Monday, December 9
4pm, CSIC 1115
University of Maryland

Abstract

In 2001 Eric Davidson published his "Genomic Regulatory Systems"
book where he reports on 30 years of work, together with his colleagues,
on purple sea urchin. Their work provided a general experimental framework
for the study of a gene¹s cis-regulatory region (an upstream DNA sequence
containing a series of consecutive binding sites). Their approach consisted
of systematic, almost exhaustive, series of mutations of individual binding
sites, together with the associated measurements of the transcription rates.
By quantitative analysis, they were able to infer a complete set of minimal functional units of regulation and their interrelations. They proceeded hierarchically to uncover "modularity" and "hardwired information processing
logic" of a gene¹s cis-region. Most of their work was focused on the endo16
gene. Their extraordinary technology and the inference of the underlying
"network" for this gene resulted in the most completely understood
transcriptional system to date.

It is quite remarkable how combinatorial and robust their approach is. We
will present an analysis and a mathematical formalism for the Davidson
transcriptional network inference technology. We will also present a glace
into our recent work with Eric Davidson towards the identification of the
regulatory "programming language."

Monday, October 14
4pm, CSIC 1115
University of Maryland

Abstract

The human genome has been called the "book of life," a natural extension of the long-standing metaphor of DNA as a language. Taking this conceit seriously, we can ask to what extent the genome may profitably be viewed as a work of literature, subject to critical exegesis. While seemingly at opposite poles from the "hard science" of molecular biology, in fact such an approach is not so far from the increasingly hermeneutic role of the bioinformatician, insofar as both are concerned with comparing texts, detecting subtle patterns and relationships, elucidating theme and variation, etc. In this talk I will explore literary and linguistic aspects of the genome, by means of a "genomic" textual analysis of Lewis Carroll's Jabberwocky.

Wednesday, December 4
3pm, AVW 1112
University of Maryland

Abstract

There seems to be no question that biologists believe sequence comparison is useful. The BLAST server at NCBI alone performs over 70,000 database searches daily and over 120,000 scientific papers refer to some aspect of biological sequence comparison. Furthermore, one of the most compelling yet implicit justifications for the investment in high throughput genome sequencing projects has been the expectation that many of the gene products within this growing inventory will match previously studied proteins.

It was not always so - the first papers describing useful discoveries from sequence database searches often termed this detection of evolutionary relationships as "serendipitous" or "unexpected". Subsequent studies on protein sequences and structures showed that detectable conservation over hundreds of millions and even billions years of evolution is a rule, rather than an exception, in biology. Extrapolations made by several groups using different methods suggested that there are only about 1000 basic protein folds and a complete classification of all protein families is a realistic goal for the near future.

Though we don't yet know why most proteins evolve so slowly, it is important to realize that the conservative mode of protein evolution determines our very ability to make sense out of genome comparisons and that theoretical and empirical studies in molecular evolution are directly relevant for the practical goals of functional genomics. I will review some notable case stories from the early days of database searching and our growing understanding of the universe of protein families.

Friday, December 14
Primer 10:15-10:55
Seminar 11:00-12:00
3258 A.V. Williams Bldg
University of Maryland

There are numerous online databases of sequence data--genomic DNA, cDNAs, open reading frames, and proteins. The sequencing of the entire genomes of over 800 organisms have been completed and the sequences placed online, including drosophila (fruit fly), human, mouse, and arabidopsis (thale cress). Numerous microarray gene expression data sets are also available through the Internet. This abundance of biological data demands computational resources for managing, searching, analyzing, and mining that data, giving rise to the interdisciplinary field of bioinformatics. Bioinformatics, in turn, presents major new career and research opportunities for computer scientists.

In this talk, we give an overview of some of the key biological concepts needed by computer scientists to understand the challenges and opportunities of bioinformatics. We will also give a succinct list of the bioinformatics challenges we currently find most interesting in our bioinformatics group.

SEMINAR ABSTRACT:
(50 minutes)
In this talk, we discuss the application of microarray technology and bioinformatics to studying successful resistance of loblolly pine trees to drought stress. Microarray technology gives biologists access to information about gene expression for thousands of genes simultaneously. The computational component of the study is supported by an NSF-funded project named Expresso. Expresso is a problem solving environment that is being developed by computer scientists at Virginia Tech to support the management of the process of microarray experiment design, data capture, and data analysis. It is being developed in parallel with several biological studies involving microarray technology, including a large study of drought stress in pine. We describe both that biological study and the computational ideas being developed by our bioinformatics collaborators at Virginia Tech and elsewhere.

Wednesday, December 5
2:00 PM
1112 A.V. Williams
University of Maryland

October 4, 2001
10:00 AM
2460 A.V. Williams
University of Maryland