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Course Criteria
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3.00 Credits
An intensive review of those aspects of biochemistry, molecular biology and cell biology necessary to begin research in bioinformatics and to enter graduate courses in biology. Areas covered include cell structure, intracellular sorting, cellular signaling (receptors), Cytoskelton, cell cycle, DNA replication, transcription and translation. This course makes extensive use of computer approaches to convey the essential computational and visual nature of the material to be covered. Prerequisites: CM102, general chemistry, general physics, organic chemistry, calculus or instructor's permission.
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3.00 Credits
Computer representations of nucleic acid and protein sequences, pairwise and multiple alignment methods, available databases of nucleic acid and protein sequences, database search methods, scoring functions for assessment of alignments, nucleic acid to protein sequence translation and codon usage, genomic organization and gene structure in prokaryotes and eukaryotes, introns and exons, prediction of open reading frames, alternative splicing, existing databases of mRNA, DNA protein and genomic information. An overview of available programs and of resources on the web. Lab is an integral part of this course. Prerequisites: None.
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3.00 Credits
Protein folding representations, databases of protein folding classes, secondary structure prediction, tertiary structure prediction via computer folding experiments threading, and homology model building, prediction of post-translation modification sites, active and binding sites in proteins, representations of contiguous and non-contiguous epitopes on protein surfaces at the sequence level, representations of functional motifs at the three dimensional and at the sequence level. Lab is an integral part of this course. Prerequisite: BI 7533.
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3.00 Credits
Functional classifications of proteins, prediction of function from sequence and structure, Orthologs and paralogs, representations of biological pathways, available systems for the analysis of whole genomes and for human-assisted and automatic functional prediction. Lab is an integral part of this course. Prerequisite: BI 7543.
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3.00 Credits
Review of database theory, chemical structure representation; connection tables, line notations, structure diagrams, representations of chemical reactions, structure manipulation: graph theory, structure analysis: ring perception, structural fingerprints, symmetry perception, molecular modeling algorithms, genetic algorithms, simulated annealing, QSAR historical approaches, structural search of chemical databases, commercial chemical information databases, combinatorial chemistry and diversity assessment.
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3.00 Credits
Bioinformatics: Presentation at intervals of various advanced or specialized topics in chemo- or bioinformatics. BI7583/-93 Guided Studies in Bioinformatics As arranged.
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12.00 Credits
As arranged Original research, which serves as basis for master's degree. Minimum research registration requirements for the master's thesis: 12 units. Registration for research required each semester consecutively until students have completed adequate research projects and acceptable theses and have passed required oral examinations. Research credits registered for each semester realistically reflect time devoted to research. Prerequisites for MS candidates: Degree status and consent of graduate adviser and thesis director.
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3.00 Credits
This course explains the functioning of basic circuit elements in transcription regulation, signal transduction, and developmental networks of living cells, using simplified mathematical models. The course focuses on design principles and information processing in biological circuits. It discusses network motifs, modularity, robustness, evolutional optimization and error minimization by kinetic proofreading in specific applications to bacterial chemotaxis, developmental patterning, neuronal circuits, and immune recognition in several well-studied biological systems. Prerequisites: Undergraduate courses in elementary calculus and physical chemistry.
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3.00 Credits
Fundamentals of biology. Physical, chemical and biochemical bases of life on various organizational levels, cellular morphology, complementarity of form and function, including reproduction, development and genetics.
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3.00 Credits
Fundamentals of biology, continued. Emphasis on evolutionary theory, phylogeny and comparative physiology including homeostasis, regulation, integration and coordination of organisms at the systems level. Prerequisite: BMS 1004 or instructor's permission.
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