USF Bioinformatics Lecture Series
Computer Science Department
Fall 2010

Ian Korf
Sean Mooney
Bob Horton
John Irwin
Thurs, September 9, 2010 11:45-12:40pm
Thurs, October 28, 2010 11:45-12:40pm
Thurs, November 11, 2010 6:30-7:30pm
Thurs, December 2, 2010 6:30-7:30pm
Harney 235 (Kudlick room)
Harney 235 (Kudlick room)
Harney 235 (Kudlick room)
Harney 235 (Kudlick room)
        directions to campus
        campus map (Harney is HR on Golden Gate Avenue).
        Parking information is available at the main gate, which is on on Golden Gate Avenue between Kittredge Terrace and Roselyn Terrace.

Dr. Ian Korf: Playing word games with DNA: IMEter and Bind-n-Seq    September 9
Ian is Associate Professor in the Department of Molecular and Cellular Biology at the UC Davis Genome Center. His research interests range from developmental biology to high performance computing. His research group is currently working on problems in gene finding, DNA-protein interactions, intron function, ChIP-seq analysis, sequence alignment, and epigenetics. Ian is an author of Bioinformatics tools and texts: BioPerl, BLAST (O'Reilly), and Unix and Perl to the Rescue (Cambridge University Press).
Abstract: To the untrained eye, DNA can look like gibberish. When confronted with millions or billions of nucleotides, even the expert eye strains. Where are the "good parts"? Why is there so much garbage? What does it all mean? While our understanding of DNA sequence is still in its infancy, we are learning some parts of the language. In this talk, I will describe how the combination of high-throughput biology and relatively simple statistical models can give us some insight into biological function.
Dr. Sean Mooney: Beyond the genomes: understanding the molecular functions of genetic variants    October 28
Sean is Associate Professor and Director of Bioinformatics at the Buck Institute for Age Research. His research focuses on the underlying molecular causes of inherited genetic diseases and cancer. His laboratory consists of scientists and engineers working together to construct new algorithms, generate new scientific hypotheses, and build electronic systems that enable research activities through the Internet.
Abstract: With the rise of whole genome sequencing and personal genomics, an important challenge in bioinformatics is understanding how genetic disease-causing mutations give rise to the molecular changes that lead to the disease phenotype. We are identifying and modeling variants that are likely to disrupt function and assessing whether they improve identification of phenotype and clinical outcome. We have applied this approach to inherited disease causing mutations, somatic amino acid substitutions in cancer and polymorphisms in the human population. Our work has identified proteomic and genomic attributes that improve prediction of disease causing variants using machine learning methods. In this presentation, I will discuss our approach to identify regulatory and protein variants involved in disease. Furthermore, I will describe our efforts to annotate and describe disease causing genes and variants and our toolbox of computer science methods that we use to accomplish this.

Dr. Bob Horton : An Overview of Technologies for Biological Sequence Determination    November 11

Bob is director of the Cybertory project, a collection of educational molecular biology simulations ( and a virtual molecular biology laboratory ( He is co-inventor of a genetic engineering technique (PCR mediated gene recombination) that is widely used in the biopharmaceutical industry, particularly for "humanizing" monoclonal antibodies. He was the original author and editor of a monthly "Internet OnRamp" column in the journal BioTechniques, and has edited books on molecular biology ("Genetic Engineering with PCR", Horizon Scientific Press) and bioinformatics ("The Internet for Molecular Biologists", Oxford University Press).
Abstract: This will be an overview of classic, current, and emerging technologies for reading sequence information from biological polymers: protein, RNA, and (most importantly) DNA. We will examine techniques based on enzymatic polymerization, sequential degradation, ligation, and hybridization, as well as physical methods. Progress in microfabrication, robotics, and molecular detection are rapidly changing what we can think of as feasible. We study past as well as present approaches because older ideas often inspire future work. Since any experimentally determined measurement includes some degree of experimental uncertainty, we will consider general approaches to describing the probability of error in sequence data, and how this affects its interpretation. Finally, we will discuss some applications and implications of economical high-throughput sequencing to epigenomics, metagenomics, human genetics, and personalized medicine.
Bob's lecture slides

Dr. John Irwin: Interpreting protein structure to discover new small molecules for biology    December 2
John is an adjunct associate professor in the Department of Pharmaceutical Chemistry at the University of California San Francisco. His research focuses on developing tools for ligand discovery, and using those tools for biological research projects. He develops the ZINC database of commercially available compounds for virtual screening (, the DOCK Blaster virtual screening server ( and the DUD database for virtual screening benchmarking ( He is also part of the team that develops the Similarity Ensemble Approach for predicting the biological targets of molecules (
Abstract: Molecular docking is a pragmatic and widely-used technique for discovering new small molecules that bind to proteins. The program orients molecules in many poses in the protein binding site and evaluates the intermolecular interaction energy, ranking the database. Compounds chosen from the best scorers are purchased and tested experimentally. Although there are a growing number of successes of this approach, the method has numerous weaknesses that limit its usefulness. This talk will focus on our efforts to make molecular docking easier to use, more reliable, and more widely applicable
John's lecture slides