Samirkumar B. Amin

Inferring ecDNA Evolution from Allele Frequency Spectra

This paper introduces ecEvol, a method to infer ecDNA emergence time and other parameters from bulk whole-genome sequencing data, finding that ecDNA typically emerges early and is associated with poorer survival.

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

The paper identifies enhancer subtypes in cancer cell lines and tumors, revealing distinct epigenetic patterns and potential therapeutic targets.

Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

This study identifies genetic changes in IDH-mutant gliomas that correlate with treatment response and tumor evolution using longitudinal genomic data from 206 patient samples.

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Integrative pathway enrichment analysis of multivariate omics data

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

Process-specific somatic mutation distributions vary with three-dimensional genome structure

The paper examines how somatic mutation distributions vary across chromatin folding domains in cancer genomes, revealing distinct patterns associated with different mutational processes.

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

The paper identifies and characterizes coding and non-coding driver mutations across 2,500 cancer genomes, revealing new candidates and questioning previous findings.

Flowr: Robust and efficient pipelines using a simple language-agnostic approach

Flowr provides a robust, scalable, and portable framework for designing computing pipelines using a simple language-agnostic approach.