BCB 442X. Bioinformatics and Computational Biology A,B,C,D. Bioinformatics and Computational Biology Techniques Cr. 0.5. S. Prereq: Junior standing. Modular minicourses consisting of guided tutorials and hands-on computer software exercises focused on fundamental problems, approaches, and software applications in bioinformatics and computational biology. Nonmajor graduate credit. Satisfactory – Fail only.
A. Sequence Database Searching
B. Protein Structure Databases, Visualization, and Prediction.
C. Phylogenetic Analysis.
D. Microarray Analysis
Website: http://bindr.gdcb.iastate.edu/BCBio442/
BCB 444. Introduction to Bioinformatics. (Dual-listed with 544). (Cross-listed with Com S, Cpr E, Gen, Biol). (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. Nonmajor graduate credit.
Fall 2009 Class Website
BCB 490. Independent Study. Cr. 1-5. Repeatable. F.S.SS.Prereq: Permission of instructor.
BCB 495. Molecular Biology for Computational Scientists. (Cross-listed with Gen). (3-0) Cr. 3. F.Survey of molecular cell biology and molecular genetics for nonbiologists, especially those interested in bioinformatics/computational biology. Basic cell structure and function; principles of molecular genetics; biosynthesis, structure, and function of DNA, RNA, and proteins; regulation of gene expression; selected topics. Provides biological background for BCB 594. Credit for graduation will not be allowed for more than one of Gen 411 and Gen/BCB 495. Nonmajor graduate credit.
BCB 538. Computational Genomics and Evolution. (Cross-listed with GDCB). (3-0) Cr. 3. Alt. S., offered 2011.Prereq: Biol 313. Introduction to evolutionary sequence analysis at the genome level. Topics include sequence alignment, phylogenetic inference, molecular clock analysis, ancestral state inference, sequence/structure relation, functional divergence and prediction, evolutionary development, genome duplication, and comparative genomics. Focus will be on data analysis and biological interpretation.
BCB 539. Statistical Methods for Computational Biology. (Cross-listed with GDCB). (2-0) Cr. 2. Alt. S., offered 2010.Prereq: BCB 568. Gu. Advanced discussion about statistical modeling of DNA and amino acid sequences, microarray expression profiles and other genome-wide data interpretation.
BCB 542. Introduction to Molecular Biology Techniques. (Cross-listed with GDCB, BBMB, B M S, FS HN, Hort, NutrS, VDPAM, EEOB, NREM, V MPM). Cr. 1. Repeatable. F.S.SS.Prereq: Graduate classification. Workshops in basic molecular biology techniques and related procedures. Satisfactory-fail only.
A. DNA Techniques. Includes genetic engineering procedures, sequencing, PCR, and genotyping. (F.S.SS.)
B. Protein Techniques. Includes fermentation, protein isolation, protein purification, SDS-PAGE, Western blotting, NMR, confocal microscopy and laser microdissection, immunophenotyping, and monoclonol antibody production. (S.SS.)
C. Cell Techniques. Includes immunophenotyping, ELISA, flow cytometry, microscopic techniques, and image analysis. (F.S.)
D. Plant Transformation. Includes Agrobacterium and particle gun-mediated transformation of tobacco, Arabidopsis, and maize, and analysis of transformants. (S.)
E. Proteomics. Includes two-dimensional electrophoresis, laser scanning, mass spectrometry, and database searching. (F.)
F. Metabolomics. Includes
chromatographic methods along with tandem mass spectrometry as the main analytical tools.
Offered for the first time in Spring 2009. Syllabus.
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 2009 Class Website
BCB 549. Advanced Algorithms in Computational Biology. (Cross-listed with Cpr E, Com S). (3-0) Cr. 3. S.Prereq: Com S 311 and either 208 or 228. Design and analysis of algorithms for applications in computational biology, pairwise and multiple sequence alignments, approximation algorithms, string algorithms including in-depth coverage of suffix trees, semi-numerical string algorithms, algorithms for selected problems in fragment assembly, phylogenetic trees and protein folding. No background in biology is assumed. Also useful as an advanced algorithms course in string processing.
BCB 550. Evolutionary Problems for Computational Biologists. (Cross-listed with Com S). (3-0) Cr. 3. Alt. F., offered 2009.Prereq: Com S 311 and some knowledge of programming. Discussion and analysis of basic evolutionary principles and the necessary knowledge in computational biology to solve real world problems. Topics include character and distance based methods, phylogenetic tree distances, and consensus methods, and approaches to extract the necessary information from sequence-databases to build phylogenetic trees.
BCB 551. Computational Techniques for Genome Assembly and Analysis. (Cross-listed with Com S). (3-0) Cr. 3. Alt. F., offered 2009.Prereq: Com S 311 and some knowledge of programming. Huang. Introduction to practical sequence assembly and comparison techniques. Topics include global alignment, local alignment, overlapping alignment, banded alignment, linear-space alignment, word hashing, DNA-protein alignment, DNA-cDNA alignment, comparison of two sets of sequences, construction of contigs, and generation of consensus sequences. Focus on development of sequence assembly and comparison programs.
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.
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 2009 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 2009 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 2009 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 2009 BCB 570 Website
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.
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 597. Introductory Computational Structural Biology. (Cross-listed with Math). (3-0) Cr. 3. S.Prereq: Math 561 and 562. Mathematical and computational approaches to protein structure prediction and determination. Topics include molecular distance geometry, potential energy minimization, and molecular dynamics simulation.
BCB 599. Creative Component. Cr. arr.
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BCB 690. Student Seminar in Bioinformatics and Computational Biology. Cr. 1. Repeatable. S.Student research presentations.
BCB 691H. Faculty Seminar in Bioinformatics and Computational Biology. (Cross-listed with GDCB). (1-0) Cr. 1. Repeatable.Faculty research series.
H. Bioinformatics and Computational Biology. (Same as GDCB 691H).
Fall 2009 Schedule for BCB 691
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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