Cell Systems

(The TQCC of Cell Systems is 23. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection429
Large-Scale Multi-omic Analysis of COVID-19 Severity395
Learning the protein language: Evolution, structure, and function192
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing165
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer152
MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities129
A time-resolved proteomic and prognostic map of COVID-19124
Fast and Flexible Protein Design Using Deep Graph Neural Networks119
A platform for experimental precision medicine: The extended BXD mouse family113
Artificial intelligence for proteomics and biomarker discovery109
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning103
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data99
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus96
Informed training set design enables efficient machine learning-assisted directed protein evolution96
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design92
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks89
Hotspot identifies informative gene modules across modalities of single-cell genomics81
Biophysics of Temporal Interference Stimulation78
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis74
Encoding Membrane-Potential-Based Memory within a Microbial Community73
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells69
A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences69
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions67
Perfect adaptation in biology65
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions64
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis62
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy62
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome59
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids59
Functional attractors in microbial community assembly58
SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks58
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains58
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program57
Codon Usage and Splicing Jointly Influence mRNA Localization57
SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses56
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins56
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism56
The Genetic Makeup of the Electrocardiogram54
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer53
Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer52
NAD+ flux is maintained in aged mice despite lower tissue concentrations52
Machine learning for perturbational single-cell omics52
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies52
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing50
Consciousness depends on integration between parietal cortex, striatum, and thalamus50
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering48
SCHEEPDOG: Programming Electric Cues to Dynamically Herd Large-Scale Cell Migration48
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions47
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition46
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain45
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma44
ProGen2: Exploring the boundaries of protein language models43
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling42
Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast41
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies40
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus40
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors39
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution38
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors38
MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing37
Database-independent de novo metaproteomics of complex microbial communities37
Noise distorts the epigenetic landscape and shapes cell-fate decisions37
Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics36
The context-dependent, combinatorial logic of BMP signaling36
Human plasma IgG1 repertoires are simple, unique, and dynamic36
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees36
Context-aware synthetic biology by controller design: Engineering the mammalian cell36
Morphology and gene expression profiling provide complementary information for mapping cell state36
Biological feedback control—Respect the loops36
Ultrasensitive molecular controllers for quasi-integral feedback35
CELLector: Genomics-Guided Selection of Cancer In Vitro Models34
Ligand-receptor promiscuity enables cellular addressing33
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets32
Degradation of host translational machinery drives tRNA acquisition in viruses32
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals31
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures31
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity31
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning31
A tale of two rhythms: Locked clocks and chaos in biology31
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays30
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis30
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines30
Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging30
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data30
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes29
Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity29
The sound of silence: Transgene silencing in mammalian cell engineering28
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity28
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation27
Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons26
Best Practices for Making Reproducible Biochemical Models26
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles26
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks26
Quantifying the Central Dogma in the p53 Pathway in Live Single Cells25
Multiomic profiling of the liver across diets and age in a diverse mouse population24
Deciphering the signaling network of breast cancer improves drug sensitivity prediction24
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles24
Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens24
Diploid hepatocytes drive physiological liver renewal in adult humans24
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease24
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation23
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods23
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants23
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells23
The community-function landscape of microbial consortia23
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma23