Cell Systems

Article	Citations
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection	423
Large-Scale Multi-omic Analysis of COVID-19 Severity	391
Learning the protein language: Evolution, structure, and function	178
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	163
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer	152
MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities	127
A time-resolved proteomic and prognostic map of COVID-19	119
Fast and Flexible Protein Design Using Deep Graph Neural Networks	116
A platform for experimental precision medicine: The extended BXD mouse family	110
Gut-Liver Physiomimetics Reveal Paradoxical Modulation of IBD-Related Inflammation by Short-Chain Fatty Acids	108
Artificial intelligence for proteomics and biomarker discovery	101
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning	100
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data	96
Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe	95
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus	94
Informed training set design enables efficient machine learning-assisted directed protein evolution	93
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design	91
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks	89
Biophysics of Temporal Interference Stimulation	75
Hotspot identifies informative gene modules across modalities of single-cell genomics	72
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis	72
Encoding Membrane-Potential-Based Memory within a Microbial Community	70
A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences	69
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells	67
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions	63

D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions	63
Perfect adaptation in biology	62
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis	62
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy	61
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome	59
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program	56
Functional attractors in microbial community assembly	56
A Live-Cell Screen for Altered Erk Dynamics Reveals Principles of Proliferative Control	56
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks	56
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	56
Codon Usage and Splicing Jointly Influence mRNA Localization	56
SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses	55
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains	55
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins	54
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism	53
The Genetic Makeup of the Electrocardiogram	52
NAD+ flux is maintained in aged mice despite lower tissue concentrations	52
Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer	51
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies	51
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv	50
Machine learning for perturbational single-cell omics	50
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer	50
Consciousness depends on integration between parietal cortex, striatum, and thalamus	48
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering	48
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing	48
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions	47
SCHEEPDOG: Programming Electric Cues to Dynamically Herd Large-Scale Cell Migration	45
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition	45
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma	44
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain	43
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling	42
Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast	41
ProGen2: Exploring the boundaries of protein language models	40
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus	39
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies	38
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors	38
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors	37
Noise distorts the epigenetic landscape and shapes cell-fate decisions	37
Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish	37
The context-dependent, combinatorial logic of BMP signaling	36
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution	36
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees	35
Biological feedback control—Respect the loops	35
Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics	35
Mitochondrial Fission and Fusion Dynamics Generate Efficient, Robust, and Evenly Distributed Network Topologies in Budding Yeast Cells	35
Database-independent de novo metaproteomics of complex microbial communities	35
Context-aware synthetic biology by controller design: Engineering the mammalian cell	35
CELLector: Genomics-Guided Selection of Cancer In Vitro Models	34
Ultrasensitive molecular controllers for quasi-integral feedback	34
Human plasma IgG1 repertoires are simple, unique, and dynamic	34

