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Athletic Training |
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ATRN 6113 - Therapeutic Exercise of the Upper Extremity
Application of rehabilitation techniques and modalities to upper extremity injuries.
Credit Hours: (3)
Corequisite(s): ATRN 6111
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6114 - General Medicine and Pharmacology I
The first part of students learning how to evaluate, diagnose, and treat common non-orthopedic medical conditions.
Credit Hours: (3)
Prerequisite(s): ATRN 5105 or ATRN 6105
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6116 - General Medicine and Pharmacology II
Second part of students learning how to evaluate, diagnose, and treat common non-orthopedic medical conditions.
Credit Hours: (2)
Prerequisite(s): ATRN 6114
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6118 - Athletic Healthcare Administration
The business management principles associated with athletic training clinical practice, as well as leadership and professional development.
Credit Hours: (3)
Prerequisite(s): ATRN 6114 and ATRN 6116
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6119 - Diagnostic Procedures for Rehabilitation Professionals
Identifies and describes various modes of imagine techniques and tests used in sports medicine. Diagnostic procedures covered include, but are not limited to: X-Ray, CT Scan, MRI, bone scan, fluoroscopy, and PET.
Credit Hours: (2)
Prerequisite(s): ATRN 6114 and ATRN 6116
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6121 - Behavioral Health in Sports Medicine
Integrates physiological, psychological, and social understanding of humans in relationship to physical activity as a lifelong pursuit. Topics include: physical fitness, nutrition, stress reduction, socialization, and individual differences in human behavior.
Credit Hours: (3)
Prerequisite(s): ATRN 6118
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6401 - Clinical Rotation I
A semester-long clinical rotation that focuses on the needs of pediatric/adolescent athletes. Students spend approximately 20 hours per week at their clinical site.
Credit Hours: (1)
Prerequisite(s): ATRN 6101 and ATRN 6102
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6402 - Clinical Rotation II
A semester-long clinical rotation that focuses on the healthcare needs of collegiate athletes. Students spend approximately 20 hours per week at their clinical site.
Credit Hours: (1)
Prerequisite(s): ATRN 6401
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6403 - Clinical Rotation III
A clinical rotation in an orthopedic physician practice, including working with an inter-professional healthcare team focused on orthopedic assessment, clinical procedures, and surgical observations with patients across the lifespan. Students are required to gain a minimum of 100 hours of patient care experience.
Credit Hours: (1)
Prerequisite(s): ATRN 6402
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6404 - Clinical Rotation IV
A clinical rotation in a primary care or urgent care center, including working with an inter-professional healthcare team focused on assessing, diagnosing, and treatment of general medical conditions. Students are required to gain a minimum of 100 hours of patient care experience.
Credit Hours: (1)
Prerequisite(s): ATRN 6403
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6405 - Clinical Rotation V
A semester-long, full-time, clinical immersion rotation that focuses on the healthcare needs of collegiate athletes. It is designed to facilitate synthesis and the integration of knowledge, skills, and clinical decision-making into patient care. The rotation allows students to participate in the full scope of athletic training clinical practice (e.g., emergency and acute care, assessment and diagnosis, rehabilitation, reconditioning, return to sport) as part of an inter-professional sports medicine team. Students are required to gain a minimum of 300 hours of patient care experience with physically active individuals and includes team travel.
Credit Hours: (3)
Prerequisite(s): ATRN 6404
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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ATRN 6406 - Clinical Rotation VI
A semester-long, full-time, clinical immersion rotation that provides the athletic training student the opportunity to gain experience in a specific area of clinical practice that they are interested in pursuing post-graduation. These can include, but are not limited to: out-patient rehabilitation, orthopedic clinics, primary care settings, emergency and acute care, dance medicine, industrial and occupational health, and athletic performance. Students are required to gain a minimum of 300 hours of patient care experience with physically active individuals.
Credit Hours: (6)
Prerequisite(s): ATRN 6405
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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Bioinformatics |
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BINF 5171 - Business of Biotechnology
Introduces students to the field of biotechnology and how biotech businesses are created and managed. Students should be able to define biotechnology and understand the difference between a biotech company and a pharmaceutical company. Additional concepts covered will include platform technology, biotechnology’s history, biotechnology products and development processes, current technologies used by biotech companies today, biotechnology business fundamentals, research and development within biotech companies, exit strategies, and careers in the biotech field.
Credit Hours: (3)
Restriction(s): Admission to a graduate program.
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 5191 - Life Sciences and the Law
Law and regulations permeate our daily lives, and nowhere is this truer than in areas of life sciences. This course explores what the law is, how our current laws developed, and factors currently affecting the evolution of the law. It provides a general overview of U.S. law, including constitutional law, criminal law, contract law, tort law, property law (especially intellectual property law), business law (especially legal aspects of forming a new company), and administrative law. It then focuses on specific aspects of the law affecting the life sciences, such as ownership of tissues and organisms, regulation of drugs and medical devices, regulation of research in the life sciences, the history and regulation of medicine, the economics and various types of health care delivery, and food production.
Credit Hours: (3)
Restriction(s): Admission to a graduate program.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6010 - Topics in Bioinformatics
Topics in bioinformatics and genomics selected to supplement the regular course offerings. A student may register for multiple sections of the course with different topics in the same semester or in different semesters.
Credit Hours: (3)
Restriction(s): Permission of department.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6100 - Biological Basis of Bioinformatics
This course provides a foundation in molecular genetics and cell biology focusing on foundation topics for graduate training in bioinformatics and genomics.
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics and undergraduate training in Computer Science or other non-biological discipline.
