Program in Bioinformatics & Proteomics/Genomics

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We are proud of our program alumni! 

The Program in Bioinformatics is part of the School of Biomarkers Research and Individualized Medicine (BRIM), a State of Ohio-recognized Center of Excellence at the University of Toledo. They provide students and researchers with the advanced analytical tools and approaches needed for state-of-the-art biomedical research. The Bioinformatics Program is associated with independent, but cooperating programs at Bowling Green State University and the University of Findlay.

Welcome! This page focuses on the degree programs we offer. In addition, the following pages on our site may be helpful:

We offer four degree programs:  

  1. Certificate in Bioinformatics & Biomarkers 
  2. Masters in Biomedical Sciences (MSBS)
  3. Dual degree bachelors/masters pipeline
  4. Professional Science Masters (PSM)

Frequently-asked questions:

CERTIFICATE DEGREE IN BIOINFORMATICS AND BIOMARKERS

The Bioinformatics and Biomarkers Certificate Program introduces students to the newly evolving fields of
bioinformatics, proteomics and genomics, and provides a core knowledge of analytical approaches used in these fields. The curriculum is designed to complement coursework and research of students enrolled in the University of Toledo Ph.D. in Biomedical Sciences Program, but also is open to other qualified students. 

Students can take one or two courses per term, earning the Certificate in one or two years.

Currently enrolled UT PhD in Biomedical Sciences or MSBS students may take individual BPG courses as electives, with permission of the instructor. To receive a Certificate in Bioformatics and Biomarkers, an online application must be submitted here: https://apply.utoledo.edu.

The Program is a joint effort of the University of Toledo and Bowling Green State University.

Requirements
Students enrolled in the Bioinformatics and Biomarkers Certificate Program must take four courses covering the following subject areas:

1)  Introduction to the scope of bioinformatics, proteomics and genomics: "BIPG5100/7100 "Fundamentals of BPG"
2) Training in statistical methods used in BPG: BIPG5200/7200"Statistical Methods in Bioinformatics"
3) Handling and manipulation of databases and introduction to computer programming skills needed to manipulate
    large quantities of nucleic acid  and protein sequence data: BIPG6100/7100 "Intro to Bioinformatic Computation".
4) EITHERBIPG6400/8400 Applications of BPG, in which faculty members using these methodologies will discuss
    and demonstrate how these techniques are utilized to solve research problems:
    OR: BRIM6200/8200 "Biomarker Discovery, Validation and Implementation", in which faculty provide an overview of
    biomedical discovery and validation techniques followed by application in selected aspects of individualized
    medicine. Upon completion of the Program, students will be prepared to utilize BPG research techniques and
    be able to interact with specialists in each BPG subdiscipline.

Curriculum
The curriculum consists of four, 3-credit courses (listed below). If you are in a doctoral program, the second (higher) course number is the one for which you should register.

Course No.                       Course Title, Description & Credits

Fall Year 1
BIPG5100/7100               Fundamentals of Bioinformatics and Proteomics/Genomics, 3 cr
                                        Introduction to scope of bioinformatics, proteomics and genomics

BIPG5200/7200                Statistical Methods in Bioinformatics, 3 cr
                                        Training in statistical methods used in BPG

Spring Year 1
BIPG6100/8100                Introduction to Bioinformatic Computation, 3 cr
                                        Handling and manipulation of databases and introduction to computer programming skills
                                        needed to manipulate large quantities of nucleic acid and protein sequence data.

 EITHER:  BIPG6400/8400              Application of Bioinformatics and Proteomics/Genomics, 3 cr
                                                     Faculty members using these methodologies will discuss and demonstrate
                                                     how these techniques are utilized to solve research problems.    

OR:        BRIM6200/8200             Biomarker Discovery, Validation & Implementation, 3cr
                                                    Faculty provide an overview of biomedical discovery and validation techniques
                                                    followed by application in selected aspects of individualized medicine. 

