Pathogen Discovery
Software:
We pioneered a computational approach to detect non-human organisms in human diseased tissues, in cancer and other diseases, using DNA sequencing information from these specimens. We next went on to create a cloud-based algorithm, PathSeq, that applies this approach to analysis of next-generation DNA sequencing data from tissue samples.
Discovery of novel pathogens in human disease:
Search for pathogens in other cancers and syndromes:
We have applied PathSeq to discover possible pathogenic bases for several human diseases of unknown origin, such as:
We pioneered a computational approach to detect non-human organisms in human diseased tissues, in cancer and other diseases, using DNA sequencing information from these specimens. We next went on to create a cloud-based algorithm, PathSeq, that applies this approach to analysis of next-generation DNA sequencing data from tissue samples.
Discovery of novel pathogens in human disease:
- Via application of the PathSeq algorithm, we uncovered an association of Fusobacterium nucleatum in human colon cancer and have gone on to confirm the ability of F. nucleatum to potentiate intestinal tumorigenesis in animal models.
- We have discovered a hitherto unknown bacterium- since named Bradyrhizobium enterica- in tissue specimens of patients suffering from cord colitis syndrome, a debilitating gastrointestinal condition often accompanying stem cell transplantation.
- We are currently exploring the role of Fusobacterium in other cancers of the gastrointestinal tract to understand its role in GI-specific tumorigenesis.
Search for pathogens in other cancers and syndromes:
We have applied PathSeq to discover possible pathogenic bases for several human diseases of unknown origin, such as:
- Giant cell arteritis (Bhatt et al., Arthritis Rheumatol., 2014)
- Head and neck cancers (Parfenov et al., Proc. Natl Acad. Sci USA, 2014)
- Oral tongue carcinoma (Li et al., Head Neck, 2015)
- AIDS-related lymphomas (Arvey, Ojesina et al., Blood, 2015)
- Crohn's Disease (Pedamallu et al., Cell Mol Gastroenterol Hepatol., 2016)