Kenji Kamimoto

The paper shows H3K9me3 represses lineage-specific enhancers in progenitor cells, restricting transcription factor access to prevent inappropriate activation during development.

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

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.

The paper defines the cellular and transcriptional features of cardiac recovery using snRNA-seq, identifying RUNX1 downregulation as a key predictor and potential therapeutic target.

Gene regulatory networks inferred from single-cell transcriptome and epigenome data are perturbed in silico to predict transcription-factor perturbation outcomes and to nominate factors that raise reprogramming yield.

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

The paper uses single-cell RNA sequencing to show that mice adapt to small bowel resection by reprogramming distal intestinal enterocytes to a proximal identity, driven by retinoid metabolism and Creb3l3.

This paper introduces a lineage-tracing method called CellTagging to study clonal dynamics in direct lineage reprogramming from fibroblasts to induced endoderm progenitors, revealing rare successful reprogramming events and clonal instability.