Andrew D Smith PhD
Assistant Professor
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California
email: andrewds@usc.edu
phone: (213) 821-4142
Brief Bio
Prior to joining the Molecular and Computational Biology section at USC, I was a postdoc in Michael Zhang's group at Cold Spring Harbor Laboratory. From 2000 until 2004 I completed my PhD at the Faculty of Computer Science, University of New Brunswick. My PhD supervisor was Patricia Evans. The topics of my doctoral dissertation were algorithms and complexity analyses for certain problems of approximate pattern discovery in strings. During 2002 and 2003 I also worked in Elisabeth Tillier's lab at the Ontario Cancer Institute. I attended UNB as an undergrad from 1995 to 2000, completing a BA (major in psychology) and a BCS (Bachelor of Computer Science).
Open Positions
Information about open positions in my lab can be found here
Research Interests
- Genomics of transcriptional regulation and regulatory sequence analysis
- Algorithms and statistical methods for analyzing data from second-generation sequencers
- Models of molecular evolution for functional non-coding sequences
- Discrete algorithms and complexity (parameterized complexity and approximability)
Bioinformatics Software and Resources
- DME program for motif discovery
- CREAD suite of regulatory sequence analysis tools
- TCat tissue specific regulatory motifs
- RMAP program for mapping reads from the Solexa sequencer
- Simprot program for simulating protein evolution (available from Elisabeth Tillier)
