The curriculum for BCB's graduate program at Iowa State University has developed over the last ten years to incorporate and keep pace with the expanding body of knowledge associated with this dynamic discipline. A recent course addition, Selected Topics in BCB, will continue the program's ability to present cutting-edge topics to BCB graduate students. This course is offered Fall 2011. See the details below.
Core Courses
BCB 567. Bioinformatics I (Fundamentals of Genome Informatics). (Cross-listed with Com S, Cpr E). (3-0) Cr. 3. F.Prereq: Com S 208; Com S 330; Stat 341; credit or enrollment in Biol 315, Stat 430. Biology as an information science. Review of algorithms and information processing. Generative models for sequences. String algorithms. Pairwise sequence alignment. Multiple sequence alignment. Searching sequence databases. Genome sequence assembly.
Fall 2011 BCB567 Website
BCB 568. Bioinformatics II (Advanced Genome Informatics). (Cross-listed with GDCB, Stat, Com S). (3-0) Cr. 3. S.Prereq: BCB 567, BBMB 301, Biol 315, Stat 430, credit or enrollment in Gen 411. Advanced sequence models. Basic methods in molecular phylogeny. Hidden Markov models. Genome annotation. DNA and protein motifs. Introduction to gene expression analysis.
Spring 2011 BCB568 Website
BCB 569. Bioinformatics III (Structural Genome Informatics). (Cross-listed with BBMB, Com S, Math, Cpr E). (3-0) Cr. 3. F.Prereq: BCB 567, Gen 411, Stat 430. Algorithmic and statistical approaches in structural genomics including protein, DNA and RNA structure. Structure determination, refinement, representation, comparison, visualization, and modeling. Analysis and prediction of protein secondary and tertiary structure, disorder, protein cores and surfaces, protein-protein and protein-nucleic acid interactions, protein localization and function.
Fall 2010 BCB569 Syllabus
BCB 570. Bioinformatics IV (Computational Functional Genomics and Systems Biology). (Cross-listed with Com S, GDCB, Stat, Cpr E). (3-0) Cr. 3. S.Prereq: BCB 567, Biol 315, Com S 311 and either 208 or 228, Gen 411, Stat 430. Algorithmic and statistical approaches in computational functional genomics and systems biology. Analysis of high throughput gene expression, proteomics, and other datasets obtained using system-wide measurements. Topological analysis, module discovery, and comparative analysis of gene and protein networks. Modeling, analysis, simulation and inference of transcriptional regulatory modules and networks, protein-protein interaction networks, metabolic networks, cells and systems: Dynamic systems, Boolean, and probabilistic models. Ontology-driven, network based, and probabilistic approaches to information integration.
Spring 2012 BCB 570 Website
The Core BCB course in molecular genetics is:
GDCB 511. Molecular Genetics. (Cross-listed with MCDB). (3-0) Cr. 3. S.Prereq: Biol 313 and BBMB 405. The principles of molecular genetics: gene structure and function at the molecular level, including regulation of gene expression, genetic rearrangement, and the organization of genetic information in prokaryotes and eukaryotes.
Additional Courses of Interest to BCB Students
Required Background Course for BCB majors:
Stat 430. Empirical Methods for Computer Science. (3-0) Cr. 3. F. Prereq: Stat 330 or an equivalent course, Math 166, knowledge of linear algebra. Programs and systems as objects of empirical studies; exploratory data analysis; selected topics from analysis of designed experiments - analysis of variance, hypothesis testing, interaction among variables; linear regression, logistic regression, Poisson regression; parameter estimation, prediction, confidence regions, dimension reduction techniques, model diagnostics and sensitivity analysis; Markov chains and processes; simulation techniques and bootstrap methods; applications to performance assessment - comparison of multiple systems; communicating results of empirical studies. Statistical software: R. Nonmajor graduate credit.
View prerequisite and background coursework for the BCB PhD degree here.
