Cell Systems

Article	Citations
Leveraging attention-based deep multiple instance and multiple task learning for improved neoepitope identification	384
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	194
Statistical modeling and analysis of cell counts from multiplexed imaging data	119
Engineering functional materials through bacteria-assisted living grafting	113
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	110
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	107
A combinatorial transcription factor screening platform for immune cell reprogramming	104
Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites	92
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	86
A framework for ultra-low-input spatial tissue proteomics	81
Pitfalls of genotyping microbial communities with rapidly growing genome collections	70
Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE	62
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	60
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	58
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	58
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	56
Context-informed subgraph foundation models enable interpretable protein-function prediction	54
Identifying maximally informative signal-aware representations of single-cell data using the information bottleneck	52
Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling	50
What are the current bottlenecks in developing and applying CRISPR technologies?	47
Diclofenac and acetaminophen dim the acute-phase response but amplify expression of the iron regulator hepcidin in liver cancer cells	46
Evolutionary paths that link orthogonal pairs of binding proteins	45
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	44
From modality-specific to compositional foundation models for cell biology	44
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	44

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	43
How can concepts from ecology enable insights about cellular communities?	42
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	42
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	41
Mapping combinatorial expression perturbations to growth in Escherichia coli	41
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	38
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	36
The electrostatic landscape of MHC-peptide binding revealed using inception networks	36
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	35
Modeling elucidates context dependence in adipose regulation	35
The structure is the message: Preserving experimental context through tensor decomposition	34
Translation elongation as a rate-limiting step of protein production	33
NOT-gated chimeric antigen receptor circuits in T and NK cells	32
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	30
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	30
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	30
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	29
Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells	29
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	29
Identifying microbial protease allergens through protein language model-guided homology	29
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	29
A top variant identification pipeline for protein engineering	29
Environmental modulators of algae-bacteria interactions at scale	28
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	28
A complete allosteric map of a GTPase switch in its native cellular network	28
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	28
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	27
Coupled oscillator cooperativity as a control mechanism in chronobiology	27
DynamicGT: A dynamic-aware geometric transformer model to predict protein-binding interfaces in flexible and disordered regions	26
Ectopic expression to synthetic design: Deriving engineering principles of lncRNA-mediated epigenetic regulation	25
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	25
Transcriptional competition biases the effects of second messengers in Escherichia coli	24
A multi-scale map of protein assemblies in the DNA damage response	24
The substrate quality of CK2 target sites has a determinant role on their function and evolution	24
Systematic screening for functional exon-skipping isoforms using the CRISPR-RfxCas13d system	24
Recent progress of gene circuit designs in immune cell therapies	24
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	24
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	23
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	23
Recurrent neural chemical reaction networks that approximate arbitrary dynamics	23
Self-organization of plasticity and specialization in a primitively social insect	23
Observations and implication of thermal tolerance in the Arabidopsis proteome	23
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	22
Tumor-adipose assembloids reveal cell-fate-transition-triggered multistage collective invasions	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
Harnessing heterogeneity for the rational design of cell manufacturing	22
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	22
The need for speed: Migratory cells in tight spaces boost their molecular clock	21

