctuations	14
A molecular clock controls periodically driven cell migration in confined spaces	14
Refactoring two-component systems for tunable gene expression regulation and upgraded bacterial sensing	14
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	14
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models	14
Emerging questions in transcriptional regulation	14
A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells	13
What limits our ability to study the effects of microbial diversity on health and the environment?	13
BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences	13
Assessing generative model coverage of protein structures with SHAPES	13
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	13
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	13
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	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 metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering	12
High-throughput mapping of modular regulatory domains in human RNA-binding proteins	12
Risk-averse optimization of genetic circuits under uncertainty	12
We wait for disease to shout—What if we listened when biology whispered?	12
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	12
Periodic spatial patterning with a single morphogen	12
Interpretable data integration for single-cell and spatial multi-omics	12
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	12
The in silico lab: Improving academic code using lessons from biology	12
Reproducibility metrics for context-specific CRISPR screens	12
Systemic rhythmicity of host and bacterial bile acid amidates in the mouse	12
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	11
Parallel engineering and activity profiling of a base editor system	11
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	11
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces	11
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	11
A new age in protein design empowered by deep learning	11
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	11
Versatile system cores as a conceptual basis for generality in cell and developmental biology	11

Integrase enables synthetic intercellular logic via bacterial conjugation	10
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	10
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	10
Biophysical metabolic modeling of complex bacterial colony morphology	10
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	10
What do you most hope spatial molecular profiling will help us understand? Part 2	10
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	10
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	10
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	10
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	10
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	10
What questions currently beyond reach do you hope systems approaches will enable addressing in the next decade?	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 we will achieve with mammalian synthetic biology within the next decade?	10
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	9
Information theory entering soils and tissues	9
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	9
Truncated protein isoforms generate diversity of protein localization and function in yeast	9
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	9
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	9
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	9
The time-resolved genomic impact of Wnt/β-catenin signaling	9
Lighting up hidden microbial enzyme diversity and functional opportunities from fermented foods	8
The hierarchical timescale hypothesis: Functional and structural convergence of biological networks and artificial neural nets	8
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	8
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
Control points for design of taxonomic composition in synthetic human gut communities	8
High-throughput functional characterization of combinations of transcriptional activators and repressors	8
The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community	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	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
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
Modes and motifs in multicellular communication	7
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	7
Reframing the role of the objective function in its proper context for metabolic network modeling	7
On knowing a gene: A distributional hypothesis of gene function	7
TarDis: Achieving robust and structured disentanglement of multiple covariates	7
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes	7
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	7
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	7
Cracking the code of adaptive immunity: The role of computational tools	7
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	7
Cell-free recombinase-integrated Boolean output system	6
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	6
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	6
IgLM: Infilling language modeling for antibody sequence design	6
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	6
Fusing imaging and metabolic modeling via multimodal deep learning in ovarian cancer	6
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	6
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	6
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	6
Data-driven batch detection enhances single-cell omics data analysis	6
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	6
Modeling non-genetic adaptation in tumor cells	6
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	6
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities	6
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	6
Phased fragility and stability of non-genetic B cell states in the germinal center accelerate the genetic evolution of antibodies	6
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	6
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	6
What is the current bottleneck in mapping molecular interaction networks?	5
What problem do you hope bioengineering or synthetic biology approaches will enable us to tackle in the next decade?	5
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	5
An adversarial scheme for integrating multi-modal data on protein function	5
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	5
Protein surface chemistry encodes an adaptive tolerance to desiccation	5
Dynamics of genetic circuits in Pseudomonas protegens	5
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle	5
Convolutions are competitive with transformers for protein sequence pretraining	5
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	5
Highly parallel production of designer organoids by mosaic patterning of progenitors	5
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	5
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	5
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones	5
Multilevel relations among plankton stitched together with an eco-evolutionary needle	5
What is the key challenge in engineering microbiomes?	5
DeST-OT: Alignment of spatiotemporal transcriptomics data	5
Molecular armor: Simple rules to keep proteins (re)soluble	5
Antithetic integral feedback control redesigned for improved dynamics and lower noise	5
How do you anticipate computational protein design will change biotechnology and therapeutic development?	5
Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems	5