Most Recently Offered (Day): Fall 2018, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6101 - Energy and Interaction in Biological Modeling
This course covers: (a) the major organic and inorganic chemical features of biological macromolecules; (b) the physical forces that shape biological molecules, assemblies and cells; (c) the chemical driving forces that govern living systems; (d) the molecular roles of biological macromolecules and common metabolites; (e) and the pathways of energy generation and storage. Each section of the course builds upon the relevant principles in biology and chemistry to explain the most common mathematical and physical abstractions used in modeling in the relevant context.
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6111 - Bioinformatics Programming I
Introduces fundamentals of programming for bioinformatics using a high-level object-oriented language such as Java or Python. Introduces object-oriented programming, analysis of algorithms, and fundamental sequence alignment methods. Students learn productive use of the Unix environment, focusing on Unix utilities that are particularly useful in bioinformatics. Course grade includes performance in BINF 6111L .
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics or permission of instructor.
Corequisite(s): BINF 6111L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6111L - Bioinformatics Programming I Laboratory
Hands-on experience in programming to solve bioinformatics problems.
Credit Hours: (0)
Corequisite(s): BINF 6111 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6112 - Bioinformatics Programming II
In this second semester, students practice and refine skills learned in the first semester. New topics include: (a) programming as part of a team, using sequence analysis algorithms in realistic settings; (b) writing maintainable and re-usable code; and (c) graphical user interface development. Course grade includes performance in BINF 6111 .
Credit Hours: (3)
Prerequisite(s): BINF 6111 or permission of instructor.
Corequisite(s): BINF 6112 . Continuation of BINF 6111 .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6112L - Bioinformatics Programming II Laboratory
Hands-on experience in programming to solve bioinformatics problems.
Credit Hours: (0)
Corequisite(s): BINF 6112L or permission of instructor.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6151 - Professional Communication
Principles and useful techniques for effective oral presentations, poster presentations, scientific writing, use of references and avoiding plagiarism. Students in the course critique and help revise each other’s presentations and learn how to avoid common pitfalls. In addition, students learn how to properly organize and run a meeting.
Credit Hours: (1)
Cross-listed Course(s): GRAD 6151.
Most Recently Offered (Day): Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6152 - Program and Professional Orientation
Students learn to identify key Bioinformatics skill sets and where they are applied in research and industry settings, join appropriate professional networks, use the major professional and research journals in the field, identify key organizations and companies driving intellectual and technology development in bioinformatics, and achieve beginner level proficiency with key molecular data repositories.
Credit Hours: (1)
Most Recently Offered (Day): Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6153 - Career Development in Bioinformatics
Students prepare intensively for the job search, from developing a resume, to identifying appropriate opportunities, to preparing for the interview. Students are expected to complete a final interview practicum with faculty and members of the PSM Executive Board.
Credit Hours: (1)
Most Recently Offered (Day): Spring 2016, Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6200 - Statistics for Bioinformatics
Introduces students to statistical methods commonly used in bioinformatics. Basic concepts from probability, stochastic processes, information theory, and other statistical methods are introduced and illustrated by examples from molecular biology, genomics and population genetics with an outline of algorithms and software. R is introduced as the programming language for homework. Course grade includes performance in BINF 6200L .
Credit Hours: (3)
Restriction(s): Permission of department.
Corequisite(s): BINF 6200L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6200L - Statistics for Bioinformatics Laboratory
Introduces R and its application in solving common statistical problems in bioinformatics. Basic relevant concepts from probability, probability distributions, and statistical inference are introduced and illustrated by examples from bioinformatics applications using R.
Credit Hours: (0)
Corequisite(s): BINF 6200 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6201 - Molecular Sequence Analysis
Introduction of the basic computational methods and open sources software commonly used in molecular sequence analysis. Topics include: biological sequence data formats and major public databases, concepts of computer algorithms and complexity, introductions to principle components analysis and data clustering methods, dynamics of genes in populations, evolutionary models of DNA and protein sequences, derivation of amino acid substitution matrices, algorithms for pairwise sequence alignments and multiple sequence alignments, algorithms for fast sequence database search, methods for molecular phylogenetic analysis, hidden Markov models and neural networks for sequence pattern and family recognition, and introductions to genome evolution and comics data analysis. Course grade includes performance in BINF 6201L .
Credit Hours: (3)
Prerequisite(s): BINF 6100 or equivalent.
Corequisite(s): BINF 6201L .
Most Recently Offered (Day): Spring 2018, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6201L - Molecular Sequence Analysis Laboratory
Hands-on experience with common software methods for biological sequence data analysis. Topics include: Basic UNIX utilities, principle component analysis, clustering analysis, global and local pair-wise sequence alignments, multiple sequence alignments, sequence database search methods, phylogenetic tree constructions, hidden Markov models, and neural networks.
Credit Hours: (0)
Prerequisite(s): BINF 6100 or equivalent.
Corequisite(s): BINF 6201 .
Most Recently Offered (Day): Fall 2015, Spring 2018, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6202 - Computational Structural Biology
Topics include: (a) the fundamental concepts of structural biology (chemical building blocks, structure, superstructure, folding, etc.); (b) structural databases and software for structure visualization; (c) Structure determination and quality assessment; (d) protein structure comparison and the hierarchical nature of biomacromolecular structure classification; (e) protein structure prediction and assessment; and (f) sequence and structure-based functional site prediction. Course grade includes performance in BINF 6202L .
Credit Hours: (3)
Prerequisite(s): BINF 6101 and BINF 6201 or their equivalents.
