The Ph.D. Program in Computational Biology & Bioinformatics (CBB) is an integrative, multi-disciplinary training program that encompasses biology using computational and quantitative methods. In and out of the classroom, students learn to apply the tools of statistics, mathematics, computer science and informatics to biological problems. Vibrant and innovative research in these fields provides exciting interactions between biological and computational scientists. Because CBB is based in the Duke Center for Genomic and Computational Biology (GCB), it offers a unique opportunity for students to become tomorrow's leaders in genome sciences.
<p>My laboratory is interested in fungal genomics.<br /><br />In particular we use genomic sequencing of fungal strains and species in comparative analysis. Starting with the sequencing of <i>Saccharomyces cerevisiae</i> strain S288C, I have been involved in the genome sequencing and annotation of <i>Ashbya gossypii</i>, <i>Cryptococcus neoformans</i> var. <i>grubii </i>and ~100 additional <i>S. cerevisiae</i> strains. We currently use Illumina paired end and mate paired sequencing, as this is at presently the most cost effective widely used technology capable of generating high accuracy, zero gap whole genome sequences. The 100-genomes <i>S. cerevisiae</i> data as well as the fully updated fully annotated <i>A. gossypii</i> sequence (Genbank numbers AE016814-AE016820), which spans all seven chromosomes from telomere to telomere, were generated using Illumina data. In my laboratory we strive to utilize comparative genomics data to understand aspects of basic fungal biology. Some of our specific areas of interest are filamentous growth, mapping of complex traits, horizontal gene transfer, and identification of RNA coding genes. This work involves a combination of experimental work and bioinformatics analysis. Research in <i>S. cerevisiae</i> has greatly benefitted from an accurate, annotated <i>S. cerevisiae</i> reference genome, and that research into the tremendous diversity in this organism will similarly benefit from the availability of a large number of accurate, fully annotated genome sequences. The use of genomic information to better understand the biology of these organisms, and this is what students in my laboratory generally work on.</p>
<br /> <br />What is the set of genes found in a pathogenic fungus such as Cryptococcus? <br /> <br />Our interest in this human pathogen is to expand beyond looking at one isolate and to investigate the diversity in the population. Are there genes found in some Cryptococcus neoformans isolates but not in others? Are there regions of the genome or individual genes which are highly diverged between Cryptococcus isolates? Efforts are now underway at Stanford University to sequence the genome of the JEC21 strain of Cryptococcus. This is a strain that has been agreed upon by the community of Cryptococcus researchers as a reference strain. Obtaining the DNA sequence of this strain is only the start however. From that sequence identifying the complete set of genes will be a considerable challenge requiring both bioinformatic as well as experimental tools. While this work on gene identification is going on we plan on addressing the question of how much do other Cryptococcus isolates differ from JEC21. <br /> <br />What is the set of genes in humans? <br /> <br />The complete DNA sequence of human and mouse will become available soon. This does not mean that we will know the complete set of human or mouse genes. Our current state of knowledge does not allow us to accurately predict human genes directly from DNA sequence. We are interested in applying to the human genome some of the experimental and bioinformatic tools we are developing and utilizing in fungal systems.