{"doi":"10.1101/2023.11.11.566719","title":"Joint representation and visualization of derailed cell states with Decipher","abstract":"Biological insights often depend on comparing conditions such as disease and health, yet we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":390856,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9128,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":624322,"name":"Joy Linyue Fan","orcid":null,"position":1,"is_corresponding":false},{"id":226863,"name":"Vincent‐Philippe Lavallée","orcid":"0000-0001-9095-0066","position":2,"is_corresponding":false},{"id":559372,"name":"Cassandra Burdziak","orcid":"0000-0001-6008-7783","position":3,"is_corresponding":false},{"id":817989,"name":"Andrew Cornish","orcid":"0000-0001-6703-8503","position":4,"is_corresponding":false},{"id":1162679,"name":"Vaidotas Kiseliovas","orcid":"0000-0002-5431-7316","position":5,"is_corresponding":false},{"id":297426,"name":"Robert L. Bowman","orcid":"0000-0002-8294-8748","position":6,"is_corresponding":false},{"id":50787,"name":"Ignas Masilionis","orcid":"0000-0001-7937-9014","position":7,"is_corresponding":false},{"id":618644,"name":"Jaeyoung Chun","orcid":"0000-0002-4164-0691","position":8,"is_corresponding":false},{"id":716346,"name":"Shira E. Eisman","orcid":null,"position":9,"is_corresponding":false},{"id":405175,"name":"James Z. Wang","orcid":"0000-0003-4379-4173","position":10,"is_corresponding":false},{"id":571474,"name":"Justin Hong","orcid":"0000-0003-2115-9101","position":11,"is_corresponding":false},{"id":647883,"name":"Lingting Shi","orcid":"0000-0002-4751-4135","position":12,"is_corresponding":false},{"id":35287,"name":"Ross L. Levine","orcid":"0000-0002-7884-1905","position":13,"is_corresponding":false},{"id":50789,"name":"Linas Mazutis","orcid":"0000-0002-5552-6427","position":14,"is_corresponding":false},{"id":374554,"name":"David M. Blei","orcid":"0000-0002-5588-4611","position":15,"is_corresponding":false},{"id":104368,"name":"Dana Pe’er","orcid":"0000-0002-9259-8817","position":16,"is_corresponding":false},{"id":559371,"name":"Elham Azizi","orcid":"0000-0001-5059-6971","position":17,"is_corresponding":false},{"id":70402,"name":"Achille Nazaret","orcid":"0000-0002-5428-9810","position":0,"is_corresponding":true}],"reference_count":143,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:18:37.743462Z","pmid":"38014231","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,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}