Corequisite(s): BINF 6202L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6202L - Computational Structural Biology Laboratory
The use and application of: (a) structural classification databases; (b) software for visualization of biological structures; (c) computational methods to evaluate and compare biological structures; (d) computational methods to align biological structures; and (f) computational methods to predict biological structures from sequence.
Credit Hours: (0)
Corequisite(s): BINF 6202 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6203 - Genomics
Surveys the application of high-throughput molecular biology and analytical biochemistry methods and data interpretation for those kinds of high volume biological data most commonly encountered by bioinformaticians. The relationship between significant biological questions, modern genomics technology methods, and the bioinformatics solutions that enable interpretation of complex data is emphasized. Topics include: genome sequencing and assembly, annotation, and comparison; genome evolution and individual variation; function prediction; gene ontologies; transcription assay design, data acquisition, and data analysis; and metabolic pathways and databases and their role in genome analysis. Course grade includes performance in BINF 6203L .
Credit Hours: (3)
Prerequisite(s): BINF 6100 or equivalent.
Corequisite(s): BINF 6203L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6203L - Genomics Laboratory
Hands-on experience with software methods for genome-scale data analysis. Topics include: Genome sequencing and assembly, genome annotation, genome comparison. Functional classification and gene ontologies. Genome evolution and individual variation. Transcriptomic and epigenetic assay design, data acquisition, and data analysis.
Credit Hours: (0)
Prerequisite(s): BINF 6100 or equivalent.
Corequisite(s): BINF 6203 .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6204 - Mathematical Systems Biology
Introduces basic concepts, principles and common methods used in systems biology. Emphasizes molecular networks, models and applications, and covers the following topics: (a) the structure of molecular networks; (b) network motifs, their system properties and the roles they play in biological processes; complexity and robustness of molecular networks; (c) hierarchy and modularity of molecular interaction networks; kinetic proofreading; (d) optimal gene circuit design; and (e) the rules for gene regulation.
Credit Hours: (3)
Prerequisite(s): BINF 6200 and BINF 6210 or equivalents.
Most Recently Offered (Day): Spring 2016, Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6205 - Computational Molecular Evolution
Covers major aspects of molecular evolution and phylogenetics with an emphasis on the modeling and computational aspects of the fields. Topics will include: models of nucleotide substitution, models of amino acid and codon substitution, phylogenetic reconstruction, maximum likelihood methods, Bayesian methods, comparison of phylogenetic methods and tests on trees, neutral and adaptive evolution and simulating molecular evolution. Students will obtain an in-depth knowledge of the various models of evolutionary processes, a conceptual understanding of the methods associated with phylogenetic reconstruction and testing of those methods and develop an ability to take a data-set and address fundamental questions with respect to genome evolution.
Credit Hours: (3)
Prerequisite(s): BINF 6201 and BINF 6200 or permission of instructor.
Most Recently Offered (Day): Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6210 - Machine Learning for Bioinformatics
Introduction of commonly used machine learning methods in the field of bioinformatics. Topics include: dimension reduction using principal component analysis, singular value decomposition, and linear discriminant analysis, clustering using kmeans, hierarchical, expectation maximization approaches, classification using k-nearest neighbor and support vector machines. To help understand these methods, basic concepts from linear algebra, optimization, and information theory are explained. Application of these machine learning methods to solving bioinformatics problems are illustrated using examples from the literature.
Credit Hours: (3)
Prerequisite(s): BINF 6200 , BINF 6200L , and Calculus.
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6211 - Design and Implementation of Bioinformatics Databases
The fundamentals of database modeling as used in bioinformatics. By the end of the course, students should be able to: understand different types of data models, know how hierarchical and relational models work and give examples that are widely used for biological databases, understand the capabilities of a standard, open source RDBMS, understand the tasks required for data integration and how to use SQL as a research tool. Introduction to ML, XML Schema, and BioOntologies as widely used data exchange and organization tools in bioinformatics databases. Course grade includes performance in BINF 6211L .
Credit Hours: (3)
Restriction(s): Permission of instructor.
Corequisite(s): BINF 6211L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6211L - Design and Implementation of Bioinformatics Databases Laboratory
Practice of skills described in the lecture, particularly design principles for the relational model and using SQL. Students complete projects in which they design, implement, prototype, and use a research biological database. Students obtain correctly formatted data from public repositories and use XML, XML Schema, and BioOntologies as tools in the data integration process. The use of SQL to create, populate, and perform complex queries on genomics databases.
Credit Hours: (0)
Restriction(s): Permission of instructor.
Corequisite(s): BINF 6211 .
Most Recently Offered (Day): Spring 2018, Spring 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6215 - Bioinformatics Pipeline Programming
The concept of pipelines assemblies of basic bioinformatics tools and data sources to solve complex data processing problems. The pipeline concept is introduced with simple UNIX command line methods, and then extended to the use of preconfigured commercial and extensible open-source workflow management systems. Reproducibility of analysis, collection of analytic provenance information, and database integration is also covered.
Credit Hours: (3)
Prerequisite(s): BINF 6203 .
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6310 - Advanced Statistics for Genomics
Canonical linear statistics (t-test, ANOVA, PCA) and their non-parametric equivalents. Examines application of Bayesian statistics, Hidden Markov Models and machine learning algorithms to problems in bioinformatics. Students should have fluency in a high-level programming language (PERL, Java, C#, Python or equivalent) and are expected, in assignments, to manipulate and analyze large public data sets. Utilizes the R statistical package with the bioconductor extension. Course grade includes performance in BINF 6310L .
Credit Hours: (3)
Prerequisite(s): BINF 6200 or equivalent.
