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485 lec1 general_introduction


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A general introduction to the genomics course

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485 lec1 general_introduction

  1. 1. Lecture 1: General Introduction Course 485 Introduction to Genomics
  2. 2. AIMS • You and I. • What is the class all about? • Class webpage and lectures. • Textbook and readings. • Attendance. • Lecturing style. • Exams and questions’ style. • Grade distribution. • Project details.
  3. 3. Who am I? • My name is Hasan Alhaddad. • Ph.D. in Genetics from UC Davis. • Studied insects and cats and does population and evolutionary genetics for fun. • I love science and I like to share this love with everybody especially you.
  4. 4. Where you find me? • My office is in 1KH room # 45. • My lab is in 2KH room # 103. • I mostly stay in the lab!
  5. 5. When you find me? • My office hours: TBA. • My email is: • • • If you cannot make it to office hours, email me and we can arrange an alternative time.
  6. 6. Who are you? State your name
  7. 7. Class Material and Announcements
  8. 8. Class Material and Announcements
  9. 9. Assigned Textbook • Buying and reading the book is your responsibility. • Please DON’T ask me if you need the book.
  10. 10. Resources I studied genomics at UC Davis and learned a lot from professors there. I will be adopting ideas and materials they provided for their lectures and shared via open sources, personal websites, and by direct contact.
  11. 11. Dr. Ian Korf
  12. 12. Dr. Keith Bradnam Twitter:@kbadnam
  13. 13. Lecturing Style • You will be RESPONSIBLE for the chapters’ readings. • I may use material that is not included in the book. Make sure you follow me in the class and check webpage frequently. • My powerpoint slides will be uploaded to class webpage (check table). It is YOUR JOB to print them and take notes during my lecture. • There are no stupid questions. So ask me and do not get lost.
  14. 14. Attendance I DON’T take attendance. You are a responsible student and you want to learn. No points only for showing up!
  15. 15. Testing style • My exams are composed of multiple choice, matching, and short answer questions. • Questions vary in difficulty. • Exams dates are fixed (see syllabus). • I WILL NOT change the dates of the exams. • If study and read the questions carefully, you can get a full mark.
  16. 16. Grade distribution Exam 1 20% 60% Exam 2 20% Data collection 10% Presentation 10% Final Exam 40% Total 100% Cumulative Final !
  17. 17. Your Project
  18. 18. Model Organisms
  19. 19. Danio rerio (zebrafish) Mus musculus (mouse) Arabidopsis thaliana (plant) Zea mays (corn) Bacteriophage (virus) Escherichia coli (intestines’ bacterium) Saccharomyces cerevisiae (budding yeast) Caenorhabditis elegans (worm) Drosophila melanogaster (fruit fly) Your Project Homo sapiens (You and I) • You will be (randomly) assigned a model organism. • You will get the genome paper of your model organism and all supplementary material.
  20. 20. Your Project • Links to the model organisms genome papers can be found on the class webpage. • You will select 2 additional genome papers of organisms that are closely related to your model organism. • One of the genome papers must be published after 2010.
  21. 21. Your Project • The three papers will be the base of your project. • During the course, I will be asking for items that you need to extract from the papers (for example: # genes, %GC et.) • The data for each organism will be collected from you periodically (worth 10% of your grade).
  22. 22. Your Project • You need to keep track of the data your collected. • If you fail to submit data when I ask for it, you will lose points. • Your objective is to compare between the three genomes of your related organisms in parameters defined later.
  23. 23. Your Project • You will be presenting your findings in oral presentation at the end of the semester (worth 10% of your grade). • DO NOT PANIC. • I will guide you to make your presentation a fun 15 min experience. • The data of all organisms will be jointly presented by me or my research students.
  24. 24. About the course I will use the chronology of findings in genetics and molecular biology as the base of a brief review of concepts needed for the course.
  25. 25. Expectations • You know me, my office location, my contacts and that my job is to teach and help you. • You understand your rights and responsibilities. • You understand my lecturing style, your project, and my grading system. • You know it is going to be a fun learning experience.
  26. 26. Disclaimer Figures, photos, and graphs in my lectures are collected using google searches. I do not claim to have personally produced the material (except for some). I do cite only articles or books used. I thank all owners of the visual aid that I use and apologize for not citing each individual item. If anybody finds the inclusion of their material in my lectures a violation of their copy rights, please contact me via email.