BME 225 Function in Biology and Bioinformatics

• Lecture 1 (introduction): Course overview and introductory remarks; HW1 assignment. (pdf)

• Lecture 2 (function classification schemes): 2a, Overview and Enzyme Classification (E.C.) scheme, a little about FunCat (MIPS); 2b, GO (Gene Ontology) and other "proper" Ontologies (= more than standardized vocabularies of terms). ( 2a.pdf | 2b.pdf)

• Project assignment, see link from front page for list of suggested servers. (pdf)

• Lecture 3a (enzymes): 3a, Preparatory/grounding lecture; more to follow upcoming class sessions. ( 3a.pdf)

• Lecture 3b (enzymes): 3b, overview of enzyme function and regulation. (3b.pdf)

• Lecture 3c (enzymes): 3c, mechanisms (including voluntary additional "hands-on" problems). (pdf)

• Hands-on In-class Exercise of Oct22+27+29 (link)

• Lecture 3d (enzymes): 3d, systematic/recurring aspects in enzyme mechanisms. (pdf)

• Paper Discussion Nov 3: Bartlett et al. 2002. J Mol B iol 324:105-121 (also of interest but not discussed on slides: Gutteridge et al. 200 3. J Mol Biol 330:719-734). (pdf)

• Lecture 4 (DNA-binding proteins): DNA-binding proteins overview + a bit of hands-on. (pdf)

• Lecture 5 (Orthology prediction; slides extracted from a talk by Ann-Charlotte Berglund-Sonnhammer, Uppsala): Orthology prediction overview. ( pdf)

• Method Discussion Nov 24: Kimmen SjÃlander's group's PhyloFacts"

Please direct any enquiries to Dietlind Gerloff (gerloff@soe.ucsc.edu; 9x4833; PSB320)