Dahlquist:Courses

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This information can also be found at the Dahlquist Lab Courses page at Loyola Marymount University.

Fall 2010 Courses

Biology 201: Cell Function

Section BIOL 201-01 MWF 9:00-9:50 AM, St. Robert's 353

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)

Protein Structure Exploration exercises are hosted here on this wiki. NOTE: these are currently under construction.

Biology / Computer Science 367-01/ Honors 398-05: 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 on the CS network.

BIOL367/F10 site on this wiki

Spring 2010 Courses

Biology 398-01: Bioinformatics Laboratory

T 8:00 AM - 12:00 PM, Seaver 120

See course web site on this wiki.

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 MyLMU Connect, formerly known as Blackboard (or via MYLMU)

Previous Courses

• Fall 2009 Courses
  • Biology 201-01, -02: Cell Function
  • Biology / Computer Science / Honors 398-01: Biological Databases
    • Course wiki (for students in the course only).
• Spring 2009 Courses
  • Biology 478: Molecular Biology of the Genome
  • Honors 240-01: On the Nature of Things
    • Course Google Site (for students in the course only).
• Fall 2008 Courses
  • Biology 201-01: Cell Function
  • Biology / Computer Science / Honors 398-01: Biological Databases
    • Course web site
  • Biology 398-01: Bioinformatics Laboratory
    • Course Google Site (for students in the course only).

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:
  1. LaTulippe E, Satagopan J, Smith A, Scher H, Scardino P, Reuter V, and Gerald WL. Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res. 2002 Aug 1;62(15):4499-506.

• Review article on prostate cancer:
  2. Nelson WG, De Marzo AM, and Isaacs WB. Prostate cancer. N Engl J Med. 2003 Jul 24;349(4):366-81. DOI:10.1056/NEJMra021562 |

• 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.
  1. Launch GenMAPP.
  2. Select the menu item, Data > Download Data from GenMAPP.org
  3. Expand the "Expression Datasets" folder, and click on "Homo sapiens" to see the file.
  4. Check the box next to the filename.
  5. Click the Start button to download.