BIOI 7601 Selected Studies in Biomedical Science for Bioinformatics Students I.
Credits: 3 semester Hours.
Prerequisite: permission of Bioinformatics faculty.
Status: required.
Selected topics in structural, cellular and molecular biology chosen among the lectures offered in IDPT 7801.
 
BIOI 7602 Selected Studies in Biomedical Science for Bioinformatics Students II.
Credits: 3 semester Hours. Prerequisite: permission of Bioinformatics faculty.
Status: required.
Selected topics in structural, cellular and molecular biology chosen among the lectures offered in IDPT 7802.
 
BIOI 7603 Selected Studies in Biomedical Science for Bioinformatics Students III.
Credits: 3 semester Hours. Prerequisite: permission of Bioinformatics faculty.
Status: required.
Selected topics in structural, cellular and molecular biology chosen among the lectures offered in IDPT 7803.
 
BIOI 7606 Biology, Mathematics or Computer Science.
Credits: minimum 2 semester Hours. Prerequisite: permission of Instructor.
Status: required.
This requirement is designed to fill in one or two of the deficient areas of study that a student may have after transferring and completing the required courses for the degree. Most often, based on the type of student who applies to the program, the topic of this course will include some aspect of biology. However, for students with a master’s degree in the biological sciences, this requirement will include either mathematics, statistics or computer sciences topics.
 
BIOI-7711 Bioinformatics I.
Credits: 4 semester hours.
Prerequisite: permission of instructor.
Status: required.
What is bioinformatics, and why study it? How is large scale molecular biology data generated, how can researchers gain access to it, and what is the quality of the data? Topics discussed include nucleotide sequence data such as: genomic sequencing, expressed sequence tags, gene expression, transcription factor binding sites and single nucleotide polymorphisms.
Metadata: summary and reference systems, finding new types of data online, likely growth areas. Private and future data sources. Computational representations of molecular biological data, data storage techniques: databases (flat, relational and object oriented), and controlled vocabularies.
General data retrieval techniques: indices, Boolean search, fuzzy search and neighboring. Biological data types and their special requirements: sequences, macromolecular structures, chemical compounds, genetic variability, and connections to clinical data. Representations of patterns and relationships: alignments, regular expressions, hierarchies, and graphical models (including Markov chains and Bayes nets).
Visualization: methods for presenting large quantities of biological data, particularly sequence viewers, 3D structure viewers, anatomical visualization, and database-driven web sites.
Interoperability: the challenges of data exchange and integration, including ontologies, interchange languages and standardization efforts. XML, UMLS, CORBA and OMG/Life Sciences.
Inference problems and techniques for molecular biology with an overview of key inference problems in biology, including: homology identification, genomic sequence annotation, protein structure prediction, protein function prediction, gene expression characterization, network identification, and drug discovery.
 
BIOI-7712 Bioinformatics II.
Credits: 4 semester hours.
Prerequisite: BIOI 7711.
Status: required.
This course continues to define and discuss inference problems and techniques for molecular biology. Overview of key inference problems in biology: homology identification, genomic sequence annotation, protein structure prediction, protein function prediction, gene expression characterization, network identification, and drug discovery. Machine learning: neural networks, genetic algorithms, simulated annealing. Evaluation of prediction methods: parametric tests, cross-validation and empirical significance testing. Sequence alignment methods: dot plots, dynamic programming, hidden Markov models. Current alignment methods: PSI-BLAST, Needleman–Wunsch, Smith–Waterman. Protein structure predictions: secondary structure, fold recognition, new fold methods. Computer simulation methods: molecular dynamics, Monte Carlo.

Additionally, this course addresses recent developments in bioinformatics and focus on advanced issues in specific areas including (but not limited to) information extraction from biomedical literature, inference of biochemical networks from high–throughput data, and prediction of protein function.
 
PHCL-7605 Ethics in Research.
Credits: 1 semester hour.
Prerequisite: permission of instructor.
Status: required.
This is a course designed to introduce graduate students and postdoctoral fellows to issues related to ethics of research, publication, and reviewing of manuscripts and grants. Lectures and class discussions in small groups of the history of scientific fraud, examples from recent cases, examples of ethical dilemmas and consequences of fraud will be covered.
 
BIOI-8990 Doctoral Thesis.
Credits: Minimum 30 semester hours.
Prerequisite: successful completion of required bioinformatics courses.
Status: required
Doctoral study for the Ph.D. degree by students in the AHS/Bioinformatics program only.