Biological context networks:
viewing biology via multiple functionalities and milieux

Simon Kasif
Boston University


In this talk we will focus on
the need to build new methodologies for studying
the vast diversity of molecular mechanisms found in nature.

For various historical reasons much of bionformatics research,
originating from sequence alignments has been focused on identifying
conserved domains, conserved  motifs and conserved networks.

While SNPs and polymorphisms have been a major focus for biological and
clinical research, this research is primarily aimed at understanding
micro-evolution and its profound implications.

It is much more challenging to identify relationship among fast evolving
genes and systems.

We describe our preliminary research aimed at elucidating or modeling such
mechanisms, their biological implications and the challenges involved in
in this study.

Speculating and using the analogy between biology and language, both
evolutionary artifacts, we hypothesize a heavy tail (Zipf) distribution
over frequencies of basic components found in nature.

Consequently if we only focus on the highly conserved, we will learn a
a relatively significant but incomplete parts of biology which are by
some measure already reasonably "well" understood.

This research is in parts joint work with Richard J. Roberts
Charles Cantor, Zak Kohane, Yu Zheng, John Rachlin, Noga Alon.