Dahlquist:Courses
This information can also be found at the Dahlquist Lab Courses page at Loyola Marymount University.
Fall 2009 Courses
Biology 201-01: Cell Function
Section BIOL 201-01 MWF 10:00-10:50 AM, Pereira 120
Section BIOL 201-02 MWF 12:00-12:50 PM, Pereira 200
Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.
Currents Students: For syllabus and course information login to MyLMU Connect, formerly known as Blackboard (or via MYLMU)
Biology / Computer Science / Honors 398: Biological Databases
T 4:30-7:00 PM, Doolan 219
Description: The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput fashion. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.
Currents Students: For syllabus and course information, login to the course wiki.
Spring 2009 Courses
Biology 478: Molecular Biology of the Genome
MW 1:00-4:50 PM, Seaver 207 and 215
Description: The completion of the Human Genome Project 50 years after Watson and Crick first described the structure of DNA marks a fundamental shift in the way we view ourselves and practice biology. This course will examine the fundamental concepts in molecular biology required to understand the biotechnology that has brought us to the genomics era and beyond. In the laboratory, students will become proficient in the basic techniques of molecular biology and then will get to work with cutting-edge genomics technology. Students will design and carry out a DNA microarray experiment. Students will then use bioinformatics tools to analyze their DNA microarray data and to model biological pathways and networks. By the end of this course, students will be working independently on a research project. Currents Students: For syllabus and course information login to Blackboard (or via MYLMU)
Honors 240-01: On the Nature of Things
MWF 10:00-10:50 AM, Seaver 202
Descripton: The purpose of this course is to examine the history, philosophy, and nature of scientific discovery, theory, and practice. The completion of the Human Genome Project 50 years after Watson and Crick first described the structure of DNA marks a fundamental shift in the way we view ourselves and in the way biology is practiced. Thus, we will focus on case studies of recent advances in biology, specifically biotechnology and genomics. Ultimately, we will explore the question, “How do I know that I know something?” Furthermore, in the popular media, "the genome is the new soul." We will explore biological (genetic) determinism in relation to what biologists really know about our genes. Currents Students: For syllabus and course information login to our Google Site.
Fall 2008 Courses
Biology 201-01: Cell Function
MWF 10:00-10:50 AM, Pereira 120
Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function. Currents Students: For syllabus and course information login to Blackboard (or via MYLMU)
Biology / Computer Science / Honors 398-01: Biological Databases
TR 9:25-10:50, Doolan 219
Description: The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput fashion. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own. Currents Students: For syllabus and course information, see the course web site or login to the wiki.
Problem Space: Analysis of Prostate Cancer DNA Microarray Data
- GenMAPP and MAPPFinder are available from http://www.genmapp.org
- Data for this exercise was published in this paper:
- Review article on prostate cancer:
- GenMAPP Prostate Cancer Exercise Part 1
- This is the link to the data file, <Hs_ED_ProstateCancer_edited.txt>, mentioned in step 3 of the protocol.
- GenMAPP Prostate Cancer Exercise Part 2 (MAPPFinder)
- This part of the exercise can be completed independently of Part 1 by downloading the GenMAPP Expression Dataset <Hs_ED_ProstateCancer_20060130.gex> from GenMAPP.org using the Data Acquisition Tool from within the GenMAPP program.
- Launch GenMAPP.
- Select the menu item, Data > Download Data from GenMAPP.org
- Expand the "Expression Datasets" folder, and click on "Homo sapiens" to see the file.
- Check the box next to the filename.
- Click the Start button to download.
Biology 398-01: Bioinformatics Laboratory
TR 3:00-5:00 PM, Seaver 120
Description: Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a “one gene at a time” approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include biological databases, sequence alignment and phylogeny, comparative genomics, protein structure prediction, modeling pathways and networks, and the analysis of high-throughput genomic and proteomic data. Currents Students: For syllabus and course information login to our Google Site.
