| # | Title | Journal | Year | Citations |
|---|
| 1 | The Molecular Signatures Database Hallmark Gene Set Collection | Cell Systems | 2015 | 7,719 |
| 2 | Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments | Cell Systems | 2016 | 2,057 |
| 3 | DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors | Cell Systems | 2019 | 1,648 |
| 4 | Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data | Cell Systems | 2019 | 1,274 |
| 5 | Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom | Cell Systems | 2016 | 1,199 |
| 6 | A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure | Cell Systems | 2016 | 1,098 |
| 7 | A Single-Cell Transcriptome Atlas of the Human Pancreas | Cell Systems | 2016 | 966 |
| 8 | Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines | Cell Systems | 2018 | 605 |
| 9 | Plasma Proteome Profiling to Assess Human Health and Disease | Cell Systems | 2016 | 549 |
| 10 | Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis | Cell Systems | 2017 | 457 |
| 11 | Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection | Cell Systems | 2020 | 439 |
| 12 | Large-Scale Multi-omic Analysis of COVID-19 Severity | Cell Systems | 2021 | 438 |
| 13 | Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures | Cell Systems | 2017 | 414 |
| 14 | An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes | Cell Systems | 2017 | 413 |
| 15 | A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease | Cell Systems | 2017 | 381 |
| 16 | Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome | Cell Systems | 2018 | 349 |
| 17 | Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity | Cell Systems | 2016 | 332 |
| 18 | The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations | Cell Systems | 2018 | 327 |
| 19 | Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks | Cell Systems | 2016 | 320 |
| 20 | MHCflurry: Open-Source Class I MHC Binding Affinity Prediction | Cell Systems | 2018 | 311 |
| 21 | Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing | Cell Systems | 2015 | 294 |
| 22 | Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas | Cell Systems | 2018 | 284 |
| 23 | End-to-End Differentiable Learning of Protein Structure | Cell Systems | 2019 | 278 |
| 24 | Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry | Cell Systems | 2018 | 272 |
| 25 | Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data | Cell Systems | 2018 | 271 |
| 26 | Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota | Cell Systems | 2015 | 267 |
| 27 | Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas | Cell Systems | 2015 | 266 |
| 28 | Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome | Cell Systems | 2016 | 261 |
| 29 | Four Key Steps Control Glycolytic Flux in Mammalian Cells | Cell Systems | 2018 | 249 |
| 30 | NDEx, the Network Data Exchange | Cell Systems | 2015 | 247 |
| 31 | Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow | Cell Systems | 2017 | 247 |
| 32 | Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics | Cell Systems | 2015 | 241 |
| 33 | Systems Biology of Cancer Metastasis | Cell Systems | 2019 | 233 |
| 34 | Matched-Comparative Modeling of Normal and Diseased Human Airway Responses Using a Microengineered Breathing Lung Chip | Cell Systems | 2016 | 227 |
| 35 | SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species | Cell Systems | 2019 | 225 |
| 36 | BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud | Cell Systems | 2018 | 217 |
| 37 | Systematic Evaluation of Molecular Networks for Discovery of Disease Genes | Cell Systems | 2018 | 215 |
| 38 | Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry | Cell Systems | 2018 | 214 |
| 39 | Compact Integration of Multi-Network Topology for Functional Analysis of Genes | Cell Systems | 2016 | 207 |
| 40 | A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism | Cell Systems | 2016 | 205 |
| 41 | Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications | Cell Systems | 2016 | 201 |
| 42 | hctsa : A Computational Framework for Automated Time-Series Phenotyping Using Massive Feature Extraction | Cell Systems | 2017 | 197 |
| 43 | Learning the protein language: Evolution, structure, and function | Cell Systems | 2021 | 194 |
| 44 | Integrative Personal Omics Profiles during Periods of Weight Gain and Loss | Cell Systems | 2018 | 183 |
| 45 | The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy | Cell Systems | 2018 | 183 |
| 46 | The Biomarker GlycA Is Associated with Chronic Inflammation and Predicts Long-Term Risk of Severe Infection | Cell Systems | 2015 | 179 |
| 47 | A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models | Cell Systems | 2017 | 178 |
| 48 | Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast | Cell Systems | 2017 | 178 |
| 49 | Stem Cell Differentiation as a Non-Markov Stochastic Process | Cell Systems | 2017 | 178 |
| 50 | Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats | Cell Systems | 2015 | 176 |
