Ulas Karaoz



I got my Ph.D. from Boston University in Bioinformatics and Systems Biology with Zhiping Weng. My background is in understanding how genes are regulated in higher order organisms. During my Ph.D. work, I worked on the identification of transcriptional regulatory elements using epigenomics. My work was focused on understanding tissue-specific gene regulation in the human genome and was part of the ENCODE (ENCyclopedia Of DNA Elements) Consortium.

Research Interests

My research interests are twofold: (1) understanding the factors influencing the phylogeny of microbial communities and how the phylogenetic changes translate into function. To this aim, I am involved in projects where we are studying at a wide range of microbial systems encompassing contaminated aquifers, bioreactors, human digestive system, and biochar amended soils using massive amounts of 16S, metagenome, and metatranscriptome data. (2) using novel high-throughput techniques to elucidate sequence determinants of antibiotic resistance in clinical environments especially focusing on the emerging drug resistant bacteria. In this context, I am aspiring to achieve a predictive understanding of drug resistance phenotypes from sequence.

Selected Current Projects

  • Metagenomics and Metatranscriptomics of a Chromate-Reducing Aquifer Microbial Community
  • Microbial Ecology of the Gastroesophageal Reflux Disease
  • BARChip: A High Density Resequencing Microarray for Simultaneous Detection of Antibiotic Resistance Genes from dozens of Organisms
  • Database of Sequence Determinants of Antibiotic Resistance using a new Ontology of Antibiotic Resistance Mechanisms, Genes, and Drug Targets
  • Metatranscriptomics of a stable tricholoroethene-degrading microbial community

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