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Introduction to Protein Informatics Bioe C144/C244, Spring 2012 Lecture 1, part 1 Kimmen Sjölander

Introduction to Protein Informatics Bioe C144/C244, Spring 2012 Lecture 1, part 1 Kimmen Sjölander. Syllabus organization. Overview of genomics & biology (weeks 1-2). Predicting functional sites (week 9). Homolog identification & multiple sequence alignment (weeks 3-4).

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Introduction to Protein Informatics Bioe C144/C244, Spring 2012 Lecture 1, part 1 Kimmen Sjölander

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  1. Introduction to Protein InformaticsBioe C144/C244, Spring 2012Lecture 1, part 1Kimmen Sjölander

  2. Syllabus organization Overview of genomics & biology (weeks 1-2) Predicting functional sites (week 9) Homolog identification & multiple sequence alignment (weeks 3-4) Basic math/CS/stats concepts (week 5) Transmembrane helix prediction (week 12) Reconstructing evolutionary trees & ortholog identification (weeks 6-7) Protein structure prediction & hidden Markov models (week 8) Protein-protein interaction & pathway prediction (week 13)

  3. Grading • Grading: Exams (80%), short paper (10%), participation (discussion section and classroom) (10%). • Exams: Three in-class quizzes (15 points each) and a take-home final exam (35 points). Please check the posted dates and see KS immediately if you have conflicts with any dates so that we can try to accommodate your schedule. • Paper: Short (2-3 page) paper or grant proposal on a bioinformatics topic. Papers are due to KS on April 16 (hardcopy, in class).

  4. Constructing alignments and trees Predicting cellular localization Protein structure prediction & functional site identification Predicting orthologs and phylogenomic inference of function Prediction of biological pathways and networks Topics included in Bioe144

  5. Learn what’s going on under the hood Acquire the skills to develop new bioinformatics methods Learn how to use the most popular and powerful bioinformatics methods Explore biology Bioe C144/C244 and Bioe C144L/C244L

  6. "Nothing in Biology Makes Sense Except in the Light of Evolution" Theodosius Dobzhansky (1973)

  7. Adaptation at organismal level

  8. Evolution: finches

  9. Tree of life

  10. Revised tree of life including horizontal transfer Horizontal transfer Endosymbiosis Reticulate evolution

  11. Hominidae

  12. Our believed family tree (circa 1979)

  13. Orangutan Gorilla Chimpanzee Homo sapiens Baboon

  14. Phylogenomic methods of species tree estimation

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