Corequisite(s): BINF 6310L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6310L - Advanced Statistics for Genomics Laboratory
Hands-on experience with using the R programming language.
Credit Hours: (0)
Prerequisite(s): BINF 6200 or equivalent.
Corequisite(s): BINF 6310 .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6311 - Biophysical Modeling
Topics include: (a) overview of mechanical force fields; (b) energy minimization; (c) dynamics simulations (molecular and coarse-grained); (d) Monte-Carlo methods; (e) systematic conformational analysis (grid searches); (f) classical representations of electrostatics (Poisson-Boltzmann, Generalized Born and Colombic); (g) free energy decomposition schemes; and (h) hybrid quantum/classical (QM/MM) methods.
Credit Hours: (3)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6312 - Computational Comparative Genomics
Introduces computational methods for comparative genomics analysis. Topics include: (a) the architecture of prokaryotic and eukaryotic genomes; (b) the evolutionary concept in genomics; (c) databases and resources for comparative genomics; (d) principles and methods for sequence analysis; evolution of genomes; (e) comparative gene function annotation; (f) evolution of the central metabolic pathways and regulatory networks; (g) genomes and the protein universe; (h) cis-regulatory binding site prediction; (i) operon and regulon predictions in prokaryotes; and (j) regulatory network mapping and prediction.
Credit Hours: (3)
Prerequisite(s): BINF 6201 or equivalent.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6313 - Structure, Function, and Modeling of Nucleic Acids
Topics include: (a) atomic structure, macromolecular structure-forming tendencies and dynamics of nucleic acids; (b) identification of genes which code for functional nucleic acid molecules, cellular roles and metabolism of nucleic acids; (c) 2D and 3D abstractions of nucleic acid macromolecules and methods for structural modeling and prediction; (d) modeling of hybridization kinetics and equilibria; and (e) hybridization-based molecular biology protocols, detection methods and molecular genetic methods, and the role of modeling in designing these experiments and predicting their outcome.
Credit Hours: (3)
Prerequisite(s): BINF 6100 and BINF 6101 , or their equivalents.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6318 - Computational Proteomics and Metabolomics
Introduces commonly used computational algorithms, software tools, and databases for analyzing mass spectrometry-based proteomics and metabolomics data. Students learn how to: 1) implement algorithms for processing raw mass spectrometry data and extracting qualitative and quantitative information about proteins and metabolites; 2) align multiple datasets; 3) perform differential analysis of proteomics and metabolomics datasets; and 4) use commonly used protein and metabolite databases. Introduction of chromatography, mass spectrometry, and isotopic patterns of proteins and metabolites to provide background information for students to understand the nature of mass spectrometry data.
Credit Hours: (3)
Prerequisite(s): BINF 6200 or equivalent.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6350 - Biotechnology and Genomics Laboratory
Introduction of the molecular biological methods by which samples are converted to a state from which sequence information can be produced. When sequence data is produced in a highly parallel fashion across a large fraction of a genome it is the basis of genomics. For historical reasons, the sample put on a sequencer is called a library, and the art of genomics lies in library construction. The experimental design and the technical details of library construction significantly affect the analyses that are appropriate and the conclusions that can be made. Lectures cover the design of experiments, how to critically read the literature to select an appropriate protocol for a variety of experimental purposes, and follow it to transform a sample into high quality sequence data. Quality control and library validation methods are explained. Topics include: selecting applications tuned to the experiment design to ensure proper data analysis and interpretation. Course grade includes performance in BINF 6350L .
Credit Hours: (3)
Prerequisite(s): A background in molecular biology and biochemistry or permission of instructor.
Corequisite(s): BINF 6350L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6350L - Biotechnology and Genomics Hands on Laboratory
Hands-on experience producing sequencing templates and libraries. Introduction to the practical skills needed to carry out a series of experiments that result in sequence data. The unifying concept is to characterize allelic variants of selected genes from related organisms. Students purify nucleic acid and then produce a selected subset of each genome using PCR. Quality control via spectroscopy, gel electrophoresis and quantitative PCR are performed. Sequencing libraries are produced and run on the Ion Torrent PGM and the ABI 3130 Genetic Analyzer. The CLCbio Genomics Workbench software for assessing data quality and identifying polymorphisms will be utilized. Students expected to keep laboratory notebooks that allow all aspects of experiments to be reconstructed.
Credit Hours: (0)
Corequisite(s): BINF 6350 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6380 - Advanced Bioinformatics Programming
Advanced algorithms in bioinformatics with an emphasis placed on the implementation of bioinformatics algorithms in the context of parallel processing. Topics covered depend on instructor expertise and student interest, but may include assembly of short read fragments from next-generation sequencing platforms, clustering algorithms, machine learning, development of multi-threaded applications, developing for multi-core processors and utilization of large clusters and “cloud” supercomputers. Students are expected to complete a significant independent project. Course includes hands-on experience with multi-threaded programming.
Credit Hours: (3)
Prerequisite(s): BINF 6112 or equivalent or permission of instructor.
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BINF 6382 - Accelerated Bioinformatics Programming
Computationally intensive algorithms in bioinformatics with an emphasis placed on the implementation of bioinformatics algorithms in the context of parallel processing using modern hardware processor accelerators such as GPUs and FPGAs. Topics covered depend on instructor expertise and student interest but may include multi-threaded applications and developing for multi-core processors and for large clusters and other “cloud” computers. Students are expected to complete a significant independent project. Course grade includes performance in BINF 6382L .
Credit Hours: (3)
Prerequisite(s): BINF 6112 or equivalent or permission of instructor.