*BMSP6340 Current Problems & Research Approaches in Genes and Genomes, or equivalent course approved by the BPG Program, is required for admission into the BPG Certificate Program. 

APPLYING TO THE BIOINFORMATICS AND BIOMARKERS CERTIFICATE PROGRAM:
Applicants who are University of Toledo students must submit the following after applying online here: https://apply.utoledo.edu.

1) Official transcripts
2) Statement of purpose
3) One letter of recommendation is required. It must be signed, and on official letterhead. Two additional letters
    are optional, HOWEVER, in the event that a student decides to pursue the BPG MSBS degree, it will save time to have
    the required total of three letters of recommendation already on file.

Applicants who are NOT presently enrolled in classes at The University of Toledo must follow the requirements below, and submit the following through the online application here https://apply.utoledo.edu

1) Earned baccalaureate and GRE, or earned graduate degree from an accredited college or university
2) Minimum 3.0 undergraduate GPA; degree in process will be considered.
3) Minimum GRE 300 or minimum requirements set for the UT Ph.D. in Biomedical Sciences or MSBS programs
4) Official transcripts
5) Three (3) letters of recommendation, signed, and on official letterhead
6) Completed electronic application and $45.00 application fee 

All applications will be reviewed by the BPG/BRIM Program Admissions Committee. 

To receive a Certificate in Bioinformatics and Biomarkers, application must be submitted online at the following link:
https://apply.utoledo.edu.

Electronic, online application must be filed ONLY for those seeking a Certificate.  If a student takes all four courses, and does not formally apply online, they will NOT receive a Certificate. 

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MASTERS DEGREE IN BIOINFORMATICS

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.

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. Completed online application form, at http://apply.utoledo.edu, and accompanying application fee.
  3. 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). 
  4. GRE  

a) GRE has been waived for the following:

    • US students with GPA above 3.0
    • UT or University of Findlay pipeline students
    • Students who can substitute recent MCAT scores (25 or higher)

b) For all others our requirements are:

    • 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). The GRE is not required if you have MCAT scores as an alternative (taken by medical science and MD/PhD Program applicants as a national equivalent).


5. Official transcripts for undergraduate and any graduate education.
6. Three letters of recommendation from college faculty or research supervisors

International Students
     a) 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.  

     b) Visa requirements and admission guidelines for International students can be found at the following links:
         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

BPG MSBS Course Schedule (in full PDF format ) OR  Click here for HTML format

Approved ELECTIVES for BPG Masters and Pipeline Degrees 

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 o f
    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 semesters 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.

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UT DUAL-DEGREE (PIPELINE) PROGRAM
The Bioinformatics & Proteomics/Genomics Program along with the Department of Biological Sciences offers a Dual-Degree BS/MS in Biological Sciences and Bioinformatics. This "Pipeline" program is available to students at the end of their second year at the University of Toledo. For description of the "pipeline" program and curriculum information, click here for,  (HTML version)  OR  (pdf fully-formatted version).  The pipeline program is part of the new UT School of Biomarker Research & Individualized Medicine (BRIM), and the Colleges of Medicine & Life Sciences and of Natural Science & Mathematics.

How the Pipeline Program Works:
IN 5.5 YEARS, you can receive a Bachelors degree in Biological Sciences AND a Masters degree in Bioinformatics
If you are in UT's BSc program in Biological Sciences, you can take up to 9 semester credit hours of graduate coursework that can count towards BOTH the BSc degree AND the MSc in Bioinformatics. Getting both degrees this way allows you to:

  • Save between 1 and 2 years over what it would take to earn both degrees separately
  • Save the tuition and housing costs associated with that extra time
  • The GRE is not required for the pipeline program.
  • Improve job prospects or your chances of getting into top-tier graduate/professional programs
  • An online video about UT's program is here: http://www.youtube.com/watch?v=F7ZcXsUrk4M

Who Can Apply:

  • You need to have completed ≥4 semesters as a full-time student (or equivalent in credit hours), and to have declared your major as biological sciences.
  • You need a total GPA of ≥3.0 (4-point scale), and ≥3.3 in biology courses taken to date.

