Systems Biology and Bioinformatics, PhD
BRB 9th Floor, School of Medicine
Phone: 216.368.5961
sybb@case.edu
Degree: Doctor of Philosophy (PhD)
Field of Study: Systems Biology and Bioinformatics
Program Overview
Do you want to convert big data into understandable models that just might change the world? With a graduate degree in systems biology and bioinformatics, you can combine your love of math, statistics, computers, biology, and medicine to develop computational models with which to provide new insight and understanding of big data, leading to big discoveries in both laboratory and clinical settings.
Data science is the convergence of data engineering, math, statistics, advanced computing, the scientific method and subject-matter expertise. It involves the collection, management and transformation of "big data" into actionable information that can answer some of the world's most pressing problems. Yet there is a distinct need for data science experts who can efficiently interpret data into information that is useful for strategic decision-making. It is the goal of the Systems Biology and Bioinformatics program to produce the scientists that are needed to assist in extracting meaning from the burgeoning biological 'omics field.
The Case Western Reserve University School of Medicine established the first PhD and MS programs in Systems Biology and Bioinformatics (SYBB) in the State of Ohio in 2011, and has since graduated 28 PhD students from the program. Based in the School of Medicine, with the Department of Nutrition as its administrative home, the faculty cohort includes faculty from multiple departments and schools across the CWRU campus, as well as at our partner teaching hospitals such as Cleveland Clinic and University Hospitals, to provide a diverse training environment for our students. The SYBB program offers a multidisciplinary training program personally customized to the student leading to an MS or PhD. The program draws training faculty (currently over 55 trainers) from more than 12 departments and 6 schools across the CWRU campus and the Cleveland Metropolitan area, ensuring students in the program acquire the core competencies needed to succeed in the bioinformatics analysis of biological big data.
The SYBB participating departments and centers include:
- Biochemistry
- Biology
- Biomedical Engineering
- Case Comprehensive Cancer Center
- Cleveland Clinic Lerner College of Medicine
- Center for Global Health
- Center for Proteomics and Bioinformatics
- Computer and Data Sciences
- Department of Medicine
- Genetics and Genome Sciences
- Mathematics
- Nutrition
- Pathology
- Pharmacology
- Physiology and Biophysics
- Population and Quantitative Health Sciences
Program Competencies
The specific academic requirements of the SYBB Program are intended to provide students with a required core curriculum in Systems Biology and a set of electives designed both to assure minimum competencies in Fundamental Core Competencies and equip them for their particular thesis research discipline. Each trainee will be guided in their customized course of study by a mentoring committee to ensure the completion of training in the program competencies as well as maintenance of a focus on molecular systems theory. These competencies include:
- Evaluation of the scientific discovery process and of the role of bioinformatics in it in detail, including data generation steps and understanding biology
- Application of computational and statistical methods appropriate to solve a given scientific problem
- Construction of software systems of varying complexity based on design and development principles
- Effective teamwork to accomplish a common scientific goal
- Building knowledge in local and global impact of bioinformatics and systems biology on individuals, organizations, and society
- Effective communication of bioinformatics and systems biology problems to a range of audiences, including, but not limited to, other bioinformatics professionals
Admissions
Students are admitted to this PhD program through the Biomedical Sciences Training Program (BSTP) or the Medical Scientist Training Program (MSTP).
Biomedical Sciences Training Program (BSTP)
The BSTP offers a common entry point to most of the School of Medicine's biomedical PhD programs. BSTP students can choose among research mentors in many different PhD programs in the School of Medicine.
Medical Scientist Training Program (MSTP)
Students in the MSTP earn the dual MD/PhD degree. MSTP students also have the choice of mentors in many different PhD programs. The admission requirements of those programs can be viewed on their pages in the Bulletin. Program requirements for the dual can be found on the Medical Scientist Training Program, PhD/Medicine, MD program page.
PhD Policies
For PhD policies and procedures, please review the School of Graduate Studies section of the General Bulletin.
Program Requirements
The Systems Biology and Bioinformatics program differs from current CWRU programs in the comprehensive requirement for an understanding of biological systems, bioinformatics, and quantitative analysis & modeling. The program includes a minimal set of required courses including (SYBB 501) and a course in the Responsible Conduct of research (IBMS 500). Additional required courses for the Translational Bioinformatics and Molecular and Computational Biology tracks are SYBB 459 and SYBB 555. At least six additional courses will be required based upon individualized student interests. Other requirements include a qualifier exam, a PhD Dissertation, and oral defense. The total credits required for the PhD is at least 54 credit hours: 24 graded credit hours, 12 pre-dissertation research credit hours, and at least 18 dissertation research credit hours. Admissions to this program may be obtained through the integrated Biomedical Sciences Training Program, by direct admission to the department in rare cases or via the Medical Scientist Training Program.