Optional BCB courses:
BCB 596. Genomic Data Processing. (Cross-listed with Com S, GDCB). (3-0) Cr. 3. F. Prereq: Some knowledge of programming. Study the practical aspects of genomic data processing with an emphasis on hand-on projects. Students will carry out major data processing steps using bioinformatics tools. Topics include base-calling, raw sequence cleaning and contaminant removal; shotgun assembly procedures and EST clustering methods; genome closure strategies and practices; sequence homology search and function prediction; annotation and submission of GenBank reports; and data collection and dissemination through the Internet. Useful post-genomic topics like microarray design and data analysis will also be covered.
BCB 660. Selected Topics in Bioinformatics and Computational Biology. (2-0) Cr. 0-2. Repeatable, maximum of 4 credits. F.S.SS. Prereq: Permission of Instructor. Topics of interest in the major research areas of computational molecular biology, including genomics, structural genomics, functional genomics, and computational systems biology.
Fall 2011 Offering: "Applications of NGS data processing software in genomics."
Tu/Th 11am - 12:20pm, MBB 1340, August 30 - November 15, 2 credits
V. Brendel and A. Toth
Web page: http://brendelgroup.org/teaching/bcb660F11.php
Synopsis: The course will be a hands-on, working group style course covering data processing and analysis of "Next Generation Sequence" data. Students will be given access to virtual machine instances tailored to course from the iPlant Collaborative research environment. Students will then install software on their machines and initially analyze sample data. The course will cover the entire range of genomic analysis, from genome assembly, transcript assembly, transcript mapping, and genome annotation to annotation visualization and evaluation. At each step, participant will work together to generate installation and How-to documentation. There will be opportunity to analyze original data as well as the provided sample data. The course recommended programs and generated documentation will form the basis for a new virtual machine image for wider distribution through iPlant, including use at a public workshop conducted in collaboration with iPlant colleagues at the end of the class.
BCB Course for non-majors:
BCB 544. Introduction to Bioinformatics. (Dual-listed with 444). (Cross-listed with Com S, Cpr E, GDCB). (4-0) Cr. 4. F. Prereq: Math 165 or Stat 401 or equivalent. Broad overview of bioinformatics with a significant problem-solving component, including hands-on practice using computational tools to solve a variety of biological problems. Topics include: database searching, sequence alignment, gene prediction, RNA and protein structure prediction, construction of phylogenetic trees, comparative and functional genomics.
Fall 2011 Class Website
To fulfill Ethics Requirement:
BCB 565. Professional Practice in the Life Sciences. (Cross-listed with Pl P, Agron, An S, Hort, Micro, V MPM). Cr. arr. S.Prereq: Graduate classification. Professional discourse on the ethical and legal issues facing life science researchers. Offered in modular format; each module is four weeks.
A. Professional Practices in Research. (Cr. 1.0) Good scientific practices and professional ethics in the life sciences.
B. Intellectual Property and Industry Interactions. (Cr. 0.5) Ethical and legal issues facing life scientists involved in research interactions with industry.
Special Topics, Workshop, Seminar
and Research Courses -- current information here
BCB 590. Special Topics. Cr. arr. Repeatable.Prereq: Permission of instructor.
BCB 593. Workshop in Bioinformatics and Computational Biology. (1-0) Cr. 1. Repeatable. F.S.Current topics in bioinformatics and computational biology research. Lectures by off-campus experts. Students read background literature, attend preparatory seminars, attend all lectures, meet with lecturers.
Spring 2012 Class Website
BCB 690. Student Seminar in Bioinformatics and Computational Biology. Cr. 1. Repeatable. S. Student research presentations.
Spring 2012 Class Website
BCB 691H. Faculty Seminar in Bioinformatics and Computational Biology. (Cross-listed with GDCB). (1-0) Cr. 1. Repeatable. F. Faculty research series.
H. Bioinformatics and Computational Biology. (Same as GDCB 691H).
Fall 2011 Class Website
BCB 697. Graduate Research Rotation. Cr. arr. F.S.SS.Graduate research projects performed under the supervision of selected faculty members in the Bioinformatics and Computational Biology major.
BCB 699. Research. Cr. arr. Repeatable. (BCB 699 reference numbers.)
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