Program in Bioinformatics & Proteomics/Genomics

MASTERS PROGRAM IN BPG                           

PROGRAM DESCRIPTION
The Master's in BPG provides a solid basic background in bioinformatics. The computatoral and research training positions graduates well for further training (PhD, MD or other doctoral programs), or for jobs in academic or industrial research areas.

STUDENT LEARNING OBJECTIVES (SLO'S) FOR BIOINFORMATICS MSBS DEGREE

ADMISSION REQUIREMENTS
1. Earned bachelor’s degree or earned graduate degree from an accredited college or university. Applicants with a degree in progress will be considered.

2. GPA of 3.0 or above (on a 4-point scale). Students with a GPA of 2.5 or above, but below 3.0, may apply for provisional acceptance. This will change to Regular (non-probationary) status, if their first term graduate coursework has a GPA of 3.0 or above (4-point scale). 

3. The GRE has been waived for all U.S. students who have a GPA of 3.0 or above, or for students who can submit MCAT scores of 25 or higher. For all other students, the GRE requirements are as follows: Minimum GRE composite score of 300 (combined verbal and quantitative) and 3.5 (analytical). GRE scores are required and they must be current (within the past five years).  

4. Official transcripts for undergraduate and any graduate education.

5. Three letters of recommendation from college faculty or research supervisors

6. Completed online application form, at https://apply.utoledo.edu, and accompanying application fee (or waiver) *

7. TOEFL scores for applicants whose native language is not English.  We require a score of 550 or higher for the paper-administered version, 213 or higher for the computer-administered version, and 80 or higher for the Internet-administered version. 

Information for International Students can be found here: http://www.utoledo.edu/graduate/prospectivestudents/admission/guidelines.html

Previous research experience is considered, but not required.  Students can begin at the start of any term, though Fall entry is recommended.  Admissions are made on a rolling basis until the class is filled. There is no fixed deadline. 

* Students who have already applied to the Program can check their application status online at this link http://application.utoledo.edu.  If a student's application is incomplete, this site will indicate which documents are missing.

Click here for BPG MSBS COURSE SCHEDULE (in full PDF format ) OR  Click here for HTML format.

APPROVED ELECTIVES FOR BPG MASTER'S AND PIPELINE DEGREES

GRADUATE STUDENT TRAVEL SUPPORT
Our students are encouraged to attend appropriate regiohnal and national meetings. One commonly attended meeting is annual GLBIO meeting found here, http://www.iscb.org/glbio2015.  Please see the Graduate Studies Handbook for additional student travel information: http://www.utoledo.edu/graduate/hsc/hsc_handbook10/FinancialSupport.html 

SELECTING A MAJOR ADVISOR AND RESEARCH PROJECT
1) Before selecting a major advisor for the Research Project, the student spends two 6-week rotations with two different faculty members.  In each rotation, the student participates in an ongoing research program.  The student selects a major advisor from among approved faculty members.

2) A Scholarly Project (BIPG 5900) or Thesis in Bioinformatics (BIPG 6990) is required with a minimum of 10 credit hours. Each student has an advisory committee composed of at least 3 members; the major advisor, plus a minimum of two others, one of whom should be a BPG faculty member.

3) The student submits a Project Proposal for review and approval by the advisory committee prior to beginning work on the project.

MENTORS for BPG Students (full PDF format)
Note: Faculty members not currently on the approved list can be added, if the faculty member and Program both agree.

REQUIRED FORMS for current Graduate Students: (click form name to access)

1)  Partially-completed Plan of Study form for the BPG Master's Degree.  You will complete the top portion and obtain the required signatures on Page 2. This form is required to be submitted BEFORE the student completes 12 credit hours (during the Fall 1 term).

(Fully blank form from the Graduate School: Plan of Study for the Master's Degree.)

2)  G.R.A.D. Form (Graduate Research Advisory Committee Approval & Assurances Form) is required prior to the student beginning any research (by the end of the Fall 1 term).

3)  Acceptance of Thesis form: Please review this page on the Graduate School website for specific instructions on preparing your thesis, and required forms before and after your defense. Please keep in mind that the Qualifying Exam must be taken BEFORE thesis research begins.   During the semester you are doing your thesis, you must be registered for at least one credit. This is a Graduate School requirement.  This should be a bioinformatics courseIf you wish to take a course from another program, please discuss this with your advisor and Program Director before registering.

SUGGESTED COURSE OPTIONS 
Students are likely to have diverse backgrounds.  For example, some might have a background in computer science or statistics, while others may have a background in the biological sciences. The same core courses are taken by all students.  However, the electives chosen will be different.  

BUSINESS SELECTIVES
For the MSBS in BIPG, up to two of the following College of Business & Innovation courses may be used as electives, if your Thesis Committee agrees.

