Marghoob Mohiyuddin

Functional Role of Small Extrachromosomal Circular DNA in Colorectal Cancer

This study investigates the role of small extrachromosomal circular DNA (eccDNA) in colorectal cancer, finding that it contributes to gene expression, immune cell recruitment, and poor patient outcomes.

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

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.

ecTMB: a robust method to estimate and classify tumor mutational burden

This paper introduces ecTMB, a statistical framework for estimating and classifying tumor mutational burden, identifying a new TMB subtype associated with patient survival.

Robust Cancer Mutation Detection with Deep Learning Models Derived from Tumor-Normal Sequencing Data

This study develops and validates deep learning strategies for robust cancer mutation detection using tumor-normal sequencing data across multiple technologies and scenarios.

Deep convolutional neural networks for accurate somatic mutation detection

NeuSomatic is a convolutional neural network for somatic mutation detection that outperforms existing methods across various sequencing platforms and tumor purities.

svclassify: a method to establish benchmark structural variant calls

svclassify classifies structural variants as true or false positives using multi-technology annotations, achieving high concordance with PCR validation and MetaSV.