How to Apply:

  • Contact the Biology Advisor for the Pipeline Program, Dr. John Gray.
  • Complete Application form and submit
  • Supply two letters of recommendation. One must be from your faculty advisor in the Department of Biological Sciences, and the other can be from any UT faculty member who knows you well enough to write a meaningful letter.
  • Submit a Statement of Purpose
  • Submit your resume
  • If your native language is not English, then supply TOEFL scores (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). As of Spring 2014 admissions, IELTS will no longer be accepted.

Funding: 
Even with no scholarship support, this program will save you a substantial amount of money compared to separately completing the two degree programs (see Cost Comparison below). In the past, tuition scholarships were available for the graduate portion of the pipeline program for Ohio residents, made possible by the Choose Ohio First Tuition Scholarship Program.  These scholarships are no longer guaranteed, but will depend on the availability of funds.  For more information about this, and about UT's Program in Bioinformatics & Proteomics/Genomics, see: http://www.utoledo.edu/med/depts/bioinfo/index.html

COST COMPARISON:  Pipeline vs. BS + MSBS Taken Separately
$56,625 = approximate cost of tuition only for BS and MSBS taken separately
$49,103 = approximate costs of tuition only for the Pipeline Program
$7,522 Savings

UT/FINDLAY DUAL DEGREE (PIPELINE) PROGRAM
The Bioinformatics & Proteomics/Genomics Program along with the Department of Natural Sciences at the University of Findlay is now offering a dual-degree in Biology and Bioinformatics BS/MS, in as little as five years, starting in the Fall 2014.  The GRE score is NOT required for this Program.   

Curriculum for UT/Findlay Pipeline can be found here.

The link to the University of Findlay website is:  http://www.findlay.edu/sciences/biology/Bioinformatics

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PROFESSIONAL SCIENCE MASTERS PROGRAM IN BIOMARKERS AND DIAGNOSTICS (PSM)

Advantages of a PSM degree
The Professional Science Master provides students advanced training in science without a Ph.D., and highly-valued business skills without an MBA. PSMs prepare students for science careers in business, government, or nonprofit organizations, where workforce needs are increasing. Programs are characterized by “science-plus,” combining rigorous study in science or mathematics with skills-based coursework in management, policy, or law. Our students have a “real-world” internship in a business or public sector enterprise, instead of the more typical thesis. 

Admission Requirements
Applicants to the PSM degree with a concentration in  Biomarkers and Diagnostics must meet the following requirements, in addition to those of the UTHSC Graduate School:

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

2. GPA of 3.0 or above (on a four-point scale) GPA of 2.5 or above may apply for provisional acceptance that
    would change to Regular (non-probationary) status, if their first term graduate coursework has a GPA of
    3.0 or above. 

3. GRE
     a) GRE has been waived for the following:
           * U.S. students with GPA of 3.0 or above
           * UT or University of Findlay pipeline students
           * Students who can submit MCAT scores of 25 or higher.  

     b) For all others our requirements are:
           * Minimum GRE composite score of 300 (combined verbal and quantitative), and 3.5 (analytical). GRE scores
             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. Statement of Purpose
7. Resume

International Students
 a) 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.  

     b) Visa requirements and admission guidelines for International students can be found at the following links:
         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.  

Selecting an Internship
During the first semester, students will be required to meet with Dr. Keith Crist to identify specific areas of interest and make contact with sponsoring companies.  Selection of an internship project should be completed early in the second semester.

Required forms for current Graduate Students: (click form name to access)
1)  Plan of Study for the Professional Science Master's Degree form is required to be submitted BEFORE
     the student completes 12 credit hours (during the Fall 1 term).

