Koichi Takahashi

LLM-PathwayCurator transforms enrichment terms into audit-gated decision-grade claims

LLM-PathwayCurator converts pathway enrichment results into auditable claims with quality assurance, showing variable coverage across cancer cohorts.

LLM-scCurator: Data-centric feature distillation for zero-shot cell-type annotation

LLM-scCurator improves zero-shot cell-type annotation by reducing biological noise and enhancing accuracy without training data.

Rapid clonal selection within early hematopoietic cell compartments presages outcome to ivosidenib combination therapy

This study shows that resistant clones are rapidly selected in hematopoietic cell compartments with leukemic stem cell potential before relapse in patients treated with ivosidenib combination therapy.

The long-term effects of chemotherapy on normal blood cells

This study examines the long-term effects of chemotherapy on normal blood cells by analyzing mutation burdens and cell population structure in treated individuals.

Clonal evolution of hematopoietic stem cells after cancer chemotherapy

This study examines how chemotherapy affects clonal diversity and mutation patterns in hematopoietic stem cells, finding that melphalan increases mutational burden and promotes clonal aging, potentially leading to therapy-related myeloid neoplasms.

Bayesian inference of fitness landscapes via tree-structured branching processes

FiTree infers fitness landscapes from single-cell tumor mutation trees using Bayesian methods, outperforming existing models and identifying epistatic effects in leukemia data.

transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks

The paper introduces transomics2cytoscape, an R package for automated 2.5D visualization of trans-omics networks, enabling rapid and dynamic interpretation of multi-omics data.

Joint copy number and mutation phylogeny reconstruction fromsingle-cell amplicon sequencing data

This paper introduces COMPASS, a method to jointly reconstruct mutation and copy number phylogenies from single-cell amplicon sequencing data, showing it detects both clonal and subclonal alterations in leukemia patients.

Clonal hematopoiesis is associated with increased toxicity in large B-cell lymphoma patients treated with chimeric antigen receptor T cell therapy

This study finds that clonal hematopoiesis mutations, particularly in DNMT3A, TET2, and ASXL1, are linked to increased toxicity in patients undergoing anti-CD19 CAR T-cell therapy for large B-cell lymphoma.

High-throughput single-cell DNA sequencing of AML tumors with droplet microfluidics

This study develops a microfluidic method for single-cell DNA sequencing of AML tumors, revealing clonal evolution not detectable by bulk sequencing.