HURM6700  HUMAN RESOURCES MANAGEMENT  3cr  (Fall)  UT Department of Management 
A survey of the functions and current trends in human resources management.  Special emphasis on research methods, tools and techniques for in-depth understanding of problems and challenges faced by medium-sized firms.

HURM6720  ADVANCED NEGOTIATIONS AND CONFLICT RESOLUTION  3cr  (Fall)  UT Department of Management NOT OFFERED FALL 2015
This course is designed to improve students' skills in all phases of negotiation and conflict resolution strategies and techniques.  The course is based on a series of simulated negotiations in a variety of contexts.

HURM6730  PERFORMANCE MANAGEMENT  3cr  (Spring)   UT Department of Management  
This course is designed to provide practical working knowledge of the processes of setting expectations, monitoring performance, coaching and developing employees, and assessing and rewarding good performance in rapidly changing organizations

MGMT6160  LEADING WITH POWER AND INFLUENCE  3cr  (Fall)   UT Department of Management
The primary focus of this course is the effective use of political and social influence in organizations. This course will develop the ability to recognize, analyze, and apply sources of power and influence beyond formal authority.

MGMT6150  LEADING AND DEVELOPING YOURSELF  3cr  (Fall)   UT Dept. of Management   
The course explores how one's own leadership competencies can be developed and applied most effectively in a variety of situations.

MOLECULAR SELECTIVES
The Molecular Selective will be selected from the following courses offered by various departments at UT and BGSU.  The course selected will depend on availability, scheduling and student background, with approval of the student's advisor, and Thesis Committee.  Note that tuition for any courses designated as Undergraduate courses (course number <5000) will have to be paid for by the student.

BMSP6310  SYSTEMS PATHOPHYSIOLOGY I:  2.5cr  (Spring: 1st half of term)   UT Biomedical Sciences Program
The course will cover the fundamentals and current research efforts in biomedical sciences, emphasizing diseases of the cardiovascular, immune, and nervous systems, as well as metabolic and infectious diseases. 

BMSP6320  SYSTEMS PATHOPHYSIOLOGY II:  2.5cr  (Spring: 2nd half of term)   UT Biomedical Sciences Program
The course will cover the fundamentals and current research efforts in biomedical sciences, emphasizing diseases of the cardiovascular, immune and nervous systems, as well as metabolic and infectious diseases.

BMSP6330  CURRENT PROBLEMS AND RESEARCH APPROACHES IN PROTEIN STRUCTURE  2.5cr  (Fall)   UT Biomedical Sciences Program
The course will cover principles of protein structure/function relationships in proteins, protein folding, ligand-protein interactions and mechanism of enzyme-catalyzed reactions. Special emphasis will be given to the present-day research.

BMSP6380  METHODS IN BIOMEDICAL SCIENCES  3cr  (Fall)  UT Biomedical Sciences Program
This course will cover the basic principles and applications, of sate-of-the-art technology in molecular biology, protein chemistry, and studies with culture cells, tissue explants and transgenic animal models.

CHEM8980 Section 001   SPECIAL TOPICS IN CHEMISTRY: MOLECULAR MODELING   4cr   (Spring)
UT Department of Chemistry    
Discussions of newly-developing areas in chemistry research.

PUBH6130  MOLECULAR EPIDEMIOLOGY  3cr  (Fall)   UT Dept. Public Health/Preventative Medicine
The course focuses on the application of epidemiological techniques to the study of effects of occupational and environmental exposures.

PUBH6180/8180   CANCER EPIDEMIOLOGY   3cr   (Summer - Online)   UT Dept. Public Health/Preventative Medicine
Focuses on a number of cancers, including the most incident cancers in the United States. Provides a broad overview of cancer epidemiology, and basic substantive knowledge regarding many cancers and their risk factors, prevention and biology and pathogen.

BGSU:  BIOL5660  BGSU  GENOMICS  Graduate Students  3cr  (Fall 2014, and bi-annually thereafter) BGSU College of Arts/Sciences
A contemporary analysis of the molecular biological and bioinformatic methods for the study of complete genomes of organisms.

PUBH6070 GENETIC EPIDEMIOLOGY  3cr   (Summer)  UT Department of Public Health and Preventative Medicine
Introduces genetic epidemiology methods, principles of population genetics including linkage and association studies used in assessing familial aggregation, and transmission patterns for identifying the genetic basis of common diseases. 

BGSU:  CHEM6940  WORKSHOP ON CURRENT TOPICS IN CHEMISTRY  1-4cr  (Taught on demand)  BGSU College of Arts/Sciences
Workshop on current topics and issues within discipline: topics vary from semester to semester.

PROGRAMMING SELECTIVES
The Advanced Programming Selective will be selected from the following courses offered by various departments at UT and BGSU.  The course selected will depend on availability, scheduling and student background, with approval of the student's advisor and Thesis Committee.  Note that tuition for courses designated as undergraduate courses will have to be paid for by the student.