Course Schedule  
Students are likely to have diverse backgrounds, the curriculum is designed to give all students a foundation appropriate to entry into a pharmaceutical research program.  Click here for PDF version of PSM curriculum schedule.

Fall Semester
BIPG5100       Fundamentals of BPG     3cr
Introduces the student to the powerful tools developed to access and analyze biological sequence and structural information. The topics include sequence databases, sequence comparisons, database searches, phylogenetic analysis, protein structure, proteomics, RNA structure prediction, gene prediction and identification, genetic analysis of disease, and microarray studies of gene expression.

BIPG5200        Statistical Methods in BPG     3cr
This course introduces students to statistical methods commonly used in bioinformatics. Students will learn to use statistical programs and related bioinformatics resources locally and on the Internet. Lectures and lab discussions will emphasize the statistical models and methods underlying the computational tools.

BMSP6340      CPRA in Genes     2.5 cr  
Introduction to major areas of current research in genetics and molecular biology. Topics include gene structure and regulation, DNA replication, recombination, repair, mutation, and quantitative genetics.

INDI6020       On Being a Scientist     1 cr  
A series of one-hour lectures dealing with the ethics, regulations, and issues facing a modern, biomedical research scientist.

--EITHER--  HURM6720    Advanced Negotiation & Conflict Resolution     3 cr  NOT OFFERED FOR FALL 2015
Equips students to make more effective decisions in employee relations. Course emphasis is on active analysis of employee-employer relationships in terms of procedures, costs and ramifications to both organizations and people.

--OR--         HURM6700   Human Resources Management     3 cr   
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.

--EITHER--  MGMT6150   Leading and Developing Yourself     3 cr  
Explores how one's own leadership competencies can be developed and applied most effectively in a variety of situations.  

--OR--         MGMT6160   Leading with Power & Influence     3 cr  
Students will develop and understanding of the strategic use of power and influence to exercise leadership in organizations. Skill development in the diagnosis and practical use of power and influence to mobilize action, to negotiate, and to resolve conflicts will be emphasized.

TOTAL FALL:  15.5cr

SPRING SEMESTER
BMSP6350     CPRA in Cell Biology and Signaling     3 cr 
Content of this course will encompass didactic lectures on current knowledge and methodological approaches in the area of fundamental cellular processes and cell communication.

HURM6730   Performance Management     3 cr  
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.

BIPG6100      Introduction to Bioinformatic Computation     3 cr  
Content will provide basic programming skills to biological and medical students who may lack a background in computer sciences. Programming will be specifically taught using important biological examples, focusing in particular on the PERL language. Students will be made familiar with UNIX environments, including Linux and OSX.

BRIM6200     Biomarker Discovery, Validation and Implementation     3 cr 
A survey course to explore the clinical need and methodological approaches to biomarker development and validation. Unit 2 will consider biomarker use for diagnostics and treatment in individualized medicine.

TOTAL SPRING: 12cr

SUMMER SEMESTER
BIDI5200     Readings in Biomarkers     3 cr  (DL/ONLINE)
In-depth analysis of original scientific papers/seminars in the fields of biomarkers, bioinformatics,proteomics and genomics for the development of critical analysis and scientific communication skills.

BIDI5100      Internship     6 cr (Done in place of thesis)
Supervised full time work experience in Biomarker discovery and validation in a pharmaceutical oriented company. Builds upon didactic course work.

TOTAL SUMMER:  9cr

TOTAL CREDITS: 36.5cr

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CONTACT US:
BRIMEducation@utoledo.edu
Education Director
Biomarkers & Diagnostics Program
Keith A Crist, Ph.D.
Email:  Keith.Crist@utoledo.edu
Phone:  419-383-3992 

External Support:
The BPG Program could not have been developed without the generous support from external agencies and foundations. A list of this support can be found on the Grants and Awards page of this site.



Last Updated: 12/30/15