Dahlquist:Courses

Home        Research        Protocols        Notebook        People        Publications        Courses        Contact       

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

Fall 2011 Courses

Biology 201: Cell Function

Section BIOL 201-01: MWF 9:00-9:50 AM, Pereira 140

Section BIOL 201-03: MWF 10:00-10:50 PM, Pereira 207

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 368: Bioinformatics Laboratory

Section BIOL 368-01: W 1:00-4:50 PM, Seaver 120

BIOL368/F11 site on this wiki

Previous Courses

• Spring 2011 Courses
  • Biology 398-01: Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics
    • BIOL398-01/S11 site on this wiki
• Fall 2010 Courses
  • Biology 201-01, -02: Cell Function
    • 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
    • Course wiki on the CS network
    • BIOL367/F10 site on this wiki
• Spring 2010 Courses
  • Biology 398-01: Bioinformatics Laboratory
    • See BIOL398-01/S10 site on this wiki.
  • Biology 478: Molecular Biology of the Genome
• 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.