Daniel B. Lipka

This study introduces scIRES-seq to analyze CTCs from cervical cancer, revealing multimodal molecular heterogeneity through integrated genetic, epigenomic, and transcriptomic profiling.

The paper develops a hierarchical classification framework combining epigenetic and genetic data with machine learning to improve diagnosis and risk stratification in hematologic malignancies.

This study shows that HSC dormancy, not apoptosis, limits mutagenesis in aging, with dormancy disruption accelerating mutation rates.

The paper introduces Knowledge Connector, a decision support system that integrates multiomics data with clinical information to aid in precision oncology decision-making.

This study identifies oncofetal reprogramming in juvenile myelomonocytic leukemia, linking RAS-pathway activation to fetal gene expression and revealing CD52 as a therapeutic target.

This study identifies PTPN11/SHP2-driven adenosine signaling as a mechanism of immune escape in JMML, showing that CD39 inhibition can enhance T cell responses and reduce myeloproliferation.

The paper benchmarks DNA methylation sequencing workflows against an experimental gold-standard, identifying superior workflows and developing a sustainable benchmarking platform.

Pyjacker detects enhancer hijacking in AML, identifying MNX1 activation via 7q deletion as a novel oncogenic mechanism.

The paper shows MNX1 overexpression in t(7;12)(q36;p13) AML is due to enhancer hijacking, not oncofusion, and is common in pediatric cases.

This study shows that high IL-3 concentrations prime murine 32D myeloid progenitor cells for granulocytic differentiation, while intermediate concentrations reduce this potential without affecting proliferation.

The paper develops a computational framework for analyzing DNA methylation data in mouse hematopoiesis, identifying novel cis-regulatory elements associated with gene expression during differentiation.

AmpliconDesign provides a web server for designing high-throughput targeted DNA methylation assays, improving primer design and analysis workflows for epigenetic studies.