Graduate Program in Systems Biology and Bioinformatics

Selected mESC- and mEpiSC-associated protein networks.
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Data Science

The Graduate Program in Systems Biology and Bioinformatics is participating in Case Western Reserve University's Data Science initiative. We have developed new courses for the undergraduate Applied Data Science minor in the Health domain area. These courses will introduce students to healthcare data analytics and bioinformatics research.

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.

Danica Wiredja, Ph.D. student, recently won an award for her poster, Phosphoproteomic and Bioinformatic Characterization of the Signaling Alterations in Response to a PP2A Activator in Lung Cancer at the Case Comprehensive Cancer Center Annual Retreat.

HackCWRU Spring 2014

Douglas Brubaker, Ph.D. student, had written a grant proposal to the NSF Graduate Research Fellowship Program on a new way to classify anti-cancer drugs. The proposal won an honorable mention, but was not funded. He approached Elena Svenson, Ph.D. student, to collaborate on the project and Elena suggested they go to HackCWRU, an event where students spend 24 hours building a new app or software program. They recruited two undergraduate students, Joshua Tang and Kai Smith and formed a team of four. Over the next 24 hours they completed the programming and generated some sample results for a presentation to the other participants.

Following the hackathon, Doug and Elena continued work on the project which they named CAncer Drug Response nEtworks (CADREs). They recruited two more undergraduate students, Christopher Ryu and Maya Monroe, and worked through the summer on a methods paper for the Pacific Symposium on Biocomputing. The manuscript was submitted on July 31. Elena and Doug are co-first authors and 3 of the 4 undergraduate students, Chris, Maya, and Kai are co-authors for their contributions.

Doug says, "The hackathon was a great experience for us. We planned and implemented a coding project with biomedical applications and are continuing to extend the method. It also provided a great mentoring and collaboration opportunity for us early in our research careers."

The Systems Biology and Bioinformatics (SYBB) PhD program (established in 2011) requires students to combine experimental and theoretical concepts in its didactic requirements and to combine theory and experiment in each student's thesis research. Co-mentoring is common and thesis committee members available from the trainer pool span many disciplines. Journal club experiences combine literature presentation with student works in progress and hands-on application of bioinformatics tools. Many didactic courses adopt a flipped classroom model where student led learning is the norm. Students are required to complete an Individual Development Plan approved by their mentor which is updated yearly. Regular thesis committee meetings and goal setting are the norm for all students. The goal is autonomous well-rounded students with a deep appreciation of their chosen area of study combined with skill sets in a wide range of areas relevant to bioinformatics and systems biology.

The Case Western Reserve University (CWRU) graduate program in Systems Biology and Bioinformatics (SYBB) has 4 tracks:

  • Translational Bioinformatics - Equips students to apply recent advances in genomics and proteomics to solve clinical problems in a cost-effective manner
  • Clinical Research Informatics - Prepares students to analyze large clinical data repositories to derive new knowledge pertaining to health and disease
  • Molecular and Computational Biology - Provides students the cutting edge tools to tackle a variety of biological problems using computational approaches
  • Applied Health Informatics - Students learn methods and technology to translate data to information to knowledge in the healthcare ecosystem.

Students can choose 1 of the 4 tracks for both the M.S. and Ph.D. programs.

The M.S. degree is comprised of 30 total credits and is anticipated to take two years to complete, going full time. There are two routes that can be followed, allowing students to customize their experience to match their interests. The first route, gives them the opportunity for in depth study of a topic leading to a Master's thesis while the second route allows replaces the thesis with a comprehensive written exam or major project. Alternatively the Ph.D. requires 36 total credits and is anticipated to be a five year program.

The interdisciplinary program has twenty-four faculty in many departments and centers on campus such as: Biology, Biomedical Engineering, Center for Proteomics and Bioinformatics, Electrical Engineering and Computer Science, Epidemiology and Biostatistics, Genetics, Mathematics, Neurosciences, Physiology and Biophysics, and Pharmacology.