Cell Systems

Article	Citations
Evaluation of Peterson et al.: MAPK cascades don’t work in silos: MAP3K cross-activation of MAPKs and the effect of crosstalk on cellular responses	343
A digital CRISPR-dCas9-based gene remodeling biocomputer programmed by dietary compounds in mammals	221
Approaching deconvolution with Fermi’s mindset	176
Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads	159
Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics	155
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line	154
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	110
A framework for ultra-low-input spatial tissue proteomics	96
Pitfalls of genotyping microbial communities with rapidly growing genome collections	95
Engineering functional materials through bacteria-assisted living grafting	95
Which image-based phenotypes are most promising for using AI to understand cellular functions and why?	94
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture	93
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning	93
What are the current bottlenecks in developing and applying CRISPR technologies?	83
Evolutionary paths that link orthogonal pairs of binding proteins	83
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	82
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	80
How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	77
Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition	69
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	66
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation	66
Homeostasis	64
The structure of the human cell cycle	62
What differentiates a stress response from responsiveness in general?	62
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	59

Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	58
How can concepts from ecology enable insights about cellular communities?	57
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors	57
A forecast for large-scale, predictive biology: Lessons from meteorology	57
The geometry of cell fate	56
Mapping the multiscale structure of biological systems	56
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks	56
Schrödinger’s What Is Life? at 75	55
Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing	54
Modeling elucidates context dependence in adipose regulation	54
The structure is the message: Preserving experimental context through tensor decomposition	53
Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions	53
The electrostatic landscape of MHC-peptide binding revealed using inception networks	51
Mapping combinatorial expression perturbations to growth in Escherichia coli	51
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors	49
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	47
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing	47
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	44
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	43
Machine learning for perturbational single-cell omics	42
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration	40
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape	39
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities	39
Coupled oscillator cooperativity as a control mechanism in chronobiology	39
Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science	38
Consequential drug combinations for tuberculosis treatments	37
Environmental modulators of algae-bacteria interactions at scale	35
Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data	35
SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues	34
A three-node Turing gene circuit forms periodic spatial patterns in bacteria	34
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	32
A complete allosteric map of a GTPase switch in its native cellular network	32
A top variant identification pipeline for protein engineering	32
The structure of the human cell cycle	31
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	31
Identifying features of genome evolution to exploit cancer vulnerabilities	30
The substrate quality of CK2 target sites has a determinant role on their function and evolution	30
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	30
Transcriptional memory formation: Battles between transcription factors and repressive chromatin	30
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature	29
Evaluation of Williams et al.: On multiomics and mediation	29
Recent progress of gene circuit designs in immune cell therapies	28
A convergent molecular network underlying autism and congenital heart disease	28
Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition	28
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	26
Database-independent de novo metaproteomics of complex microbial communities	26
Multiomic profiling of the liver across diets and age in a diverse mouse population	26
Noise distorts the epigenetic landscape and shapes cell-fate decisions	26
Hotspot identifies informative gene modules across modalities of single-cell genomics	25
Human plasma IgG1 repertoires are simple, unique, and dynamic	25

