Cell Systems

Article	Citations
Large-Scale Multi-omic Analysis of COVID-19 Severity	420
Learning the protein language: Evolution, structure, and function	252
Artificial intelligence for proteomics and biomarker discovery	149
A time-resolved proteomic and prognostic map of COVID-19	136
A platform for experimental precision medicine: The extended BXD mouse family	123
Informed training set design enables efficient machine learning-assisted directed protein evolution	120
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	117
ProGen2: Exploring the boundaries of protein language models	115
Biophysics of Temporal Interference Stimulation	99
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	99
Hotspot identifies informative gene modules across modalities of single-cell genomics	99
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	93
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	83
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	80
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	79
Perfect adaptation in biology	76
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	74
Functional attractors in microbial community assembly	72
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	71
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	71
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	70
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	68
Machine learning for perturbational single-cell omics	67
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	67
NAD+ flux is maintained in aged mice despite lower tissue concentrations	65

Consciousness depends on integration between parietal cortex, striatum, and thalamus	65
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	61
The sound of silence: Transgene silencing in mammalian cell engineering	58
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	58
Morphology and gene expression profiling provide complementary information for mapping cell state	57
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering	57
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling	55
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	55
Noise distorts the epigenetic landscape and shapes cell-fate decisions	53
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	50
The context-dependent, combinatorial logic of BMP signaling	48
Biological feedback control—Respect the loops	46
Database-independent de novo metaproteomics of complex microbial communities	45
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	45
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies	44
Ligand-receptor promiscuity enables cellular addressing	44
Human plasma IgG1 repertoires are simple, unique, and dynamic	44
Context-aware synthetic biology by controller design: Engineering the mammalian cell	43
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus	43
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors	42
Degradation of host translational machinery drives tRNA acquisition in viruses	42
Ultrasensitive molecular controllers for quasi-integral feedback	41
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	41
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees	40
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity	39
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals	39
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes	39
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning	38
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines	37
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation	36
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	36
The community-function landscape of microbial consortia	35
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets	35
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis	35
IgLM: Infilling language modeling for antibody sequence design	34
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity	34
A tale of two rhythms: Locked clocks and chaos in biology	33
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles	33
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures	33
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	32
Diploid hepatocytes drive physiological liver renewal in adult humans	32
A new age in protein design empowered by deep learning	32
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	30
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	29
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges	29
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	29
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	29
Multiomic profiling of the liver across diets and age in a diverse mouse population	28
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles	27
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression	27

A vast evolutionarily transient translatome contributes to phenotype and fitness	27
Mapping the multiscale structure of biological systems	27
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease	26
A convergent molecular network underlying autism and congenital heart disease	26
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer	26
A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease	26
Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity	26
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations	25
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants	25
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods	25
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	23
Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits	23
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	23
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations	23
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria	23
The structure of the human cell cycle	23
Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales	22
Sparse dictionary learning recovers pleiotropy from human cell fitness screens	22
Virtual screening for small-molecule pathway regulators by image-profile matching	22
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner	21
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain	21
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals	21
Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer	21
Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention	21
Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems	21
Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain	20
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	20
Engineering molecular translation systems	20
Privacy-preserving genotype imputation with fully homomorphic encryption	20
Path to improving the life cycle and quality of genome-scale models of metabolism	19
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro	18
Fundamentals to function: Quantitative and scalable approaches for measuring protein stability	18
Efficient retroelement-mediated DNA writing in bacteria	18
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	18
The computational capabilities of many-to-many protein interaction networks	18
DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution	17
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi	17
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback	17
Privacy-preserving genotype imputation in a trusted execution environment	17
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery	17
How can Waddington-like landscapes facilitate insights beyond developmental biology?	16
Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3	16
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	16
GCN2 adapts protein synthesis to scavenging-dependent growth	16
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces	16
Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity	15
Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion	15
Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations	14
In vitro continuous protein evolution empowered by machine learning and automation	14
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	14
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	14
Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition	13
Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis	13
Studying stochastic systems biology of the cell with single-cell genomics data	13
Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks	13
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	13
Machine Learning of Hematopoietic Stem Cell Divisions from Paired Daughter Cell Expression Profiles Reveals Effects of Aging on Self-Renewal	13
Somatic XIST activation and features of X chromosome inactivation in male human cancers	13
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	13
Mapping the dynamic transfer functions of eukaryotic gene regulation	13
A multi-scale map of protein assemblies in the DNA damage response	13
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	13
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	13
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	13
Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule	13
What does the success of mRNA vaccines tell us about the future of biological therapeutics?	12
Core liver homeostatic co-expression networks are preserved but respond to perturbations in an organism- and disease-specific manner	12
The trans-regulatory landscape of gene networks in plants	12
BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences	12
Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors	12
Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers	12
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	12
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	12
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	11
The geometry of cell fate	11
Pitfalls of genotyping microbial communities with rapidly growing genome collections	11
Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references	11
Revamping Space-omics in Europe	11
Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition	11
The time-resolved genomic impact of Wnt/β-catenin signaling	11

Recent progress of gene circuit designs in immune cell therapies	10
Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics	10
A proteogenomics data-driven knowledge base of human cancer	10
BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment	10
Systematically quantifying morphological features reveals constraints on organoid phenotypes	10
Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology	10
Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle	10
Analysis of scientific society honors reveals disparities	10
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia	10
A molecular clock controls periodically driven cell migration in confined spaces	10
High-throughput functional characterization of combinations of transcriptional activators and repressors	10
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation	10
Periodic spatial patterning with a single morphogen	10
EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance	9
A framework for ultra-low-input spatial tissue proteomics	9
Bridging scales: From cell biology to physiology using in situ single-cell technologies	9
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing	9
Convolutions are competitive with transformers for protein sequence pretraining	9
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden	9
Learning protein fitness landscapes with deep mutational scanning data from multiple sources	9
A synthetic gene circuit for imaging-free detection of signaling pulses	9
The structure of the human cell cycle	8
Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection	8
Leading edge competition promotes context-dependent responses to receptor inputs to resolve directional dilemmas in neutrophil migration	8
TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression	8
Quantifying stimulus-response specificity to probe the functional state of macrophages	8
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer	8
A complete allosteric map of a GTPase switch in its native cellular network	7
Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient	7
SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays	7
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens	7
Resistor: An algorithm for predicting resistance mutations via Pareto optimization over multistate protein design and mutational signatures	6
Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions	6
H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos	6
Metabolic models of human gut microbiota: Advances and challenges	6
PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction	6
Clonally heritable gene expression imparts a layer of diversity within cell types	6
RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer	6
Protein engineering via sequence-performance mapping	6
A global genetic interaction network by single-cell imaging and machine learning	6
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth	6
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing	6
Comparing the Efficacy of Cancer Therapies between Subgroups in Basket Trials	6
Benchmarking transcriptional host response signatures for infection diagnosis	5
Schrödinger’s What Is Life? at 75	5
Genes enriched in A/T-ending codons are co-regulated and conserved across mammals	5
Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments	5
Reproducibility metrics for context-specific CRISPR screens	5
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition	5
The architecture of binding cooperativity between densely bound transcription factors	5
Engineering allosteric transcription factors guided by the LacI topology	5
High-throughput discovery and characterization of viral transcriptional effectors in human cells	5
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling	5
Simplifying complex antibody engineering using machine learning	5
Extrapolating missing antibody-virus measurements across serological studies	5
What do you most want to understand about how collective features emerge in microbial communities?	5
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation	5
Alignment of single-cell trajectories by tuMap enables high-resolution quantitative comparison of cancer samples	5