Daoud M. Meerzaman

Hybrid Semantic-Lexical Retrieval for Source-to-CDE Mapping in the NCI caDSR

The paper develops a hybrid retrieval system for mapping source data elements to CDEs, achieving high recall across multiple datasets.

Distributed Clonal Deletion Prevents Autoimmune Disease Progression

This study shows that distributed clonal deletion checkpoints prevent autoimmune disease by restricting autoreactive B cell diversification and persistence.

A simple liquid 3D cell culture paradigm models oxidative mitochondrial metabolism of epithelial breast cancer cells with relevance for lung metastases.

This paper compares two 3D culture models for breast cancer cells, finding that the EmC model better mimics lung metastasis by altering metabolism and gene expression.

Scalable generation of pure CD103⁺ cDC1 from iDC1 cultures

This paper develops a scalable method to generate pure CD103+ cDC1 from mouse bone marrow cultures, achieving high purity and yield for immunological studies.

TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers

This study shows TRAIL treatment of TNBC cells activates the NFKB2 pathway, leading to cytokine production that enhances neutrophil chemotaxis and immune suppression.

Evidence for the digital programming of cellular differentiation: characterization of binary switches in lineage-determining transcription factors

The paper identifies binary promoter switches in lineage-determining transcription factors, showing mutually exclusive sense/antisense transcription and distinct gene expression patterns in different cell states.

Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study

The paper presents whole-genome and whole-exome sequencing datasets from a multi-center, cross-platform study to benchmark NGS technologies and bioinformatics pipelines in cancer genomics.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

This study evaluates somatic CNV callers using NGS data from 91 samples with varying factors, finding that caller choice and tumor purity significantly impact call quality.

Bromodomain Protein, BRD4, Contributes to the Regulation of Alternative Splicing

This study shows BRD4 influences alternative splicing by interacting with splicing machinery during transcription elongation in thymocytes and T-ALL cells.