Cell Systems

Papers
(The TQCC of Cell Systems is 20. 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 2020-11-01 to 2024-11-01.)
ArticleCitations
Large-Scale Multi-omic Analysis of COVID-19 Severity420
Learning the protein language: Evolution, structure, and function252
Artificial intelligence for proteomics and biomarker discovery149
A time-resolved proteomic and prognostic map of COVID-19136
A platform for experimental precision medicine: The extended BXD mouse family123
Informed training set design enables efficient machine learning-assisted directed protein evolution120
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data117
ProGen2: Exploring the boundaries of protein language models115
Hotspot identifies informative gene modules across modalities of single-cell genomics99
Biophysics of Temporal Interference Stimulation99
Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design99
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis93
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions83
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells80
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions79
Perfect adaptation in biology76
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy74
Functional attractors in microbial community assembly72
The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis71
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains71
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids70
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins68
Machine learning for perturbational single-cell omics67
Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism67
NAD+ flux is maintained in aged mice despite lower tissue concentrations65
Consciousness depends on integration between parietal cortex, striatum, and thalamus65
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer61
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition58
The sound of silence: Transgene silencing in mammalian cell engineering58
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering57
Morphology and gene expression profiling provide complementary information for mapping cell state57
Diversity of the Gβγ complexes defines spatial and temporal bias of GPCR signaling55
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma55
Noise distorts the epigenetic landscape and shapes cell-fate decisions53
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution50
The context-dependent, combinatorial logic of BMP signaling48
Biological feedback control—Respect the loops46
Database-independent de novo metaproteomics of complex microbial communities45
Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors45
Human plasma IgG1 repertoires are simple, unique, and dynamic44
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies44
Ligand-receptor promiscuity enables cellular addressing44
Defining and Manipulating B Cell Immunodominance Hierarchies to Elicit Broadly Neutralizing Antibody Responses against Influenza Virus43
Context-aware synthetic biology by controller design: Engineering the mammalian cell43
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors42
Degradation of host translational machinery drives tRNA acquisition in viruses42
Ultrasensitive molecular controllers for quasi-integral feedback41
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data41
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees40
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity39
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer’s Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals39
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes39
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning38
Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines37
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation36
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation36
The community-function landscape of microbial consortia35
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets35
Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis35
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity34
IgLM: Infilling language modeling for antibody sequence design34
Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures33
A tale of two rhythms: Locked clocks and chaos in biology33
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles33
A new age in protein design empowered by deep learning32
Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells32
Diploid hepatocytes drive physiological liver renewal in adult humans32
Deciphering the signaling network of breast cancer improves drug sensitivity prediction30
Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA29
Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes29
Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset29
Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges29
Multiomic profiling of the liver across diets and age in a diverse mouse population28
Mapping the multiscale structure of biological systems27
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles27
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression27
A vast evolutionarily transient translatome contributes to phenotype and fitness27
Tissue-specific enhancer functional networks for associating distal regulatory regions to disease26
A convergent molecular network underlying autism and congenital heart disease26
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer26
A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease26
Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity26
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations25
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants25
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods25
Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits23
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions23
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations23
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity23
The structure of the human cell cycle23
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria23
Sparse dictionary learning recovers pleiotropy from human cell fitness screens22
Virtual screening for small-molecule pathway regulators by image-profile matching22
Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales22
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals21
Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer21
Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention21
Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems21
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner21
Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain21
Engineering molecular translation systems20
Privacy-preserving genotype imputation with fully homomorphic encryption20
Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain20
Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease20
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