Meeting 49, 2023-06-02
- Bengt Sennblad
When is the meeting? | 2-June-2023 at 10.00 - 11.00 |
| Where is the meeting? | Zoom video-conference: http://meet.nbis.se/aiaio |
| What is the meeting about? | Scuphr: A probabilistic framework for cell lineage tree reconstruction |
| Who is the responsible presenter? | Hazal Koptagel, KTH |
Abstract: (From BioRxiv: Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method’s robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.)
Presentation: Slides