GMS6181 - Genomics and Bioinformatics

(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 (10:40-12:35) & Thursday (10:40-11:30).

WHERE: UFGI 451A (4th floor of UF Genetics and Cancer Research Complex, between the Cancer and Genetics wings).

OFFICE HOURS: By appointment.

COURSE WEBSITE: http://bioinformatics.ufl.edu/courses/GMS6181/

COURSE PREREQUISITE: STA6166 (Statistical Methods in Research I) and PCB5065 (Advanced Genetics), or permission from the instructor.

COURSE SYLLABUS: Download here.

REFERENCES: Books:

A Primer of Genome Sciences (2nd edition, 2004), by Greg Gibson and Spencer V. Muse, Sinauer Associates, ISBN: 0878932321 (required textbook).

Discovering Genomics Proteomics and Bioinformatics (2nd edition, 2005), by A. Malcolm Campbell and Laurie J. Heyer, Cold Spring Harbor Laboratory Press and Benjamin Cummings, ISBN: 0805347224.

LECTURE SLIDES: Week 1 - DNA sequencing methods
Week 2 - Introduction to Bioinformatics
Week 2 - Computational Gene Discovery
Week 3 - DNA sequence alignments
Week 3 - Genome sequencing and assembly
Week 4 - Genetic Variation
Week 4 - SNP Genotyping platforms
Week 4 - SNP-based association
Week 5 - Population structure
Week 6 - Disequilibrium
Week 7 - Array image analysis
Week 9 - Transcriptome analysis
Week 10 - Proteomics (1)
Week 13 - Genome annotation

PROGRAMS AND DATASETS:
(password required) Structure 2.1 Installation
SNP Genotype Data
Linkage Calculator (Excel)
Tabulator (Excel)
Dataset for JMP Genomics demo
Comparative genomics to link gene and function (Examples)

PAPERS:
(password required)

Verhoeven KJF, Simonsen KL and McIntyre LM. Implementing false discovery rate control: increasing your power. Oikos 2005; 108: 643-647.

Morley M, Molony CM et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430, 743-747.

Yu J, Holland JB et al. Genetic Design and Statistical Power of Nested Association Mapping in Maize. Genetics 2008; 178: 539-551.

Yu J, Pressoir G et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 2006; 38(2):203-8.

Fu J, Swertz MA et al. MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nature Protocols 2007; 2(3):685-94.

Keurentjes JJB, Fu J et al. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. PNAS 2006; 104(5):1708-1713.

de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. 2007 Jul 23;8:245. (Pubmed)

El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. 2006 Dec 8;281(49):37586-93. (Pubmed)

Hanauer DA, Rhodes DR, Sinha-Kumar C and Chinnaiyan A. Bioinformatics Approaches in the Study of Cancer. Current Molecular Medicine 2007, 7, 133-141.

PROBLEM ASSIGNMENTS:
INSTRUCTORS:
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) 846 0900
e-mail: mkirst@ufl.edu

Dr. Sixue Chen
Department of Botany
College of Liberal Arts and Sciences
Cancer & Genetics Research Complex, Rm. 438
Phone: (352) 392 3277
e-mail: schen@ufl.edu

Dr. Lauren McIntyre
Department of Molecular Genetics and Microbiology
College of Medicine
Cancer & Genetics Research Complex, Rm. 116
Phone: (352) 273 8024
e-mail: mcintyre@ufl.edu

Dr. Alberto Riva
Department of Molecular Genetics and Microbiology
College of Medicine
Cancer & Genetics Research Complex, Rm. 117
Phone: (352) 273 6582
e-mail: ariva@ufl.edu
GRADES: Each section worth 20% of the final grade. Grading of each section will be defined by the instructor in the beginning of the section. Grading of Section "Genome Sequencing" will be calculated from two weekly (5% each) and one final session project (10%).

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".

ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES: Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of 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:

University Counseling Center, 301 Peabody Hall, 2-1575, personal and career counseling;

Student Mental Health, Student Health Care Center, 2-1171, personal counseling;

Sexual Assault Recovery Services (SARS), Student Health Care Center, 2-1161, sexual assault counseling;

Career Resource Center, Reitz Union, 2-1601, career development assistance and counseling.

