Katja Koeppen, PhD                

Research Scientist
Department of Microbiology and Immunology
The Geisel School of Medicine at Dartmouth
Remsen, Room 504
Hanover, NH 03755
USA


E-mail: Katja.Koeppen@Dartmouth.edu


Areas of expertise: bioinformatics, data analysis, cystic fibrosis, host-pathogen interactions


Research:
Katja Koeppen is a Research Scientist in the Department of Microbiology and Immunology at the Geisel School of Medicine at Dartmouth. A biochemist trained at the University of Tuebingen, her research focuses on host-pathogen interactions in the context of cystic fibrosis, and she serves as lead data analyst in the DartCF Applied Bioinformatics and Biostatics Core. Her foundational work in microbiology has identified that Pseudomonas aeruginosa selectively packages a bacterial tRNA fragment (sRNA52320) into outer membrane vesicles that deliver it to host epithelial cells. This short bacterial RNA is predicted to hybridize with host messenger RNAs in the LPS-stimulated MAPK signaling pathway leading to reduced IL-8 secretion. This prediction was validated in a mouse model. Dr. Koeppen is passionate about big data analysis and has been teaching bioinformatics and data analysis at Dartmouth and at the Mount Desert Island Biological Laboratory for more than five years. She has developed course modules for RNA-seq, exploratory data analysis, differential gene expression, pathway analysis and machine learning.


Publications

ScanGEO Web Application
ScanGEO is a tool for rapid meta-analysis of differential gene expression across NCBI Gene Expression Omnibus datasets.