| Title |
Joint representation and visualization of derailed cell states with Decipher |
| Authors |
Nazaret, Achille ; Fan, Joy Linyue ; Lavallée, Vincent-Philippe ; Burdziak, Cassandra ; Cornish, Andrew E ; Kiseliovas, Vaidotas ; Bowman, Robert L ; Masilionis, Ignas ; Chun, Jaeyoung ; Eisman, Shira E ; Wang, James ; Hong, Justin ; Shi, Lingting ; Levine, Ross L ; Mažutis, Linas ; Blei, David ; Pe’er, Dana ; Azizi, Elham |
| DOI |
10.1186/s13059-025-03682-8 |
| Full Text |
|
| Is Part of |
Genome biology.. London : BioMed Central Ltd. 2025, vol. 26, iss. 1, art. no. 219, p. [1-43].. ISSN 1474-7596. eISSN 1474-760X |
| Keywords [eng] |
acute myeloid leukemia ; cell-state trajectories ; deep generative model ; dimensionality reduction |
| Abstract [eng] |
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. |
| Published |
London : BioMed Central Ltd |
| Type |
Journal article |
| Language |
English |
| Publication date |
2025 |
| CC license |
|