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 (10:40-12:35) & Thursday (10:40-11:30).
WHERE:	UFGI 451A (4th floor of UF Genetics and Cancer Research Complex, between the Cancer and Genetics wings).
OFFICE HOURS:	By appointment.
COURSE WEBSITE:	http://bioinformatics.ufl.edu/courses/GMS6181/
COURSE PREREQUISITE:	STA6166 (Statistical Methods in Research I) and PCB5065 (Advanced Genetics), or permission from the instructor.
COURSE SYLLABUS:	Download here.
REFERENCES:	Books: A Primer of Genome Sciences (2nd edition, 2004), by Greg Gibson and Spencer V. Muse, Sinauer Associates, ISBN: 0878932321 (required textbook). Discovering Genomics Proteomics and Bioinformatics (2nd edition, 2005), by A. Malcolm Campbell and Laurie J. Heyer, Cold Spring Harbor Laboratory Press and Benjamin Cummings, ISBN: 0805347224.
LECTURE SLIDES:	Week 1 - DNA sequencing methods Week 2 - Introduction to Bioinformatics Week 2 - Computational Gene Discovery Week 3 - DNA sequence alignments Week 3 - Genome sequencing and assembly Week 4 - Genetic Variation Week 4 - SNP Genotyping platforms Week 4 - SNP-based association Week 5 - Population structure Week 6 - Disequilibrium Week 7 - Array image analysis Week 9 - Transcriptome analysis Week 10 - Proteomics (1) Week 13 - Genome annotation
PROGRAMS AND DATASETS: (password required)	Structure 2.1 Installation SNP Genotype Data Linkage Calculator (Excel) Tabulator (Excel) Dataset for JMP Genomics demo Comparative genomics to link gene and function (Examples)
PAPERS: (password required)	Verhoeven KJF, Simonsen KL and McIntyre LM. Implementing false discovery rate control: increasing your power. Oikos 2005; 108: 643-647. Morley M, Molony CM et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430, 743-747. Yu J, Holland JB et al. Genetic Design and Statistical Power of Nested Association Mapping in Maize. Genetics 2008; 178: 539-551. Yu J, Pressoir G et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 2006; 38(2):203-8. Fu J, Swertz MA et al. MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nature Protocols 2007; 2(3):685-94. Keurentjes JJB, Fu J et al. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. PNAS 2006; 104(5):1708-1713. de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. 2007 Jul 23;8:245. (Pubmed) El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. 2006 Dec 8;281(49):37586-93. (Pubmed) Hanauer DA, Rhodes DR, Sinha-Kumar C and Chinnaiyan A. Bioinformatics Approaches in the Study of Cancer. Current Molecular Medicine 2007, 7, 133-141.
PROBLEM ASSIGNMENTS:
INSTRUCTORS:	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) 846 0900 e-mail: mkirst@ufl.edu Dr. Sixue Chen Department of Botany College of Liberal Arts and Sciences Cancer & Genetics Research Complex, Rm. 438 Phone: (352) 392 3277 e-mail: schen@ufl.edu Dr. Lauren McIntyre Department of Molecular Genetics and Microbiology College of Medicine Cancer & Genetics Research Complex, Rm. 116 Phone: (352) 273 8024 e-mail: mcintyre@ufl.edu Dr. Alberto Riva Department of Molecular Genetics and Microbiology College of Medicine Cancer & Genetics Research Complex, Rm. 117 Phone: (352) 273 6582 e-mail: ariva@ufl.edu
GRADES:	Each section worth 20% of the final grade. Grading of each section will be defined by the instructor in the beginning of the section. Grading of Section "Genome Sequencing" will be calculated from two weekly (5% each) and one final session project (10%).
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".
ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES:	Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of 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: University Counseling Center, 301 Peabody Hall, 2-1575, personal and career counseling; Student Mental Health, Student Health Care Center, 2-1171, personal counseling; Sexual Assault Recovery Services (SARS), Student Health Care Center, 2-1161, sexual assault counseling; Career Resource Center, Reitz Union, 2-1601, career development assistance and counseling.