Quantitative Biology & Modeling Courses
Indexed by Department

Biochemistry and Molecular Biology

Chemical Engineering

Chemistry

Computer Science and Engineering

Genetics
Mathematics

Microbiology
Physics and Astronomy
Plant Biology

Statistics and Probability

Past Courses

• BCH 960 Genomics and Proteomics of Complex Genetic Systems
  • Provide students with a current overview of developments in the areas of structural and functional genomics/proteomics.
  • Examples from eukaryotic (animal, plant, and fungi) and, in some cases, prokaryotic organisms will be covered.
  • One emphasis will be on the demonstration of available Internet resources.
  • Prerequisites: BCH801 (or instructor approved equivalent)
  • Taught by: Christoph Benning, Dean DellaPenna, Doug Gage, John LaPres, Tim Zacharewski
  • Course: Sect. 1, 2 credits, offered every fall
  • Course: Syllabus
  • Contact: Christoph Benning benning@msu.edu

• BMB 960-001/CHE 891-003/PLB 802-002
  From Analysis of Metabolism to Systems Biology
  • Multidisciplinary approach to understanding how metabolic networks are analyzed, regulated, and manipulated
  • Course: 2 credits, offered Spring 2006
  • Course: Tuesdays & Thursdays 9:10-10:00a.m.
  • Complete Course Description
  • Taught by: Christoph Benning, Christina Chan, Syed Hashsham, Yair Shachar-Hill, and Claire Vieille

• BMB 960/GEN 800/CMB 800 Analysis of Transcriptional Networks
  • Seminar will focus on current examples from literature of network analysis and modeling in bacterial and eukaryotic systems, presented by students and instructors
  • Introductory material tailored for students from both biological and mathematical/statistical areas so both areas will profit.
  • Course will complement a Genetics Symposium to be held in May 2006 on this topic
  • Course: 2 credit course, offered spring 2006
  • Course: Meets Wednesday or Friday, depending on room availability, at 2:30p.m.
  • Complete Course Description
  • Taught by: David Arnosti, Lee Kroos, and Chichia Chiu
  • Contact: David Arnosti arnosti@msu.edu

• BMB 961 Computational Genomics Laboratory (Graduate Bioinformatics Course)

• Hands-on course on the computer analysis of DNA and protein sequences as well as microarray data.
• 50% of class time dedicated to PERL programming techniques to automate and simplify the analysis of large data sets.
• General topics include:
  1. Introduction to the UNIX operating system
  2. DNA sequence analysis using the GCG package of programs
  3. Assembly of genomic DNA sequencing projects using the Staden software suite
  4. Mutation/SNP analysis using the Staden software suite
  5. Database searching and comparison using Blast
  6. Microarray analysis using Tree View, Cluster and R
  7. Excel and Access databases for data analyses and presentation
  8. Phylogenetic analysis
• Taught by: Kevin Carr, David DeWitt, Rob Halgren, Marianne Huebner, Jeff Landgraf, Matt Larson, Tao Sang, Curtis Wilkerson
• Course: 2 credits, offered every spring
• Lecture/Lab: Wednesday & Fridays 3-4:30pm, Microlab in room 128 Hubbard Hall
• Enrollment limit: 25 (by permission)
• Complete Course Description
• Contact: David DeWitt dewittd@msu.edu
  
  
• BMB961, Advanced Topics
  • Course: offered spring 2005
  • Course Description
  • Taught by: Phillip Duxbury duxbury@pa.msu.edu and Michael Feig feig@msu.edu

• BMB 961 (formerly BCH 961), Concepts in Protein Structure Analysis and Modeling
• One hour lecture per week covers and demonstrates the techniques.
• Students have two hours of hands-on laboratory work in a project-like setting.
• Taught by: Michael Feig, Michael Garavito, Robert Halgren, Leslie Kuhn, Kaillathe Padmanabhan, Honggao Yan, and William Wedemeyer
• Course: 2 credits, offered every fall
• Complete Course Description
• Contact: Kaillathe Padmanabhan padmanab@msu.edu
  
  
• BMB 961/CEM 987, Biomolecular Spectroscopy - Theory and Applications
• Introduces students to the basic principles of biomolecular spectroscopy using a range of techniques.
• Taught by: Doug Gage, Michael Garavito, Rawle Hollingsworth, John McCracken, G.M. Strasburg, Honggao Yan, David Weliky
• Course: 3 credits, offered periodically in the fall
• Contact: Honggao Yan yanh@msu.edu

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Chemical Engineering

• CHE 883/491, Multidisciplinary Bioprocessing Laboratory (MBL)
  • Open to both undergraduates and graduate students from bioscience, chemistry, and engineering
  • To train students to work together effectively in multidisciplinary teams
  • To teach students advanced experimental techniques related to industrial biotechnology
  • Course: offered Spring 2005
  • Required: Senior or graduate standing in a department related to biotechnology
  • Previous offering Course Description
  • Recitation meets Wednesdays 9:10 - 10:00
  • Lab times will be chosen by each student team
  • Contact: Mark Worden
    
• CHE 891-003/PLB 802-002/BMB 960-001
  From Analysis of Metabolism to Systems Biology
  • Multidisciplinary approach to understanding how metabolic networks are analyzed, regulated, and manipulated
  • Course: 2 credits, offered Spring 2006
  • Course: Tuesdays & Thursdays 9:10-10:00a.m.
  • Complete Course Description
  • Taught by: Christoph Benning, Christina Chan, Syed Hashsham, Yair Shachar-Hill, and Claire Vieille
  
  

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Chemistry

• CEM 883, Computational Quantum Chemistry
• Covers computational methods in electronic structure determination of energies, structures and other molecular properties.
• Taught by: James Harrison
  
• CEM 888, Computational Chemistry
• The course is strongly computationally focused.
• Computational approaches to the electronic structure of molecules.
• Reaction dynamics.
• Molecular dynamics simulations.
• Biomolecular mechanics.
• Course: Offered in the spring of odd years
• Taught by: Robert Cukier, James Harrison, Rawle Hollingsworth, Ned Jackson and Piotr Piecuch
• Contact: Robert Cukier

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Computer Science and Engineering

• CSE 231 and CSE 232
• Provides introduction to programming and data structures.
• CSE 331
• Provides more in depth treatment of data structures and algorithum design and analysis.
• Limited capacity, currently only open to CSE majors.
• Several prerequisites needed before course can be taken.
• CSE 480
• Provides introduction to design and implementation of databases.
• Perhaps more theoretical than needed for CBM students.
• Limited capacity, currently only open to CSE majors.
• Many prerequisites needed before course can be taken.
• CSE 830
• Graduate course in design and analysis of algorithms.
• Beefed up version of CSE 331.
• Limited capacity, currently only open to CSE graduate students.
• May be more theoretical and general than what is really needed.

• CSE 960, spring semester, 2001
• For this semester, this special topics course will focus on string and tree algorithms covering topics such as string matching, alignment and phylogenetic tree construction.

• CSE 491, Digital Evolution & Biocomplexity
  • Course: Offered every spring
  • Taught by Charles Ofria