Cold and hot fibrosis define clinically distinct cardiac pathologies	21
Learning antibody sequence constraints from allelic inclusion	21
All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics	21
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation	21
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	20
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	20
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	20
Accurate top protein variant discovery via low-N pick-and-validate machine learning	20
The community-function landscape of microbial consortia	20
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	20
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning	20
Resource competition shapes CRISPR-mediated gene activation	20
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	19
Modeling chimeric antigen receptor response at the single-cell level with conditional optimal transport	19
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	19
Studying stochastic systems biology of the cell with single-cell genomics data	19
Unveiling the hidden network of STING’s subcellular regulation	19
Deep visual proteomics reveals an in vivo-like phenotype of orthotopically transplanted human colon organoids	18
Single-cell colocalization analysis using a deep generative model	18
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	18
Widespread alteration of protein autoinhibition in human cancers	18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	18
Contrastive learning of T cell receptor representations	18
Dango: Predicting higher-order genetic interactions	17
The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering	17
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	17
Disobind: A sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions	17
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states	17
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	17
Morphology and gene expression profiling provide complementary information for mapping cell state	17
Systematic genome-wide mapping of host determinants of bacteriophage infectivity	17
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	17
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth	16
How well do contextual protein encodings learn structure, function, and evolutionary context?	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
TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples	16
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models	15
The impact of package selection and versioning on single-cell RNA-seq analysis	15
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	15
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	15
Emerging questions in transcriptional regulation	15
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity	15
Enhanced cellular longevity arising from environmental fluctuations	15
A molecular clock controls periodically driven cell migration in confined spaces	15
Assessing generative model coverage of protein structures with SHAPES	15
Active learning of enhancers and silencers in the developing neural retina	15
What can recent methodological advances help us understand about protein and genome evolution?	15
Somatic XIST activation and features of X chromosome inactivation in male human cancers	15
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	15
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	14
A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells	14
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	14
The tree labeling polytope: A unified approach to ancestral reconstruction problems	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
Systemic rhythmicity of host and bacterial bile acid amidates in the mouse	13
Refactoring two-component systems for tunable gene expression regulation and upgraded bacterial sensing	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
Interpretable data integration for single-cell and spatial multi-omics	12
We wait for disease to shout—What if we listened when biology whispered?	12
Periodic spatial patterning with a single morphogen	12
Multiplex genome engineering: Methodologies and applications	12
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
Risk-averse optimization of genetic circuits under uncertainty	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
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
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	11
Versatile system cores as a conceptual basis for generality in cell and developmental biology	11
The in silico lab: Improving academic code using lessons from biology	11
Parallel engineering and activity profiling of a base editor system	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
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	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
What do you most hope spatial molecular profiling will help us understand? Part 2	10
What questions currently beyond reach do you hope systems approaches will enable addressing in the next decade?	10
Integrase enables synthetic intercellular logic via bacterial conjugation	10
A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide	10
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	10
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	10
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	10
A systems view of cellular heterogeneity: Unlocking the “wheel of fate”	10
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	9
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	9
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	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
Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models	9
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders	9
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	9
What do you most hope we will achieve with mammalian synthetic biology within the next decade?	9
Biophysical metabolic modeling of complex bacterial colony morphology	9
Lighting up hidden microbial enzyme diversity and functional opportunities from fermented foods	8
Information theory entering soils and tissues	8
Control points for design of taxonomic composition in synthetic human gut communities	8
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	8
Truncated protein isoforms generate diversity of protein localization and function in yeast	8
The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community	8
The hierarchical timescale hypothesis: Functional and structural convergence of biological networks and artificial neural nets	8
Image2Reg: Linking chromatin images to gene regulation using genetic and chemical perturbation screens	8
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	8
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	7
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	7
Modes and motifs in multicellular communication	7
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	7
Chemotherapy modulation by a cancer-associated microbiota metabolite	7
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	7
Reframing the role of the objective function in its proper context for metabolic network modeling	7
Systems genetics of metabolic health in the BXD mouse genetic reference population	7
Benchmarking transcriptional host response signatures for infection diagnosis	7
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	7
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	7
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	7
Cracking the code of adaptive immunity: The role of computational tools	7
IgLM: Infilling language modeling for antibody sequence design	7
Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes	7
High-throughput functional characterization of combinations of transcriptional activators and repressors	7
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods	7
Phased fragility and stability of non-genetic B cell states in the germinal center accelerate the genetic evolution of antibodies	7
On knowing a gene: A distributional hypothesis of gene function	7
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	7
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	7
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database	6
DeST-OT: Alignment of spatiotemporal transcriptomics data	6
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	6
Cell-free recombinase-integrated Boolean output system	6
Fusing imaging and metabolic modeling via multimodal deep learning in ovarian cancer	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
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
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	6
Data-driven batch detection enhances single-cell omics data analysis	6
Modeling non-genetic adaptation in tumor cells	6
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	6
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	6
What is the key challenge in engineering microbiomes?	6
TarDis: Achieving robust and structured disentanglement of multiple covariates	6
What problem do you hope bioengineering or synthetic biology approaches will enable us to tackle in the next decade?	6
Multilevel relations among plankton stitched together with an eco-evolutionary needle	5
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities	5
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	5
How do you anticipate computational protein design will change biotechnology and therapeutic development?	5
Protein surface chemistry encodes an adaptive tolerance to desiccation	5
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones	5
Vascular scaling: A careful balancing act between proliferation and extrusion	5
Antithetic integral feedback control redesigned for improved dynamics and lower noise	5
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle	5
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	5
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	5
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	5
Molecular armor: Simple rules to keep proteins (re)soluble	5
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	5
An adversarial scheme for integrating multi-modal data on protein function	5
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	5
What is the current bottleneck in mapping molecular interaction networks?	5
Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems	5
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	5
Convolutions are competitive with transformers for protein sequence pretraining	5
Rationally reprogramming single-cell aging trajectories and lifespan through dynamic modulation of environmental inputs	5
Rewriting endogenous human transcripts with dual CRISPR-guided 3′ trans-splicing	5
Dynamics of genetic circuits in Pseudomonas protegens	5
Fast, long-range intercellular signal propagation through growth-assisted positive feedback	5