The National Science Foundation has awarded Graduate Research Fellowships to Ph.D. students Gabriel Pratt and Kunal Bhutani in the Bioinformatics Graduate Program.
The Program and everyone who knew him was saddened today by the news of the passing of Professor Virgil Woods, an innovator of mass spectrometry and structural bioinformatics, and an engaging colleague, advisor and committee member to several of the Program students.
Wednesday, May 29th
Ph.D. Defense: Marcus Kinsella
- Start time: 10:00am
- End date: Thursday, May 30th
- End time: 12:00pm
- Where: Fung Auditorium, PFBH
UCSD Bioinformatics and Systems Biology Graduate Program
Ph.D. Dissertation Defense Announcement
"Computational Tools to Investigate Structural Variation"
Wednesday, May 29, 2013
Location: Fung Auditorium
Powell-Focht Bioengineering Hall
Chair: Vineet Bafna
Co-Chair: Kelly A. Frazer
The importance of structural variation as a source of phenotypic variation has become more and more apparent in recent years. At the same time, tools and techniques that detect structural variation using high-throughput data have proliferated. These trends have spurred interest in making increasingly sophisticated inferences about structural variation, including identifying complex or difficult to observe variants and elucidating the biological mechanisms that produce structural variants.
In this talk, we identify several challenging problems in the investigation of structural variation and discuss computational techniques that solve them. First, we examine the discovery of fusion genes in the transcriptome using paired-end reads, a task complicated by reads that have multiple mappings. We demonstrate a method to resolve these ambiguous mappings and increase the sensitivity of fusion gene detection. Second, we investigate whether the breakage-fusion-bridge mechanism leaves a reliable footprint in high-throughput data. Using novel algorithms and simulation, we identify the surprisingly limited circumstances when the presence breakage-fusion-bridge can be inferred. Finally, we examine evidence for the phenomenon known as chromothripsis, the shattering and reannealing of chromosomes. We show that there are alternative hypotheses that can account for the structural variation patterns that form the currently proposed signature of chromothripsis.