Written by Dr. Tom Schneider, Mentor to Theodore Nikolaitchik
Gene Regulation and Chromosome Biology Laboratory
Theo Nikolaitchik joined my group in the Gene Regulation and Chromosome Biology Laboratory in the summer of 2013 through the Werner H. Kirsten Student Intern Program.
Previous SIP students have built bioinformatics tools and have made a number of scientific discoveries. One of the most important was Mike Stephens and I inventing sequence logos,
which are now widely used to show patterns in DNA, RNA, and proteins.
All of our work is based on the mathematics underlying modern communications systems and information theory, developed at Bell Labs by Claude Shannon and published in 1948.
I discovered that this mathematics is a perfect fit to biological systems, with a wide variety of applications, including predicting the effect of sequence changes on
RNA splicing in various diseases such as the skin cancer Xeroderma Pigmentosum.
Theo is using our information-theory based tools, including sequence logos and sequence walkers, to construct a model of CTCF. CTCF is involved in chromosome structuring,
blocks RNA polymerase, and creates a boundary between active and inactive DNA. With luck we will build and verify a model of CTCF. We are collaborating with the laboratory
of Mikhail Kashlev who will be able to test our model.