Corequisite(s): BINF 6382L .
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6382L - Accelerated Bioinformatics Programming Laboratory
Hands-on experience with accelerated programming in bioinformatics.
Credit Hours: (0)
Prerequisite(s): BINF 6112 or equivalent, or permission of instructor.
Corequisite(s): BINF 6382 .
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6399 - Principles of Team Science
Introduction of appropriate project design, implementation, and management skills needed to function as a small team solving typical problems in Bioinformatics. Students are given realistic problems and are required to develop specifications, deliverables, timelines, and costs. Under faculty supervision, the group assigns roles, responsibilities, and deadlines in order to complete the project and then execute the project. At the end of the course, the group produces a written document with deliverables and makes a formal presentation of the project.
Credit Hours: (3)
Restriction(s): Permission of department.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6400 - Internship Project
Project is chosen and completed under the guidance of an industry partner, and results in an acceptable technical report.
Credit Hours: (1 to 3)
Restriction(s): Admission to graduate standing in Bioinformatics.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6600 - Bioinformatics Seminar
Weekly seminars are given by bioinformatics researchers from within the University and across the world.
Credit Hours: (1)
Restriction(s): Admission to graduate standing in Bioinformatics.
Cross-listed Course(s): BINF 8600 .
Most Recently Offered (Day): Fall 2018, Spring 2018, Fall 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6601 - Bioinformatics Journal Club
Each week, a student in the course is assigned to choose and present a paper from the primary bioinformatics literature.
Credit Hours: (1)
Restriction(s): Admission to graduate standing in Bioinformatics.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6880 - Independent Study
Faculty supervised research experience to supplement regular course offerings.
Credit Hours: (1 to 3)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 6900 - Master’s Thesis
Project is chosen and completed under the guidance of a graduate faculty member, and will result in an acceptable master’s thesis and oral defense.
Credit Hours: (1 to 3)
Restriction(s): 12 graduate credit hours and permission of instructor.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8010 - Topics in Bioinformatics
Topics in bioinformatics and genomics selected to supplement the regular course offerings. A student may register for multiple sections of the course with different topics in the same semester or in different semesters.
Credit Hours: (3)
Restriction(s): Permission of department.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8100 - Biological Basis of Bioinformatics
Provides a foundation in molecular genetics and cell biology focusing on foundation topics for graduate training in bioinformatics and genomics.
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics and undergraduate training in Computer Science or other non-biological discipline.
Most Recently Offered (Day): Fall 2018, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8101 - Energy and Interaction in Biological Modeling
Topics include: the major organic and inorganic chemical features of biological macromolecules; the physical forces that shape biological molecules, assemblies and cells; the chemical driving forces that govern living systems; the molecular roles of biological macromolecules and common metabolites; and the pathways of energy generation and storage. Each section of the course builds upon the relevant principles in biology and chemistry to explain the most common mathematical and physical abstractions used in modeling in the relevant context.
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8111 - Bioinformatics Programming I
Introduces fundamentals of programming for bioinformatics using a high-level object-oriented language such as Java or Python. Also introduces object-oriented programming, analysis of algorithms and fundamental sequence alignment methods. Students learn productive use of the Unix environment, focusing on Unix utilities that are particularly useful in bioinformatics. Course grade includes performance in BINF 8111L .
Credit Hours: (3)
Restriction(s): Admission to graduate standing in Bioinformatics or permission of instructor.
Corequisite(s): BINF 8111L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8111L - Bioinformatics Programming I Laboratory
Hands-on experience in programming to solve bioinformatics problems.
Credit Hours: (0)
Corequisite(s): BINF 8111 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8112 - Bioinformatics Programming II
Continuation of BINF 8111 . In this second semester, students practice and refine skills learned in the first semester. New topics include: programming as part of a team, using sequence analysis algorithms in realistic settings; writing maintainable and re-usable code; and graphical user interface development. Course grade includes performance in BINF 8112L .
Credit Hours: (3)
Prerequisite(s): BINF 8111 or permission of instructor.
Corequisite(s): BINF 8112L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8112L - Bioinformatics Programming II Laboratory
Hands-on experience in programming to solve bioinformatics problems.
Credit Hours: (0)
Corequisite(s): BINF 8112L or permission of instructor.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8151 - Professional Communications
Principles and useful techniques for effective oral presentations, poster presentations, scientific writing, use of references and avoiding plagiarism. Students critique and help revise each other’s presentations and learn how to avoid common pitfalls. In addition, students learn how to properly organize and run a meeting. Students prepare a CV, job application letter, and job talk.
Credit Hours: (1)
Cross-listed Course(s): GRAD 6151 and GRAD 8151 .
Most Recently Offered (Day): Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8200 - Statistics for Bioinformatics
Introduction of statistical methods commonly used in bioinformatics. Basic concepts from probability, stochastic processes, information theory, and other statistical methods are introduced and illustrated by examples from molecular biology, genomics and population genetics with an outline of algorithms and software. R is introduced as the programming language for homework. Course grade includes performance in BINF 8200L .
Credit Hours: (3)
Restriction(s): Permission of department.
Corequisite(s): BINF 8200L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8200L - Statistics for Bioinformatics Laboratory
Introduces R and its application in solving common statistical problems in bioinformatics. Basic relevant concepts from probability, probability distributions, and statistical inference are introduced and illustrated by examples from bioinformatics applications using R.
