Systems Biology and Bioinformatics (SYBB) PhD Program

Overview and 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 Biomedical Informatics and Systems Biology Journal Club and a course in the Responsible Conduct of research (IBMS 500 On Being a Professional Scientist: The Responsible Conduct of Research). Additional required courses for the Translational Bioinformatics and Molecular and Computational Biology tracks are SYBB 459 Bioinformatics for Systems Biology and SYBB 555 Current Proteomics.  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 PhD requires at least 54 credits: 24 graded credits, 12 pre-dissertation research credits, and at least 18 dissertation research credits.  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.

Please visit the General Bulletin for the University's full requirements for doctoral degrees.

Tracks

Case Western Reserve University's (CWRU) graduate program in Systems Biology and Bioinformatics (SYBB) has two tracks:

  • Translational Bioinformatics: The SYBB track in Translational Bioinformatics poises students to work at the interface of applied ‘omics research and clinical medicine. From integrating genomic and functional genomic data into electronic medical records, to developing meta-analysis tools for communicating genomic risk to patients to utilizing this data in personalized medicine. Students trained in the Translational Bioinformatics track work to integrate bioinformatics tools and technologies into clinical workflows. Graduates of this training track will find ample opportunities within industry and, as genomics enters the clinical arena, within hospitals, as well.
  • Molecular and Computational Biology: The SYBB track in Molecular and Computational Biology embraces the pursuit of basic science research, employing the application and development of computational approaches to address difficult questions derived from today’s “Big data” derived from ‘omics approaches. This track equips students in the acquisition of experimental data utilizing approaches including proteomics, metabolomics, genomics and structural biology and extends this work with interpretation provided by computational analysis. Graduates of this training track will find ample opportunities within the pharmaceutical industry, contract research organizations as well as more traditional academic career paths.

Students can choose one of the two tracks for the PhD program.

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 the 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.

Sample Plan of Study for the PhD: Translational Bioinformatics Track

Year 1 Fall Units Spring Units
SYBB 501: Biomedical Informatics and Systems Biology Journal Club 0  
SYBB 411A: Survey of Bioinformatics: Technologies in Bioinformatics 1  
SYBB 411B: Survey of Bioinformatics: Data Integration in Bioinformatics 1  
SYBB 411C: Survey of Bioinformatics: Data Integration in Bioinformatics 1  
CBIO 453: Cell Biology I 3  
CBIO 455: Molecular Biology I 3  
SYBB 601: Systems Biology and Bioinformatics Research 1-9  
SYBB 412: Survey of Bioinformatics: Programming for Bioinformatics   3
SYBB 555: Current Proteomics and Bioinformatics   3
SYBB 459: Bioinformatics for Systems Biology   3
BIOL 434: Structural Biology   3
SYBB 601: Systems Biology and Bioinformatics Research   1-9
SYBB 501: Biomedical Informatics and Systems Biology Journal Club   0
IBMS 500: On Being a Professional Scientist: The Responsible Conduct of Research 0 1
Semester Totals: 10-18 14-22

 

Year 2 Fall Units Spring Units
SYBB 528: Contemporary Approaches to Drug Discovery 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  
SYBB 427: BioDesign   3
PQHS 431: Statistical Methods II   3
SYBB 601: Systems Biology and Bioinformatics Research   3
SYBB 501: Biomedical Informatics and Systems Biology Journal Club   0
Semester Totals: 9

9

 

Year 3 Fall Units Spring Units
SYBB 701: Dissertation PhD 3  
SYBB 701: Dissertation PhD   3
Semester Totals: 3 3

 

Year 4 Fall Units Spring Units
SYBB 701: Dissertation PhD 3  
SYBB 701: Dissertation PhD   3
Semester Totals: 3 3

 

Year 5 Fall Units Spring Units
SYBB 701: Dissertation PhD 3  
SYBB 701: Dissertation PhD   3
Semester Totals: 3 3

Total Units in Sequence: 60-76

*Note: MSTP students would take MSTP 400 for research rotations.

Elective Courses

Genes and Proteins

PHOL/CHEM/PHRM/BIOC/NEUR 475 Protein Biophysics 3
PHOL 456 Conversations on Protein Structure and Function 2
PHOL 480 Physiology of Organ Systems 4
CBIO 453 Cell Biology I 3
CBIO 455 Molecular Biology I 3
BIOC 452 Nutritional Biochemistry and Metabolism 3
BIOC 519 Molecular Biology of RNA 3
BIOC 412 Proteins and Enzymes 3
BIOC 420 Current Topics in Cancer 3
BIOC 454 Biochemistry and Biology of RNA 3
SYBB 528 Contemporary Approaches to Drug Discovery 3
BETH 412 Ethical Issues in Genetics/Genomics 3

Bioinformatics and Computational Biology

BIOL/EECS 419 Applied Probability and Stochastic Processes for Biology 3
PQHS 451 A Data-Driven Introduction to Genomics and Human Health 3
EECS 458 Introduction to Bioinformatics 3
NEUR 478/BIOL 378/COGS/MATH 378/BIOL 478/EBME 478 Computational Neuroscience 3
SYBB 411A Survey of Bioinformatics: Technologies in Bioinformatics 1
SYBB 411B Survey of Bioinformatics: Data Integration in Bioinformatics 1
SYBB 411C Survey of Bioinformatics: Translational Bioinformatics 1
SYBB 412 Survey of Bioinformatics: Programming for Bioinformatics 3
SYBB 459 Bioinformatics for Systems Biology 3
SYBB 472 BioDesign 3

Quantitative Analysis and Modeling

MPHP 405 Statistical Methods in Public Health 3
PQHS 431 Statistical Methods I 3
PQHS 432 Statistical Methods II 3
EECS 435 Data Mining 3
PQHS 515 Secondary Analysis of Large Health Care Data Bases 3
PQHS 480 Introduction to Mathematical Statistics 3
EECS 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

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