Genomics and Bioinformatics GMS6231 (3 credits)

Transcription

1 Genomics and Bioinformatics GMS6231 (3 credits) COURSE DESCRIPTION: Principles of genomic characterization and bioinformatic analysis of eukaryotes, including an overview of analytical platforms, computational tools, experimental design, analysis methods and databases used to study DNA sequence, gene expression and protein levels. COURSE OBJECTIVES: Understanding the principles of genomic analysis of eukaryotes at various levels (DNA, mrna and protein), and bioinformatics methods used in these analysis. MEETING PERIODS: Tuesday (11:45-1:40) & Thursday (11:45-12:35) MEETING ROOM: UFGI 451A&B (4 th floor of UF Genetics and Cancer Research Complex, between the Cancer and Genetics wings) OFFICE HOURS: By appointment. COURSE WEBSITE: COURSE PREREQUISITE: STA6166 & STA6167 (Statistical Methods in Research I & II) and PCB5065 (Advanced Genetics) or permission from the instructor. COMPUTATIONAL RESOURCES ACCESS: The students need to complete a user agreement prior to be given access to the Fisher cluster. ( Access to the cluster is required for the course because several exercises will be done in the environment. User agreements need to be turned in during the first week of class. Students are also required to install JMP Genomics on their personal computers. The software is available from Taum Hanlon (taum@ufl.edu).

2 INSTRUCTORS: Dr. Sixue Chen Department of Biology College of Liberal Arts and Sciences Cancer & Genetics Research Complex, Rm. 438 Phone: (352) Dr. Lauren McIntyre Department of Molecular Genetics and Microbiology College of Medicine Cancer & Genetics Research Complex, Rm. 116 Phone: (352) Dr. Matias Kirst (Course leader) School of Forest Resources and Conservation College of Agriculture and Life Sciences Cancer & Genetics Research Complex, Rm. 320 Phone: (352) Dr. Alberto Riva Department of Molecular Genetics and Microbiology College of Medicine Cancer & Genetics Research Complex, Rm. 117 Phone: (352)

3 REFERENCES: A Primer of Genome Sciences (3 rd edition, 2009), by Greg Gibson and Spencer V. Muse, Sinauer Associates, ISBN: (required). Required reading will be indicated by the instructor throughout the semester. GRADES: 30% - Exams (genomics, transcriptomics and proteomics) 30% - Projects 30% - Paper discussions 10% - Class participation Paper discussion: For each paper discussion, students will be expected to write a summary of the strengths and weaknesses of the article. Strengths and weaknesses should be identified in two separate paragraphs of no more than 50 words each and no less than 35 words each. Assignments must be typed and printed out, and turned in at the start of the class period the paper is discussed. ed assignments will not count. Failure to have a printed copy at the start of class will result in a zero score for that assignment. Individual assignments will be graded on a scale of 0 to 10. For each grammar/spelling mistake one full point will be subtracted. You must proofread your assignment carefully before turning it in you may ask for colleagues to proofread your summary. Assignments will be graded on a progressively stricter scale as the semester progresses as students will be expected to improve in their ability to present thoughtful analyses of the literature. All of these mini-essays must be completely in your own words and quotations are to be avoided. ACADEMIC HONESTY. As a result of completing the registration form at the University of Florida, every student has signed the following statement: I understand that the University of Florida expects its students to be honest in all of their academic work. I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University. You are encouraged to review the universities materials on plagiarism and to take the online course at: The penalties for plagiarism are severe. In your professional career you may lose your job (see for a local example). In the case of this course, depending on the extent of the offense penalties will range from a zero on an assignment to failure for the course. In all cases, without exception, plagiarism will be officially reported both the individuals research mentor and to the graduate program creating a permanent record of academic dishonesty. ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES: Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of

4 Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodations. UF COUNSELING SERVICES: Resources are available on campus for students having personal problems or lacking clear career and academic goals, which interfere with their academic performance. These resources include: 1. University Counseling Center, 301 Peabody Hall, , personal and career counseling; 2. Student Mental Health, Student Health Care Center, , personal counseling; 3. Sexual Assault Recovery Services (SARS), Student Health Care Center, , sexual assault counseling; 4. Career Resource Center, Reitz Union, , career development assistance and counseling.

5 TENTATIVE CLASS SCHEDULE Week Day Topic (Instructor) 1 Jan 10 Introduction, 2 nd Generation DNA sequencing, DNA sequence alignment (K) Jan 12 Project: Short-read sequence mapping to a reference genome (Due Jan 27) (R) 2 Jan 17 3 nd Generation DNA sequencing (K) Jan 17 Project (cont.): Short-read sequence mapping to a reference genome (R) Jan 19 Paper discussion: Strategies for mapping short reads to a genome Jan 24 Genome sequencing and assembly (K) Jan 26 Genome structural annotation (R) 4 Jan 31 SNP genotyping tools and approaches (K) Feb 2 Paper discussion: SNP genotyping + review of first exercise 5 Feb 7 Association genetics (M+K) Feb 9 Project: Nucleotide variation detection (Due Mar 3) (R) Feb 11 Exam: Genome sequencing, assembly and annotation, and sequence diversity 6 Feb 14 Exercise: Association tests in JMP (Due Mar 3) (R) Feb 14 RNA-seq algorithms (M+R) Transcriptome analysis tools (M+K) Feb 16 Paper discussion: RNA-seq transcriptional variation (All) 7 Feb 21 Project: RNA-seq mapping (Due Mar 15) (R) Feb 21 Genome functional annotation (R) Feb 23 Differential gene expression and GLM (M) 8 Feb 28 Project: Transcriptome analysis (Due date TBA) (M+R) Mar 1 Project: Transcriptome analysis (Due date TBA) (M+R) Mar 2 Exam: Transcriptomics Mar3-10 Spring Break No Class 9 Mar 13 Proteomics Introduction (C) Mar 15 Protein separation and fractionation (C) 10 Mar 20 Mass spectrometry (C) Mar 22 Protein database and MS data analysis (C) 11 Mar 27 Proteomics applications (C) Mar 29 Introduction to Proteomics Databases (R) 12 Apr 3 ICBR Proteomics Lab visit Apr 3 Apr 5 Apr 7 Paper discussion: Proteomics Proteomics analysis tools (M) Exam: Proteomics 13 Apr 10 Comparative genomics Apr 12 Paper discussion: Comparative genomics 14 Apr 17 Comparative genomics Apr 19 Paper discussion: Comparative genomics 15 Apr 24 Course evaluation