Credit Hours: (0)
Corequisite(s): BINF 8200 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8201 - Molecular Sequence Analysis
Introduction of the basic computational methods and open sources software commonly used in molecular sequence analysis. Topics include: biological sequence data formats and major public databases, concepts of computer algorithms and complexity, introductions to principle components analysis and data clustering methods, dynamics of genes in populations, evolutionary models of DNA and protein sequences, derivation of amino acid substitution matrices, algorithms for pairwise sequence alignments and multiple sequence alignments, algorithms for fast sequence database search, methods for molecular phylogenetic analysis, hidden Markov models and neural networks for sequence pattern and family recognition, and introductions to genome evolution and comics data analysis. Course grade includes performance in BINF 8201L .
Credit Hours: (3)
Prerequisite(s): BINF 8100 or equivalent.
Corequisite(s): BINF 8201L .
Most Recently Offered (Day): Spring 2018, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8201L - Molecular Sequence Analysis Laboratory
Hands-on experience with common software methods for biological sequence data analysis. Topics include: Basic UNIX utilities, principle component analysis, clustering analysis, global and local pair-wise sequence alignments, multiple sequence alignments, sequence database search methods, phylogenetic tree constructions, hidden Markov models, and neural networks.
Credit Hours: (0)
Prerequisite(s): BINF 8100 or equivalent.
Corequisite(s): BINF 8201 .
Most Recently Offered (Day): Spring 2018, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8202 - Computational Structural Biology
Topics include: (a) the fundamental concepts of structural biology (chemical building blocks, structure, superstructure, folding, etc.); (b) structural databases and software for structure visualization; (c) Structure determination and quality assessment; (d) protein structure comparison and the hierarchical nature of biomacromolecular structure classification; (e) protein structure prediction and assessment; and (f) sequence and structure-based functional site prediction. Course grade includes performance in BINF 8202L .
Credit Hours: (3)
Prerequisite(s): BINF 8101 and BINF 8201 , or their equivalents.
Corequisite(s): BINF 8202L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8202L - Computational Structural Biology Laboratory
The use and applications of: (a) structural classification databases; (b) software for visualization of biological structures; (c) computational methods to evaluate and compare biological structures; (d) computational methods to align biological structures; and (f) computational methods to predict biological structures from sequence.
Credit Hours: (0)
Corequisite(s): BINF 8202 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8203 - Genomics
Surveys the application of high-throughput molecular biology and analytical biochemistry methods and data interpretation for those kinds of high volume biological data most commonly encountered by bioinformaticians. The relationship between significant biological questions, modern genomics technology methods, and the bioinformatics solutions that enable interpretation of complex data is emphasized. Topics include: genome sequencing and assembly, annotation, and comparison; genome evolution and individual variation; function prediction; gene ontologies; transcription assay design, data acquisition, and data analysis; metabolic pathways and databases and their role in genome analysis. Course grade includes performance in BINF 8203L .
Credit Hours: (3)
Prerequisite(s): BINF 8100 or equivalent.
Corequisite(s): BINF 8203L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8203L - Genomics Laboratory
Hands-on experience with software methods for genome-scale data analysis. Topics include: Genome sequencing and assembly, genome annotation, genome comparison. Functional classification and gene ontologies. Genome evolution and individual variation. Transcriptomic and epigenetic assay design, data acquisition, and data analysis.
Credit Hours: (0)
Prerequisite(s): BINF 8100 or equivalent.
Corequisite(s): BINF 8203 .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8204 - Mathematical Systems Biology
Introduces basic concepts, principles and common methods used in systems biology. Emphasizes on molecular networks, models and applications, and covers the following topics: the structure of molecular networks; network motifs, their system properties and the roles they play in biological processes; complexity and robustness of molecular networks; hierarchy and modularity of molecular interaction networks; kinetic proofreading; optimal gene circuit design; and the rules for gene regulation.
Credit Hours: (3)
Prerequisite(s): BINF 8200 and BINF 8210 , or equivalents.
Most Recently Offered (Day): Spring 2016, Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8205 - Computational Molecular Evolution
Major aspects of molecular evolution and phylogenetics with an emphasis on the modeling and computational aspects of the fields. Topics include: models of nucleotide substitution, models of amino acid and codon substitution, phylogenetic reconstruction, maximum likelihood methods, Bayesian methods, comparison of phylogenetic methods and tests on trees, neutral and adaptive evolution and simulating molecular evolution. Students obtain an in-depth knowledge of the various models of evolutionary processes, a conceptual understanding of the methods associated with phylogenetic reconstruction and testing of those methods and develop an ability to take a data-set and address fundamental questions with respect to genome evolution.
Credit Hours: (3)
Prerequisite(s): BINF 8200 and BINF 8201 , or permission of instructor.
Most Recently Offered (Day): Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8210 - Machine Learning for Bioinformatics
Introduces commonly used machine learning methods in the field of bioinformatics. Topics include: dimension reduction using principal component analysis, singular value decomposition, and linear discriminant analysis, clustering using k-means, hierarchical, expectation maximization approaches, classification using k-nearest neighbor and support vector machines. To help understand these methods, basic concepts from linear algebra, optimization, and information theory are explained. Application of these machine learning methods to solving bioinformatics problems are illustrated using examples from the literature.
Credit Hours: (3)
Prerequisite(s): BINF 8200 , BINF 8200L , and Calculus.
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8211 - Design and Implementation of Bioinformatics Databases
By the end of the course, students are able to: understand different types of data models, know how hierarchical and relational models work and give examples that are widely used for biological databases, understand the capabilities of a standard, open source RDBMS, understand the tasks required for data integration and how to use SQL as a research tool. Introduction of XML, XML Schema, and BioOntologies as widely used data exchange and organization tools in bioinformatics databases. Course grade includes performance in BINF 8211L .
