Hasan Otu

Background

About Hasan Otu

My career to date has involved research in Information Theory and Bioinformatics. My earlier work was in the areas of image compression and joint source/channel coding. With the availability of genomic sequences, my interest shifted into bioinformatics by trying to understand how information is organized in DNA sequences. Using Information Theory, I developed characterizations of this organization, with applications to fragment assembly and phylogeny reconstruction. My research at Harvard Medical School focused on management and analysis of high-throughput biological data in the context of functional genomics and proteomics. These included, but were not limited to, transcription profiling (e.g. Affymetrix GeneChip system), proteomics (e.g. SELDI TOF, MALDI TOF/TOF), and genotyping (e.g. Affymetrix SNP arrays) efforts targeting questions in computational biology, systems biology, cancer, stem cells, heart disease, diabetes, and obesity. As the director of Bioinformatics Core at BIDMC Genomics Center, I managed the core to establish a state-of-the-art computer infrastructure and a research web portal. Specifically, I focused on problems regarding data normalization, differential expression, clustering, functional group/pathway analysis and biomarker discovery. Currently I have been working on analysis of biological data within the context of networks, along the lines of systems biology. We use probabilistic graph models, e.g Bayesian Networks, to answer two questions:(i) what are the active known pathways given experimental data?(ii) what are the interaction networks based on observed data? Our goal is to incorporate existing biological knowledge in interpreting specific experimental results in the context of pathways. I have also led next-generation sequencing projects that involve RNA-seq, whole genome sequencing, and metagenomics. In addition to research efforts, I have supervised and trained summer interns, IT personnel, BS, MS, and PhD students totaling around 30 people over the last 20 years. My teaching experience involves assisting in undergraduate Electrical Engineering (EE) courses at Bogazici University and University of Nebraska-Lincoln (UNL), teaching undergraduate/graduate EE, Bioinformatics, and Bioengineering courses at UNL, Northeastern University, Yeditepe University, Sabanci University, Acibadem University and Istanbul Bilgi University. I have published over 70 journal articles,~50 conference proceedings, 5 book chapters and 6 U.S. patents, which have received around citations.