Required Core Courses
| Code | Title | Credit Hours |
|---|---|---|
| SYBB 459 | Bioinformatics for Systems Biology | 3 |
| SYBB 555 | Current Proteomics and Bioinformatics | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| SYBB 701 | Dissertation Ph.D. | 18 |
Elective Courses
Genes and Proteins Courses
| Code | Title | Credit Hours |
|---|---|---|
| PHOL/CHEM/PHRM/BIOC/NEUR 475 | Protein Biophysics | 3 |
| IBMS 453 | Cell Biology I | 3 |
| IBMS 455 | Molecular Biology I | 3 |
| BIOC 452 | Nutritional Biochemistry and Metabolism | 3 |
| BIOC 412 | Proteins and Enzymes | 3 |
| BIOC 420 | Current Topics in Cancer | 3 |
| SYBB 528 | Contemporary Approaches to Drug Discovery | 3 |
| BETH 412 | Ethical Issues in Genetics/Genomics | 3 |
Bioinformatics and Computational Biology Courses
| Code | Title | Credit Hours |
|---|---|---|
| BIOL/ECSE 419 | Applied Probability and Stochastic Processes for Biology | 3 |
| PQHS 451 | A Data-Driven Introduction to Genomics and Human Health | 3 |
| CSDS 458 | Introduction to Bioinformatics | 3 |
| NEUR 478/BIOL 378/COGS/MATH 378/BIOL 478/EBME 478 | Computational Neuroscience | 3 |
| SYBB 402 | Introduction to Scientific Computing | 1 |
| SYBB 411 | Technologies in Bioinformatics | 3 |
| SYBB 412 | Survey of Bioinformatics: Programming for Bioinformatics | 3 |
| SYBB 459 | Bioinformatics for Systems Biology | 3 |
| SYBB 461 | Cancer Systems Biology | 3 |
| SYBB 472 | BioDesign | 3 |
Quantitative Analysis and Modeling
| Code | Title | Credit Hours |
|---|---|---|
| MPHP 405 | Statistical Methods in Public Health | 3 |
| PQHS 431 | Statistical Methods I | 3 |
| PQHS 432 | Statistical Methods II | 3 |
| CSDS 435 | Data Mining | 3 |
| PQHS 515 | Secondary Analysis of Large Health Care Databases | 3 |
| PQHS 480 | Introduction to Mathematical Statistics | 3 |
| CSDS 440 | Machine Learning | 3 |
| MATH 441 | Mathematical Modeling | 3 |
| EBME 300/MATH 449 | Dynamics of Biological Systems: A Quantitative Introduction to Biology | 3 |
| MIDS 301 | Introduction to Information: A Systems and Design Approach | 3 |
| PQHS 457 | Current Issues in Genetic Epidemiology: Design and Analysis of Sequencing Studies | 3 |
| PQHS 451 | A Data-Driven Introduction to Genomics and Human Health | 3 |
| PQHS 452 | Statistical Methods for Genetic Epidemiology | 3 |
| PQHS 453 | Categorical Data Analysis | 3 |
| PQHS 459 | Longitudinal Data Analysis | 3 |
Biomedical Sciences Training Program (BSTP) Requirements
Coursework
Students take integrated courses in Cell and Molecular Biology (IBMS 453, IBMS 455). They also complete a Data Science and AI in Biomedicine course (IBMS 457). These three courses, offered in the fall semester, emphasize the molecular approaches that form the basis of modern biology. We also seek students with strong quantitative training who may have majored in physics or math, and offer alternative courses for these students to acquire foundations in biology. Qualified students also may take more specialized elective courses. All students take IBMS 500 On Being a Professional Scientist: The Responsible Conduct of Research.
Research Rotations
The research rotations allow students to explore research areas and become familiar with faculty members and their laboratories. The main purpose of these rotations is to aid students in selecting a laboratory for their thesis work. Students are encouraged to begin their rotations in July. Doing so gives them the opportunity to complete rotations during the summer before classes begin at the end of August. Students must complete at least three rotations.
Choosing a Thesis Advisor
During the first year, students select an advisor for their dissertation research. Each student also joins the PhD program with which their advisor is affiliated. Once students choose a PhD program, the requirements of that program are followed to obtain the PhD. The emphasis of the PhD work is on research, culminating in the completion of an original, independent research thesis and publishing the results in the scientific literature. PhD programs also focus on educating students to work as professional scientists.
Sample Plan of Study
Plan of study includes required courses as well as electives. Please review the Systems Biology and Bioinformatics Program webpage on the Nutrition Department's website for additional information.
Translational Bioinformatics Track
| First Year | ||
|---|---|---|
| Fall | Credit Hours | |
| IBMS 453 | Cell Biology I | 3 |
| IBMS 455 | Molecular Biology I | 3 |
| IBMS 457 | Basics of AI and Data Science in BioMedicine | 2 |
| BSTP 400 | Research Rotation in Biomedical Sciences Training Program | 1 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 9 | |
| Spring | ||
| SYBB 412 | Survey of Bioinformatics: Programming for Bioinformatics | 3 |
| SYBB 459 | Bioinformatics for Systems Biology | 3 |
| SYBB 601 | Systems Biology and Bioinformatics Research | 2 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| IBMS 500 | On Being a Professional Scientist: The Responsible Conduct of Research | 1 |
| Credit Hours | 9 | |
| Second Year | ||
| Fall | ||
| SYBB 555 | Current Proteomics and Bioinformatics | 3 |
| SYBB 421 | Fundamentals of Clinical Information Systems | 3 |
| PQHS 431 | Statistical Methods I | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 9 | |
| Spring | ||
| SYBB 472 | BioDesign | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| SYBB 601 | Systems Biology and Bioinformatics Research | 3 |
| PQHS 432 | Statistical Methods II | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 9 | |
| Third Year | ||
| Fall | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Spring | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Fourth Year | ||
| Fall | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Spring | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Fifth Year | ||
| Fall | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Spring | ||
| SYBB 701 | Dissertation Ph.D. | 3 |
| IBMS 501 | Responsible Conduct of Research for Advanced Trainees | 0 |
| SYBB 501 | Biomedical Informatics and Systems Biology Journal Club | 0 |
| Credit Hours | 3 | |
| Total Credit Hours | 54 | |