Credit Hours: (3)
Prerequisite(s): Permission of instructor.
Corequisite(s): BINF 8211L . Introduces the fundamentals of database modeling as used in bioinformatics.
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8211L - Design and Implementation of Bioinformatics Databases Laboratory
The practice of skills described in the lecture, particularly design principles for the relational model and using SQL, and complete projects in which they design, implement, prototype and use a research biological database. Students are able to obtain correctly formatted data from public repositories and use XML, XMLSchema, and BioOntologies as tools in the data integration process; and use SQL to create, populate and perform complex queries on genomics databases.
Credit Hours: (0)
Prerequisite(s): Permission of instructor.
Corequisite(s): BINF 8211 .
Most Recently Offered (Day): Spring 2018, Spring 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8310 - Advanced Statistics for Genomics
Canonical linear statistics (t-test, ANOVA, PCA) and their non-parametric equivalents. Examines the application of Bayesian statistics, Hidden Markov Models and machine learning algorithms to problems in bioinformatics. Students should have fluency in a high-level programming language (PERL, Java, C#, Python or equivalent) and are expected, in assignments, to manipulate and analyze large public data sets. Utilizes the R statistical package with the bioconductor extension. Course grade includes performance in BINF 8310L .
Credit Hours: (3)
Prerequisite(s): BINF 8200 or equivalent.
Corequisite(s): BINF 8310L .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8310L - Advanced Statistics for Genomics Laboratory
Hands-on experience with using the R programming language.
Credit Hours: (0)
Prerequisite(s): BINF 8200 or equivalent.
Corequisite(s): BINF 8310 .
Most Recently Offered (Day): Spring 2018, Spring 2017, Spring 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8311 - Biophysical Modeling
Topics include: an overview of mechanical force fields; energy minimization; dynamics simulations (molecular and coarse-grained); Monte-Carlo methods; systematic conformational analysis (grid searches); classical representations of electrostatics (Poisson-Boltzmann, Generalized Born and Coulombic); free energy decomposition schemes; and hybrid quantum/classical (QM/MM) methods.
Credit Hours: (3)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8312 - Computational Comparative Genomics
Introduces computational methods for comparative genomics analyses. The course covers the following topics: the architecture of prokaryotic and eukaryotic genomes; the evolutionary concept in genomics; databases and resources for comparative genomics; principles and methods for sequence analysis; evolution of genomes; comparative gene function annotation; evolution of the central metabolic pathways and regulatory networks; genomes and the protein universe; cisregulatory binding site prediction; operon and regulon predictions in prokaryotes; and regulatory network mapping and prediction.
Credit Hours: (3)
Prerequisite(s): BINF 8201 or equivalent.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8313 - Structure, Function, and Modeling of Nucleic Acids
The course covers the following topics: atomic structure, macromolecular structure-forming tendencies and dynamics of nucleic acids; identification of genes which code for functional nucleic acid molecules, cellular roles and metabolism of nucleic acids; 2D and 3D abstractions of nucleic acid macromolecules and methods for structural modeling and prediction; modeling of hybridization kinetics and equilibria; and hybridization-based molecular biology protocols, detection methods and molecular genetic methods, and the role of modeling in designing these experiments and predicting their outcome.
Credit Hours: (3)
Prerequisite(s): BINF 8100 - BINF 8101 or equivalent.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8318 - Computational Proteomics and Metabolomics
Introduces commonly used computational algorithms, software tools, and databases for analyzing mass spectrometry-based proteomics and metabolomics data. Students learn how to: 1) implement algorithms for processing raw mass spectrometry data and extracting qualitative and quantitative information about proteins and metabolites; 2) align multiple datasets; 3) perform differential analysis of proteomics and metabolomics datasets; and 4) use commonly used protein and metabolite databases. Also introduces chromatography, mass spectrometry, and isotopic patterns of proteins and metabolites to provide background information for understanding the nature of mass spectrometry data.
Credit Hours: (3)
Prerequisite(s): BINF 8200 or equivalent.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8350 - Biotechnology and Genomics Laboratory
Introduction to the molecular biological methods by which samples are converted to a state from which sequence information can be produced. When sequence data is produced in a highly parallel fashion across a large fraction of a genome it is the basis of genomics. For historical reasons, the sample put on a sequencer is called a library, and the art of genomics lies in library construction. The experimental design and the technical details of library construction significantly affects the analyses that are appropriate and the conclusions that can be made. Lectures cover the design of experiments, how to critically read the literature to select an appropriate protocol for a variety of experimental purposes, and follow it to transform a sample into high quality sequence data. Quality control and library validation methods are explained. Topics include selecting applications tuned to the experiment design to ensure proper data analysis and interpretation. Course grade includes performance in BINF 8350L .
Credit Hours: (3)
Prerequisite(s): A background in molecular biology and biochemistry or permission of instructor.
Corequisite(s): BINF 8350L .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8350L - Biotechnology and Genomics Hands on Laboratory
Hands-on experience producing sequencing templates and libraries, discussed in the lecture. Introduces students to the practical skills needed to carry out a series of experiments that result in sequence data. The unifying concept is to characterize allelic variants of selected genes from related organisms. Students purify nucleic acid and then produce a selected subset of each genome using PCR. Quality control via spectroscopy, gel electrophoresis and quantitative PCR is performed. Sequencing libraries are produced and run on the Ion Torrent PGM and the ABI 3130 Genetic Analyzer. The CLCbio Genomics Workbench software for assessing data quality and identifying polymorphisms is utilized. Students are expected to keep laboratory notebooks that allow all aspects of experiments to be reconstructed.
