COMPUTATIONAL MOLECULAR BIOLOGY
A Two Semester Course
at
UFC
2007
Instructor: Basilis Gidas
Brown University
USA
Location and Time:
We will have an organizational meeting on Monday March 12, 14:00 horas, sala dos
seminarios, premiero andar no Departamento de Matematica, Bloco 914. In this
meeting we will decide the day and time of the class. The class will meet one day a week for
three hours with an interval of 15 minutes.
Contact: Basilis Gidas
Sala 01, Departamento de Matematica, Bloco 914
fone: 085/96030663, e-mail: gidas@mat.ufc.br, gidas@dam.brown.edu
Course Description
With the availability of genomic, expression (microarray), ChIp-chip, structural, mass spectrom-
etry, and other biological data, modern molecular biology depends increasingly on detailed math-
ematical modeling, and mathematical/computer science/ statistical tools and algorithms for the
analysis and interpretation of the data. Basic objectives of molecular biology include: (a) Ge-
nomics: sequencing and comparing the genomes of different species, finding the genes,discovering
transcription factors motifs and other patterns in a genome, and constructing phylogenetic trees,
(b)Functional Genomics: microarray data analysis and clustering of genes and experiments, reg-
ulation of gene transcription and other biological processes, determining gene networks on the
basis of microarray data, ChIp-chip data, and cis-regulatorymodules information, (c)Proteomics:
determining protein identification and signal transduction pathways on the basis of tandem mass
spectrometry and immunoprecipitation information, (c) Structural Proteomics: determining the
structure and function of proteins, understanding protein complexes and DNA-protein com-
plexes, ligand-receptor coupling, docking, and drug design, (d) RNA structure: predicting RNA
secondary structure.
The study of these problems has involved mathematical tools, models, and algorithms from
Bayesian Statistics, Learning Theory and Data Mining, Decision Theory, Computer Science,
and even Algebraic Geometry.