CSU Pomona

Bioinformatics Program

Biology 499 Overview:

Purpose and Prerequisites for this Course:

This course presents a broad overview and introduction to the cell and molecular domains of the 

new field of bioinformatics. It is part of an intended three-course series and so will not contain an

introduction to the field, ecological, or phylogenetic domains of bioinformatics. We would like to 

acknowledge that a grant from CSUPERB (the California State University Program for Education 

and Research in Biotechnology) helped fund preparation for the course and purchase of the 

computer lab.Although we will provide brief introductions, we recommend that students already 

have a good foundation in genetics, evolution, and a strong interest in computers and their use 

in computational and systems biology before taking this course. 

Lecturers:This first test offering of Bioinformatics will be team-taught by five professors from

three departments, Biology, Chemistry, and Computer Science. They are:

· Dr. Len Troncale (Cell and Molecular Biology)

· Dr. Wei-Jen Lin (Microbiology)

· Dr. Dennis Livesay (Biochemistry)

· Dr. Chung Lee (Computer Science)

· Dr. Sep Eskandari (Physiology & Functional Genomics)

Bioinformatics is a rapidly developing, rigorously interdisciplinary new specialty, and we believe 

that this team approach will result in better coverage. Each professor will present two weeks of 

lecture.

Guiding Questionsanswered in this course include:

· What is the history of bioinformatics and can we trace trends for its future development from study 

of its recent development?

· How does bioinformatics incorporate and use the fundamental concepts of genome, genetic information 

transfer, the molecular biology of DNA, RNA, and proteins, and the fundamental principles of molecular 

evolution?

· What is the present utility of bioinformatics to basic research in medicine and biology?

· What are the differences between genomics, proteomics, and physiognomics?

· What is the practical economic and professional development benefit of student specialization in 

bioinformatics?

· How can a student use the techniques and tools of bioinformatics in conducting their own undergraduate 

or graduate research at Cal Poly Pomona?

· Which are the main bioinformatic databases and what are their basic features?

· What is the meaning and significance of the plethora of acronyms used in bioinformatics?

· What are the most useful sequence analysis software tools and how can I use them?

· What are the most useful sequence alignment techniques and how can I use them?

· What are the most useful gene identification tools and how can I use them?

· How is bioinformatics used to build molecular phylogenies?

· How is bioinformatics used to explore protein families, superfamilies, and motifs?

· How can we discover relationships between stereo structures or simulate protein structure?

· How do computer algorithms work to accomplish the searches and comparisons of bioinformatics?

· How do bioinformatic algorithms relate to SQL, JAVA, MS-Access and other software domains?

· What are the current research questions in comparative physiological networks (physiological 

genomics)?

· What techniques and tools can I use to study interactions among protein products and regulatory 

elements?

· What are the meanings of functional genomics and pharmacogenetics?

· What are the biological uses of functional genomics and pharmacogenetics?

What is bioinformatics?

Bioinformatics is the application of computer technology to the management of biological 

information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. The 

need for Bioinformatics capabilities has been precipitated by the explosion of publicly available 

genomic information resulting from the Human Genome Project. The goal of this project – 

determination of the sequence of the entire human genome (approximately three billion base pairs) - will be reached by the 

year 2002. The science of Bioinformatics, which is the melding 

of molecular biology with computer science, is essential to the use 

of genomic information in understanding human diseases and in 

the identification of new molecular targets for drug discovery. In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting 

of computational biologists and bioinformatics computer scientists. 

Such groups will be key to unraveling the mass of information 

generated by large scale sequencing efforts underway in 

laboratories around the world.

What is the Human Genome Project?

The U.S. Human Genome Project (HGP), composed of the DOE and NIH Human Genome 

Programs, is the national coordinated effort to characterize all human genetic material by 

determining the complete sequence of the DNA in the human genome. The HGP's ultimate 

goal is to discover all the more than 30,000 human genes and render them accessible for 

further biological study.Click here to learn more …

The Bioinformatics Gold Rush: A $300-million industry has emerged around turning 

raw genome data into knowledge for making new drugs.

http://www.sciam.com/2000/0700issue/0700howard.html