Bioinformatics Group

The GeMS Bioinformatics Group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to microbial scientists. The Bioinformatics Group provides a walk-in service for consultations and computational support, and a variety of training workshops.  Investigators work with the GeMS Bioinformatics Group on (1) a collaborative basis and (2) a core service basis through the GCB Genomic Analysis Bioinformatics Shared Resource. For consultations on new or existing projects, please contact Olaf Mueller, PhD or Joshua Granek, PhD.

Joshua Granek, PhD
Olaf Mueller, PhD
Dr. Granek interests are centered in interactions between organisms at the cellular and molecular scale, with a research focus on microbial communities and pathogens. Throughout his career, he has used a combination of experimental and computational approaches to address biological questions ranging from the structure, organization, and evolution of transcription regulatory sequences, through the development of GOMER, a software package for modeling transcriptional regulation on a genomic scale, to wet-lab experiments that analyzed the regulation of ploidy specific genes in the yeast Saccharomyces cerevisiae. He also developed S. cerevisiae colony biofilms as a model for understanding how microbes interact to generate multicellular behavior using a combination of genome-scale techniques, including next-generation DNA sequencing, high-throughput phenotyping, and computation. Dr. Granek’s current efforts are focused on supporting various microbial labs with the analysis of high-throughput genomic DNA and RNA sequencing data in both bacterial and fungal systems. Dr. Granek’s primary appointment is in the Department of Biostatistics and Bioinformatics and the Department of Molecular Genetics and Microbiology.Dr. Mueller is a biologist by training with a strong background in bioinformatics. He is interested in fungal and lichen genomics and evolution, and his former research focused on molecular interactions of fungi in pathogenic or symbiotic systems. His well versed in “wet lab” applications and computational methods for functional genomics, with a focus on the identification and characterization of pathogenicity related fungal genes. His expertise include the development of ‘Yeast Signal Sequence Trap’ screenings, generation and characterization of gene knockout mutants, and the development of bioinformatic tools and pipelines for in silico genome wide screenings for pathogenicity factors. More recently, he has focused exclusivelly on bioinformatic approaches to study molecular evolution in fungal meiosis and lichen symbiosis, were he implemented bioinformatic tools and pipelines for comparative genomics and various downstream phylogenetic analyses. Additional work in lichen genome projects focused on evolution of lichen symbiosis and included genome and transcriptome assemblies, de novo and functional gene annotations, mRNA-seq based transcriptome studies, and application of frameworks and databases, like GMOD components, to organize and present genomic data.
Contact:
Joshua Granek, PhD
Assistant Research Professor
Dept. of Biostatistics & Bioinformatics
joshua.granek@duke.edu
Tel: 919.684.2876
Contact:
Olaf Mueller, PhD
Bioinformatician II
Dept. of Molecular Genetics & Microbiology
om25@duke.edu
Tel: 919.660.2876