CSET4100   SERVER-SIDE PROGRAMMING  3cr  (Fall)   UT Computer Science & Engineering Technology
Covers Common Gateway Interface (CGI) programming on the Internet using the most popular scripting languages.  Topics include client-side programs, server-side programs, distributed database creation and searching.  Prerequisite: Junior standing.

INFS3380  WEB APPLICATION DEVELOPMENT I  3cr   (Summer - Online)  UT Department of Information Systems, Marketing, E-Commerce & Sales
An introduction to business application program development on the web using contemporary technologies with emphasis on client-side applications. Implications of information technology projects on organizations will be discusses. Prerequisite: INFS 3150

PUBH6110  CATEGORICAL DATA ANALYSIS  3cr   (Summer)   UT Dept. Public Health and Preventative Medicine
This course introduces the theory and application of methods for categorical data, with emphasis on biomedical and public health applications.  Topics include contingency tables, log-linear, logistic regression and Raush models, multivariate methods for matched pairs and longitudinal data.  The methods are illustrated with SAS and/or SPSS, R.

DATABASE MANAGEMENT SELECTIVES
The Database Management Selective will be selected from the following courses offered by various departments at UT and BGSU.  The course selected will depend on availability, scheduling and student background, with approval of the student's advisor and Thesis Committee.  Note that tuition for courses designated as undergraduate courses will have to be paid for by the student.

BGSU:  CS5620   DATABASE MANAGEMENT SYSTEMS   3cr  (Spring)   BGSU Department of Computer Science
Semantic models for conceptual and logical design of databases. Detailed study of relational systems: design, dependency, and normal forms. Use of interactive and embedded query languages. Overview of topics such as database connectivity, security, and object-oriented systems. Prerequisites: Admission to MS in CS program, or consent of department, plus CS202 or equivalent.

EECS 5560 DATABASE SYSTEMS I   3cr   (Fall)   UT Department of Electrical Engineering and Computer Science
The following topics are covered: relational database modeling, query languages, design issues and implementation issued of databases. An appropriate database language is introduced and used to demonstrate principles. Prerequisite: EECS1510

CMPT1420 MICROSOFT ACCESS DATABASE APPLICATIONS   2cr   (Spring)    UT Department of Business Technology
Hands-on analysis of the use of Access in solving business problems with an emphasis on the entering, updating, manipulating, storing and retrieving of information.                                                       

STUDENT LEARNING OBJECTIVES (SLO's) FOR BIOINFORMATICS MSBS DEGREE:             

Graduating students WILL BE ABLE TO:

1)     Describe mammalian and nonmammalian genome structure and function, including (for example): 

1.  Coding/non-coding sequence distribution
2.  Isochore structure
3.  Repeated element distribution
4.  Intron/exon structure and distribution
5.  Distribution and dynamics of methylation
6.  Transcription factor binding sites (for long- and short-range factors)

2)    Discuss the processes of genome evolution, including (for example): 

  1. Mechanisms of mutation
  2. Consequences and exploitation of SNPs
  3. Fixation of mutations
  4. Genetic drift
  5. Phylogenetics
  6. Major theories for the origin of novel genes
  7. Nature and basis of codon bias

3)    Describe and use analytic tools associated with systems/bioinformatic approaches, including (for example): 

  1. Transcriptomics – microarray analysis vs. deep sequencing
  2. Proteomic mass spectroscopic methods (identification and abundance)
  3. Determining statistical significance in large bioinformatic datasets
  4. Determination and structure of interaction networks
  5. Functional network maps 

4)    Carry out appropriate statistical analysis of sequence information, including (for example): 

  1. Probabilistic methods
  2. Deterministic methods
  3. Machine learning methods, including Support Vector Machines (SVMs)
  4. Cluster analysis

5)    Demonstrate competent use of existing bioinformatic and statistical software, including (for example): 

  1. R statistical tools
  2. Alignments and their interpretation
  3. Phylogenetic analyses
  4. Programs to predict genes and transcription factor binding sites
  5. Programs to display, predict and analyze 3D biomolecule structures

6)    Develop and use basic PERL programs for bioinformatic analyses, including (for example): 

  1. Familiarity with the UNIX operating system
  2. Writing scripts for extracting information from databases
  3. Creating databases
  4. Interfacing with supercomputers

7)    Apply bioinformatic methods to clinical problems, by demonstrating understanding of: 

  1. Biomarker discovery and validation
  2. Major diseases such as cancer, diabetes, and autoimmunity

8)    Communicate competently both in writing and orally 

  1. With fellow team members in research projects
  2. With the broader scientific public

9)    Demonstrate familiarity with and adherence to research ethics.

 

 

 

Last Updated: 12/29/15