Gabor Marth

Biography

My research focuses on development of DNA sequence analysis software. Over the past 15 years, my group has developed software to aid genome sequence completion (finishing), for single-nucleotide polymorphism discovery, for population genetic analysis of genomic variation data.  We have developed software packages for base calling, read mapping, variant discovery, and data visualization in high-throughput, next-generation sequencing data. My current research is aimed at developing complete, automated pipelines for sequence processing, variant detection, and variant interpretation; adapt and extend our tools for cancer sequence analysis, and at developing informatics technologies to support population, medical, and personal genome sequencing of very large numbers of samples. A major goal of genetics research is to characterize the contribution of variation in DNA sequence to differences in physical traits or disease susceptibility between individuals. Until recently, the discovery of genetic variants was the rate-limiting step in genetics research due to the prohibitive cost of obtaining DNA sequences of large numbers of individuals. Over the past five years advances in next generation sequencing (NGS) have lowered the cost of sequencing DNA. NGS has had a profound impact because it is now possible to sequence large numbers of individuals and fully describe the complete spectrum of genetic variation in a species. Genetic variation occurs at different levels within the genome. The simplest and most common type of variation is single-nucleotide polymorphisms (SNPs) or single-base changes. Often short sections of DNA can be inserted into or deleted from an individual's genome (short INDELs). Often longer regions are deleted from and individual's chromosomes; other regions may be present in multiple copies (chromosomal amplifications); sometimes long sections of chromosomes are translocated. These large-scale variations are termed structural genetic variations. Our current focus is to develop computer software to process and analyze the vast amount of sequence data generated by NGS technologies. We are actively developing software for reference-guided assembly, haplotype-based variant discovery and genotyping, as well as APIs & command-line toolkits for working with NGS data, and tools to build custom NGS analysis pipelines.

Research Interest

DNA sequence Genetics Genetic variation