Credit Hours: (0)
Corequisite(s): BINF 8350 .
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8380 - Advanced Bioinformatics Programming
Advanced algorithms in bioinformatics with an emphasis placed on the implementation of bioinformatics algorithms in the context of parallel processing. Topics covered depend on instructor expertise and student interest, but may include assembly of short read fragments from next-generation sequencing platforms, clustering algorithms, machine learning, development of multi-threaded applications, developing for multi-core processors and utilization of large clusters and “cloud” supercomputers. Students are expected to complete a significant independent project. Course includes hands-on experience with multi-threaded programming.
Credit Hours: (3)
Prerequisite(s): BINF 8112 or equivalent, or permission of instructor.
Most Recently Offered (Day): Fall 2018, Fall 2017, Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8382 - Accelerated Bioinformatics Programming
Computationally intensive algorithms in bioinformatics with an emphasis placed on the implementation of bioinformatics algorithms in the context of parallel processing using modern hardware processor accelerators such as GPUs and FPGAs. Topics covered depend on instructor expertise and student interest but may include multi-threaded applications and developing for multi-core processors and for large clusters and other “cloud” computers. Students are expected to complete a significant independent project. Course grade includes performance in BINF 8382L .
Credit Hours: (3)
Prerequisite(s): BINF 8112 or equivalent, or permission of instructor.
Corequisite(s): BINF 8382L .
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8382L - Accelerated Bioinformatics Programming Laboratory
Hands-on experience with accelerated programming in bioinformatics.
Credit Hours: (0)
Prerequisite(s): BINF 8112 or equivalent, or permission of instructor.
Corequisite(s): BINF 8382 .
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8600 - Bioinformatics Seminar
Departmental seminar. Weekly seminars will be given by bioinformatics researchers from within the University and across the world.
Credit Hours: (1)
Restriction(s): Admission to graduate standing in Bioinformatics.
Cross-listed Course(s): BINF 6600 .
Repeatability: May be repeated for credit.
Most Recently Offered (Day): Fall 2018, Spring 2018, Fall 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8601 - Bioinformatics Journal Club
Each week, a student in the class is assigned to choose and present a paper from the primary bioinformatics literature.
Credit Hours: (1)
Restriction(s): Admission to graduate standing in Bioinformatics.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8911 - Bioinformatics Research Rotation I
Faculty supervised research experience in bioinformatics to supplement regular course offerings.
Credit Hours: (2)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8912 - Bioinformatics Research Rotation II
Faculty supervised research experience in bioinformatics to supplement regular course offerings.
Credit Hours: (2)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8990 - Pre-Dissertation Research
Students conduct research in bioinformatics under the direction of one or more Bioinformatics faculty. A major goal of this course is to prepare the student for the Qualifying Examination.
Credit Hours: (1 to 6)
Restriction(s): Permission of department
Repeatability: May be repeated for credit up to 6 credit hours
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BINF 8991 - Doctoral Dissertation Research
Individual investigation culminating in the preparation and presentation of a doctoral dissertation. A student may register for multiple sections of this course in the same semester or different semesters.
Credit Hours: (1 to 9)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5000 - Advanced Topics in Biology
Courses in selected topics and advanced studies in biology. Lecture and laboratory hours will vary with the topics taught.
Credit Hours: (1 to 4)
Repeatability: May be repeated for credit with change of topic.
Most Recently Offered (Day): Fall 2018, Spring 2018, Fall 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5111 - Evolution
Theories of evolution and forces, which affect gene frequencies.
Credit Hours: (3)
Prerequisite(s): BIOL 3166.
Most Recently Offered (Day): Fall 2018, First Summer 2018, Fall 2017
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5121 - Advanced Biometry
Advanced biostatistics design and analysis of experiments. Three lecture hours and one laboratory period of three hours a week.
Credit Hours: (4)
Prerequisite(s): BIOL 2140 or equivalent, BIOL 3166 or equivalent, and one STAT course.
Most Recently Offered (Day): Spring 2017, Spring 2016, Spring 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5144 - Advanced Ecology
Energy flow, nutrient cycles, community structure, population growth and regulation. Three lecture hours and one laboratory period of three hours a week.
Credit Hours: (4)
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5162 - Advanced Biotechnology I
Problem-based learning approach where students work in teams to develop solution strategies that use biotechnology to solve real-world problems.
Credit Hours: (3)
Prerequisite(s): BIOL 3161 or BIOL 3166 with grade of C or above.
Most Recently Offered (Day): Fall 2016
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
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BIOL 5163 - Advanced Biotechnology II
Students work in teams to implement solution strategies developed in BIOL 5162 that use biotechnology to solve real-world problems. One laboratory period and two lecture hours per week.
Credit Hours: (3)
Prerequisite(s): BIOL 3161 or BIOL 3166 with grade of C or above and permission of instructor.
Most Recently Offered (Day): Course has not been offered at this time in the past 3 years
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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BIOL 5167 - Medical Genetics
Various applications of genetics to human health, including studies of the inheritance of diseases in families, mapping of disease genes to specific locations on chromosomes, analyses of the molecular mechanisms through which genes cause disease, diagnosis and treatment of genetic disease, and genetic counseling.
Credit Hours: (3)
Restriction(s): Admission to Graduate School in Biology or permission of instructor.
Most Recently Offered (Day): Fall 2017, Fall 2016, Fall 2015
Most Recently Offered (Evening): Course has not been offered at this time in the past 3 years
Schedule of Classes
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