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing	34
Ligand-receptor promiscuity enables cellular addressing	33
Morphology and gene expression profiling provide complementary information for mapping cell state	33
Degradation of host translational machinery drives tRNA acquisition in viruses	32
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets	32
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning	31
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals	31
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity	31
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines	30
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis	30
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures	30
Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging	30
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data	29
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays	29
Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity	29
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes	29
A tale of two rhythms: Locked clocks and chaos in biology	28
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity	27
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks	26
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation	26
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles	26
Best Practices for Making Reproducible Biochemical Models	25
Quantifying the Central Dogma in the p53 Pathway in Live Single Cells	25
Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons	25
Multiomic profiling of the liver across diets and age in a diverse mouse population	24
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease	24
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma	23
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles	23
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants	23
The sound of silence: Transgene silencing in mammalian cell engineering	22
Deciphering the signaling network of breast cancer improves drug sensitivity prediction	22
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells	22
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations	22
Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens	22
A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease	22
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods	22
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer	21
The community-function landscape of microbial consortia	21
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges	21
Profiling the Non-genetic Origins of Cancer Drug Resistance with a Single-Cell Functional Genomics Approach Using Predictive Cell Dynamics	21
Diploid hepatocytes drive physiological liver renewal in adult humans	21
Prediction of Signed Protein Kinase Regulatory Circuits	21
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation	20
A convergent molecular network underlying autism and congenital heart disease	20
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression	20
Loss of TET2 Affects Proliferation and Drug Sensitivity through Altered Dynamics of Cell-State Transitions	20
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals	19
Cell Mechanics at the Rear Act to Steer the Direction of Cell Migration	19
Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity	19
The structure of the human cell cycle	19
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics	19
Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits	19
Mapping the multiscale structure of biological systems	19
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain	18
Lattice Light-Sheet Microscopy Multi-dimensional Analyses (LaMDA) of T-Cell Receptor Dynamics Predict T-Cell Signaling States	18
Sparse dictionary learning recovers pleiotropy from human cell fitness screens	18
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner	18
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset	18
Collective Dynamics of Focal Adhesions Regulate Direction of Cell Motion	17
Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer	17
Virtual screening for small-molecule pathway regulators by image-profile matching	17
Engineering molecular translation systems	16
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions	16
Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales	16
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity	16
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes	16
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro	16
Path to improving the life cycle and quality of genome-scale models of metabolism	16
MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning	16
Efficient retroelement-mediated DNA writing in bacteria	15
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria	15
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery	15
The Scaffold Protein Axin Promotes Signaling Specificity within the Wnt Pathway by Suppressing Competing Kinase Reactions	15
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease	15
Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems	15
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations	15
Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain	14
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA	14
Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention	14
A vast evolutionarily transient translatome contributes to phenotype and fitness	14

Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages	14
μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells	14
Assessment of Genetic Drift in Large Pharmacogenomic Studies	14
Fundamentals to function: Quantitative and scalable approaches for measuring protein stability	13
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain	13
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution	13
Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling	13
GCN2 adapts protein synthesis to scavenging-dependent growth	12
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi	12
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback	12
Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition	12
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer	12
Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs	12
Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data	12
Privacy-preserving genotype imputation in a trusted execution environment	11
Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation	11
Machine Learning of Hematopoietic Stem Cell Divisions from Paired Daughter Cell Expression Profiles Reveals Effects of Aging on Self-Renewal	11
Privacy-preserving genotype imputation with fully homomorphic encryption	11
Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule	11
Core liver homeostatic co-expression networks are preserved but respond to perturbations in an organism- and disease-specific manner	11
The computational capabilities of many-to-many protein interaction networks	11
How Can Microfluidic and Microfabrication Approaches Make Experiments More Physiologically Relevant?	11
Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis	10
Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity	10
Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion	10
Analysis of scientific society honors reveals disparities	10
DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution	10
uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes	10
Revamping Space-omics in Europe	10
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting	9
Mapping the dynamic transfer functions of eukaryotic gene regulation	9
Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references	9
Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors	9
Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model	9
Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers	9
What does the success of mRNA vaccines tell us about the future of biological therapeutics?	9
A molecular clock controls periodically driven cell migration in confined spaces	9
EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance	9
Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation	9
Bridging scales: From cell biology to physiology using in situ single-cell technologies	9
How can Waddington-like landscapes facilitate insights beyond developmental biology?	9
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health	8
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs	8
Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection	8
Localized electrical stimulation triggers cell-type-specific proliferation in biofilms	8
Systematically quantifying morphological features reveals constraints on organoid phenotypes	8
Recent progress of gene circuit designs in immune cell therapies	8
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells	8
Studying stochastic systems biology of the cell with single-cell genomics data	8
TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression	8
A synthetic gene circuit for imaging-free detection of signaling pulses	8
SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma	8
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities	8
The structure of the human cell cycle	8
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia	8
Systematic analysis of the MAPK signaling network reveals MAP3K-driven control of cell fate	8