{"doi":"10.1016/j.cell.2019.05.031","title":"Comprehensive Integration of Single-Cell Data","abstract":"Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to \"anchor\" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.","journal":"Cell","year":2019,"id":26,"datarank":18.89532252565016,"base_score":9.71208488700598,"endowment":9.71208488700598,"self_citation_contribution":1.4568127330508973,"citation_network_contribution":17.438509792599262,"self_endowment_contribution":1.4568127330508973,"citer_contribution":17.438509792599262,"corpus_percentile":97.3,"corpus_rank":434,"citation_count":16515,"citer_count":194,"citers_with_citation_signal":194,"citers_with_endowment":194,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2019-06-01","authors":[{"id":159,"name":"Andrew Butler","orcid":"0000-0003-3608-0463","position":1,"is_corresponding":false},{"id":29313,"name":"Pejman Mohammadi","orcid":"0000-0003-4457-8552","position":2,"is_corresponding":false},{"id":161,"name":"Christoph Hafemeister","orcid":"0000-0001-6365-8254","position":3,"is_corresponding":false},{"id":162,"name":"Efthymia Papalexi","orcid":"0000-0001-5898-694X","position":4,"is_corresponding":false},{"id":163,"name":"William M. Mauck","orcid":"0000-0001-9455-7245","position":5,"is_corresponding":false},{"id":164,"name":"Yuhan Hao","orcid":"0000-0002-1810-0822","position":6,"is_corresponding":false},{"id":165,"name":"Marlon Stoeckius","orcid":"0000-0002-5658-029X","position":7,"is_corresponding":false},{"id":166,"name":"Peter Smibert","orcid":"0000-0003-0772-1647","position":8,"is_corresponding":false},{"id":167,"name":"Rahul Satija","orcid":"0000-0002-1479-664X","position":9,"is_corresponding":false},{"id":158,"name":"Tim Stuart","orcid":"0000-0002-3044-0897","position":0,"is_corresponding":true}],"reference_count":103,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}