Titles
Associate Professor, Department of Systems BiologyAffiliations
Department of Systems BiologyCenter for Computational Biology and Bioinformatics
Center for Cancer Systems Therapeutics
Department of Biomedical Informatics
Phone
(212) 851-5151Website
Vitkup LabDennis Vitkup is an associate professor in the Center for Computational Biology and Bioinformatics and the Department of Biomedical Informatics. His laboratory develops and applies novel probabilistic techniques to analyze cellular networks. Their work involves developing methods that connect network structure to function to phenotypes, and can be used to make experimentally verifiable predictions. Research in the Vitkup Lab focuses on three main topics: 1) the global probabilistic reconstruction and analysis of metabolic networks based on completely sequenced genomes, 2) the development of methods to identify new human disease genes and genetic disease modules using probabilistic functional networks, and 3) the development of methods to combine mechanistic and probabilistic approaches for the dynamic simulation of biological pathways. The Vitkup Lab developed GLOBUS, a global probabilistic method for reconstructing cellular metabolic networks, and applied it to design new drugs for malaria and understand cancer metabolism. They also created NETBAG, a novel method for considering genetic mutations in the context of molecular networks, and used it to identify networks that are perturbed in autism and schizophrenia.
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News
Research News
Diversity and Severity of Autism Symptoms Linked to Mutation Locations In a recent study, led by Dennis Vitkup, PhD, researchers at Columbia University Vagelos College of Physicians and Surgeons have made an important step towards understanding the biological mechanisms underlying the cognitive and behavioral diversity of autism cases triggered by de novo truncating mutations.
Research News
Dynamics of Gut Bacteria Follow Ecological Laws The seemingly chaotic bacterial soup of the gut microbiome is more organized than it first appears and follows some of the same ecological laws that apply to birds, fish, tropical rainforests, and even complex economic and financial markets, according to a new paper in Nature Microbiology by systems biologists at Columbia University Irving Medical Center.
Profile
Grad Spotlight: Brian Ji, PhD For Brian Ji, the big draw to systems biology stemmed from his passion for applying quantitative approaches to understanding biology. Ji studied under Dr. Dennis Vitkup in the Vitkup lab and completed his thesis defense for systems biology in the fall of 2018. Also an MD student in Columbia’s Vagelos College of Physicians and Surgeons, Ji was attracted to Columbia because of the close interplay between the Systems Biology Department and the Columbia University Irving Medical Center. “Ultimately,” he says, “the opportunity to sit at the intersection between math, biology and medicine was too good to pass up.”
Education
PhD Candidate Brian Ji Wins for Outstanding Research at Integrated Conference Brian Ji, an MD/PhD student in systems biology and a member of the Vitkup Lab, delivered the winning talk at the Biennial Integrated Program Retreat. Ji, who discussed a novel experimental and computational method to understand spatiotemporal dynamics of the human gut microbiome, was one of six systems biology students who delivered research presentations at the conference.
Awards and Grants
Columbia Awarded NCI Center for Cancer Systems Biology The Center for Cancer Systems Therapeutics (CaST) is developing a framework that can account for the dynamic nature of cancer and use this knowledge to disrupt the programs that maintain tumor survival.