Russ Altman interviews distinquished innovators in the science and art of Biomedical Informatics. Altman interviewed Marcie McClure on February 24th, 2003 at Stanford University's School of Medicine. Marcie McClure's lectures are co-sponsored by UCSF's Biological and Medical Informatics Program,  
 
 
 

Bioinformatics Studies on the Evolution
Structure and Function of RNA-based life forms 


The first lecture will introduce RNA life forms (viruses and transposons) as fast evolving quasi-species that must use RNA as an intermediate in their lifecycles. Two computational virology problems will be described: 1) the use of motif detection methods to test the hypothesis that all RNA-dependent polymerases share common ancestry; and 2) ideas on the possibility of predicting amino acid contacts among a three viral protein replication/transcription complex by a combined use of protein disorder and evolutionary dynamic analyses without knowledge of structure.

View First Lecture + Questions and Answers
The second lecture will introduce the Retroid Agents that encode at least one gene in common, the reverse transcriptase. These agents have co-evolved with Eukaryotic genomes. A bioinformatic tool, the Genome Parsing Suite, will be introduced in the context of studying the nature of how, when and where Retroid Agents came to population genomes. The human genome was used as the model system in the development of this method and, surprisingly, statistically significant low-frequency reverse transcriptase signals, not previously reported, are detectable. These discovery-based results generate new hypotheses regarding Retroid Agents in the human genome.
View Second Lecture + Questions and Answers

Russ Altman Interviews Marcie McClure on Bioinformatics ~ View Interview (12 min.)

 
 
Marcie McClure
The recent recognition of Bioinformatics as an important and necessary area of scientific research and development, and the advent of multiple organismal sequencing projects demands innovative approaches in basic research. While development of software for meaningful large-scale analytical projects is necessary, the deposition of the results of Bioinformatics analyses in appropriate databases, thereby creating new research and development tools, is increasingly important. My Bioinformatic research agenda has two components: the analysis of life-forms that require an RNA replication intermediate in their lifecycle; and the assessment and development of tools necessary for studying large amounts of sequence information in a biologically meaningful manner.

Read more about Marcie and download her lab’s recent publications at the McClure Lab web site: http://shiva.msu.montana.edu/index2.html

 
 

Russ Altman
My primary interests are in the application of computing technologies to basic molecular biological problems, now referred to as bioinformatics. I am particularly interested in the analysis of protein and RNA structure and function, both in a problem-centered manner and on a functional genomic scale. My core work has been the development of probabilistic algorithms for the determination of protein structure from sparse and uncertain experimental data. These algorithms have been shown to have some advantages over other methods of structure determination including the ability to calculate not only a protein conformation, but also an explicit estimate of the uncertainty in the position of each atom.

For more information about Russ Altman, please visit his website:
http://smi-web.stanford.edu/people/altman/