Xue Yang

Gene Regulatory Network Reconfiguration in Direct Lineage Reprogramming

The paper uses CellOracle to analyze GRN reconfiguration during fibroblast to iEP reprogramming, identifying Fos and Yap1 as key factors for successful conversion.

Multiomic single-cell lineage tracing to dissect fate-specific gene regulatory programs

The paper introduces CellTag-multi, a method for multiomic single-cell lineage tracing that combines chromatin accessibility with lineage barcodes, and applies it to study reprogramming outcomes and gene regulatory programs in mouse hematopoiesis.

Capybara: A computational tool to measure cell identity and fate transitions

Capybara measures cell identity and fate transitions using a continuum-based approach, showing improved performance in annotating cells and identifying transitions in hematopoiesis and reprogramming.

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

CellTag Indexing enables genetic barcode-based multiplexing for single-cell genomics, allowing simultaneous sample identification and transcriptional analysis across diverse cell types.