Xiaotu Ma

A structure-derived contact-network responsiveness atlas of human proteins

The paper introduces CNR, a framework to quantify how protein contact networks respond to stabilizing interaction changes, using human AlphaFold models to analyze 22,167 structures.

Tabular foundation model predicts alternative lengthening of telomeres (ALT) and identifies SMARCAL1 as a target in ALT-driven cancers

The paper develops ALTitude, a machine learning model to predict ALT status from whole genome sequencing data, identifies SMARCAL1 as a therapeutic target in ALT-driven cancers.

Reactivation of a TAL1 progenitor cell enhancer region by non-coding somatic variants in T-lineage acute lymphoblastic leukemia

The paper identifies non-coding somatic variants in TAL1 regulatory regions that reactivate enhancers normally active in hematopoietic stem cells in T-lineage acute lymphoblastic leukemia.

The landscape of structural variation in pediatric cancer

This study analyzes structural variants in 1,616 pediatric cancer genomes, revealing unique SV hotspots and patterns distinct from adult cancers.

CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies

CanID is a machine learning classifier for pediatric cancer subtypes using RNAseq data, achieving 99% accuracy for solid tumors and 92-93% for hematologic malignancies.

Clonal Evolution of Pediatric Acute Myeloid Leukemia and Its Contribution to Disease Relapse

This study analyzes genetic changes in pediatric AML relapse using whole-genome sequencing and finds that relapse is driven by the selection of pre-existing clones rather than new mutations.

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

Seq2Karyotype (S2K) enables in-silico karyotyping from whole-genome sequencing data, revealing intratumoral heterogeneity and evolutionary trajectories in cancer samples.

TP53 Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia

This study shows TP53 mutations cause resistance to revumenib in AML and suggests combining MCL-1 inhibitors with menin inhibitors could be effective.

bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis

bamSliceR enables rapid, cross-cohort variant analysis by extracting and analyzing aligned reads from GDC data, identifying clinically relevant variants in leukemia cohorts.

Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma

This study creates two mouse models with conditional c-MYC activation in specific cell types, leading to distinct neuroendocrine tumors resembling human neuroblastoma and somatostatinoma.