Self-organization of plasticity and specialization in a primitively social insect	25
Observations and implication of thermal tolerance in the Arabidopsis proteome	25
Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers	25
A multi-scale map of protein assemblies in the DNA damage response	25
Minding the gaps: The importance of navigating holes in protein fitness landscapes	25
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	25
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning	24
The need for speed: Migratory cells in tight spaces boost their molecular clock	24
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	24
Systematic analysis identifies a connection between spatial and genomic variations of chromatin states	24
To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy	24
Accurate top protein variant discovery via low-N pick-and-validate machine learning	23
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells	23
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	22
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain	22
Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs	22
The community-function landscape of microbial consortia	21
Ligand-receptor promiscuity enables cellular addressing	21
Cold and hot fibrosis define clinically distinct cardiac pathologies	20
Tissue Schematics: A framework to decipher tissue architecture and assembly	20
Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data	20
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	19
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference	19
Unveiling the hidden network of STING’s subcellular regulation	19
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	19
Widespread alteration of protein autoinhibition in human cancers	18
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria	18
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	18
Systematic thermal analysis of the Arabidopsis proteome: Thermal tolerance, organization, and evolution	18
Studying stochastic systems biology of the cell with single-cell genomics data	17
Functional attractors in microbial community assembly	17
A time-resolved proteomic and prognostic map of COVID-19	16
Morphology and gene expression profiling provide complementary information for mapping cell state	16
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	16
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities	16
Contrastive learning of T cell receptor representations	16
Single-cell colocalization analysis using a deep generative model	16
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	16
Paving the path toward genomic privacy with secure imputation	15
How well do contextual protein encodings learn structure, function, and evolutionary context?	15
Automated single-cell omics end-to-end framework with data-driven batch inference	15
Somatic XIST activation and features of X chromosome inactivation in male human cancers	15
Active learning of enhancers and silencers in the developing neural retina	15
Entrainment and multi-stability of the p53 oscillator in human cells	15
Privacy-preserving genotype imputation with fully homomorphic encryption	15
What can recent methodological advances help us understand about protein and genome evolution?	14
Artificial intelligence for proteomics and biomarker discovery	13
Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells	13
Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy	13
FlowDesign: Improved design of antibody CDRs through flow matching and better prior distributions	13
Deep-learning-based design of synthetic orthologs of SH3 signaling domains	13
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	13
MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets	13
Enhanced cellular longevity arising from environmental fluctuations	13
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	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
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	13
Emerging questions in transcriptional regulation	12
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals	12
Periodic spatial patterning with a single morphogen	12
Efficient retroelement-mediated DNA writing in bacteria	12
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	12
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	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
Reproducibility metrics for context-specific CRISPR screens	11
Transcriptional activators in the early Drosophila embryo perform different kinetic roles	11
Assembly of stool-derived bacterial communities follows “early-bird” resource utilization dynamics	11
NAD+ flux is maintained in aged mice despite lower tissue concentrations	11
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges	11
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	11
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	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
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	10
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	10
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	10
Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces	10
Parallel engineering and activity profiling of a base editor system	10
A new age in protein design empowered by deep learning	10

Evo-velocity: Protein language modeling accelerates the study of evolution	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	9
Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes	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
Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli	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
Truncated protein isoforms generate diversity of protein localization and function in yeast	8
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells	8
Evaluation of Lee et al.: Clarity and interpretation of mutual information in promoter transfer functions	8
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	8
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter	8
Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity	8
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	8
Integrase enables synthetic intercellular logic via bacterial conjugation	8
Organizing principles of the C. elegans contactome	8
Evaluation of Ravindran et al.: Real-time detection of signaling pulses in vivo: making cells monitor themselves	7
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs	7
DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods	7
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	7
Information theory entering soils and tissues	7
High-throughput functional characterization of combinations of transcriptional activators and repressors	7
Control points for design of taxonomic composition in synthetic human gut communities	7
How can Waddington-like landscapes facilitate insights beyond developmental biology?	7
Degradation of host translational machinery drives tRNA acquisition in viruses	7
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	7
Cracking the code of adaptive immunity: The role of computational tools	6
Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network	6
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment	6
IgLM: Infilling language modeling for antibody sequence design	6
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework	6
On knowing a gene: A distributional hypothesis of gene function	6
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells	6
Modes and motifs in multicellular communication	6
The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time	6
Privacy-preserving genotype imputation in a trusted execution environment	6
What does the success of mRNA vaccines tell us about the future of biological therapeutics?	6
What is the key challenge in engineering microbiomes?	6
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	6
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques	6
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	6
Benchmarking transcriptional host response signatures for infection diagnosis	6
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis	6
Tailoring microbial fitness through computational steering and CRISPRi-driven robustness regulation	6
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening	6
Highly parallel production of designer organoids by mosaic patterning of progenitors	6
Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework	6
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development	6
Systems genetics of metabolic health in the BXD mouse genetic reference population	6
What cannot be seen correctly in 2D visualizations of single-cell ‘omics data?	5
Data-driven batch detection enhances single-cell omics data analysis	5
DeST-OT: Alignment of spatiotemporal transcriptomics data	5
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing	5
Convolutions are competitive with transformers for protein sequence pretraining	5
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	5
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery	5
Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species	5
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	5
Modeling non-genetic adaptation in tumor cells	5
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	5
Tumor architecture and emergence of strong genetic alterations are bottlenecks for clonal evolution in primary prostate cancer	5
Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations	5
Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut	5
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors	5
How do you anticipate computational protein design will change biotechnology and therapeutic development?	5
Multilevel relations among plankton stitched together with an eco-evolutionary needle	5
Fundamentals to function: Quantitative and scalable approaches for measuring protein stability	5