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Syllabus For: PSGA-PLSS-PLB 426 Genomics and Bioinformatics
Credit Hours: 4 Meeting times: Tuesdays & Thursdays: 10-11:50 AM Instructor:
Khalid Meksem, PhD (click to go to
faculty page)
Catalogue description: The course is designed to introduce students from a variety of backgrounds and departments to the scope and methodology of genomic and bioinformatic sciences. Real problems and solutions from genome data analysis are studied in this course to see how high throughput genomics is driving bioinformatics, and changing the biological sciences in revolutionary ways.
Prerequisites: Enrollment in this course is by "consent of instructor". Please contact Dr. Khalid Meksem) meksemk@siu.edu. One course in the principles of genetics or biology is required.
Justification The Saint Louis and Chicago area is becoming the silicon valley of genomics and bioinformatics. Public as well as private sectors are increasing their demand for trained employees in this field. There are no courses for genomics and bioinformatics at SIUC. The course aims to teach the conceptual foundations for the student to be able to gain an understanding of genomics, bioinformatics and the challenge of the new era of life science methodologies. It seeks to teach this material through real problems and examples of solutions in agriculture, biology and medicine.
Objectives: The course is designed to introduce students from a variety of backgrounds to the scope and methodology of genomic sciences. It will cover genomics technologies, data and bioinformatics technologies. Examples from genome data analysis will be studied (e.g. "Gene sequencing, Gene Chips and genome-wide expression arrays), to demonstrate how the high throughput genomics data are driving bioinformatics, and changing the biological sciences in revolutionary ways. The course aims to teach the conceptual foundations of genomics, bioinformatics and the challenge of the new era of life science methodologies, through real problems and examples of solutions in agriculture and medicine.
Course Textbooks: We will use the following textbooks, plus additional material for many of the lectures that will be distributed in class. A Primer of Genome Science by Greg Gibson, Spencer V. Muse; ISBN: 0-87893-234-8
Recommended:
Genomes, 2nd Edition
By Terence A. Brown (Editor) Web resources: http://www.genome.ad.jp/ http://www.ncgr.org/ http://www.iscb.org/ http://www.genomicshelp.com/ http://www.tigr.org http://www.ncbi.nlm.nih.gov http://pedant.mips.biochem.mpg.de/frishman/pedant.html http://www.nbif.org
Basis for Grading: Grades will be based on: Regular attendance and active participation in class, completion of assignment(s) and exams 15% midterm exam, 35% final exam, Oral Presentation: 30%. (30 min PowerPoint Presentation) Term Paper: 20% (Topics can be related, but not identical to your oral presentation). Grading scale +90 to 100% A +80 to 89% B +70 to 79% C +60 to 69% D +60 and below F
Topical Outlines
Topic 1. Introduction to Genomics: The course proposed aims to enroll a variety of students from different backgrounds. Some of the students may have never been exposed to genomics before, so the first topic will be an introduction that aims to bring all the students to a certain level.
Topic 2. Genetic mapping: Although “Genetic Markers” is taught in different classes and colleges, the development of the genomic science is changing the way we view genetic markers. We will develop the subject from traditional genetics methods to the new sequencing based genetic markers such as: SNPs (Single Nucleotide Polymorphism), Indels (Insertion-Deletions), SCAR based AFLPs. We will compare the technologies used to score the polymorphism.
Topic 3. Physical mapping: Physical mapping can be divided into several sections that can be taught at different levels in different colleges, including: Science, Medicine, Agriculture and Engineering. However, the topic will focus on genomic methods for physical mapping utilizing BACs Bacterial Artificial Chromosomes and YACs Yeast Artificial Chromosome. We will discuss fingerprinting based methods that are combined with software such as FPC developed at the Sanger Center (UK). The utility of physical mapping for genome sequencing, genome structure, organization and comparative genomics will be discussed.
Topic 4. Genome sequencing: The technology is becoming a standard method for gene discovery in the 21st century, with the Human, Nematode, Arabidopsis and some plant pathogens genomes fully sequenced and the rice and several other agriculturally important genomes in the pipeline. It is becoming necessary to teach the class through some practical studies of sequencing, to familiarize the students not only with the chemistry and methods used for sequencing but also with the hardware and software used to generate contigs based on overlapping sequences
Topic 5. Proteomics: Will be described as a tool for gene function discovery and drug development. Proteomics is a key discipline in teaching the science of the genome and its organization, structure, functionality and integrity. The topic aims to introduce the students to the utility of Proteomics in the integrity and communication of the genome. The goal is to supplement this topic through seminars organized with the faculty members of other colleges
Topic 6. Functional genomics: Relating genes to phenotypes and vice versa is a challenging step in genetics and molecular biology. We will discuss some of the methods developed in the past decade, “gene knockout” by homologous recombination where the function of the gene can be assigned based on the analysis of the mutant phenotype. The factors limiting the adoption of the knockout techniques will be discussed; alternatives such as gene silencing and DNA chips based expression profiling will be described.
Topic 7. DNA chips: The topic aims to describe the value of this approach, its propensity for miniaturization, allowing huge numbers of gene fragments to be analyzed in parallel. For example, DNA fragments corresponding to the entire set of more than 10,000 Arabidopsis open reading frames could be contained on a single 18- _x 18-mm microscope slide (5). We will discuss the Chip production and reading and gene expression arrays.
Topic 8. High-throughput and automation: A magnificent tool kit is becoming available through the Human and Arabidopsis genome projects. We will discuss how the developed tools, robot and technologies will dramatically improve the quality of research in all disciplines of biology, the challenge in the next decade in building integrated databases and intelligent software tools required for the efficient mining of this wealth of information.
Topic 9. Introduction into Bioinformatics: The proposed topics in Bioinformatics are considered more of an introduction than an advanced course. It will serve to introduce the students to the science and algorithms behind the advanced programs used in Bioinformatics. The goal is to introduce the students to the use of computer based software to analyze DNA and protein sequences data. Databases such as GeneBank, EMBL SwissProt and data mining tools such as Blast and Fasta will be the major focus of the proposed bioinformatics topic. |