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Advanced Multidisciplinary Training Program for Systems

Biology

Yana Zavros, Ph.D.

Associate Professor

Department of Molecular and Cellular Physiology

University of Cincinnati

Background• Many degree-granting programs strive to build expertise in tightly

focused areas– isolated expertise cannot sustain adequate research progress in an era when

total information accumulates at a much faster rate than the paradigms and methods from individual disciplines can effectively utilize

• During this time of ‘big data’ (large/complex data sets):– traditional analyses are inadequate– train scientists that are not limited to techniques and ideas within a single

discipline– research approaches that transcend departmental and traditional disciplinary

boundaries

• Emerging scientists need to acquire skills:– work in research teams– continually take advantage of new methods and concepts throughout their

career

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Objective• To prime researchers to tackle complex mechanisms of human disease using cross-

disciplinary approaches– team-building: experts from diverse disciplines applying their unique perspectives to address collectively

a problem

– applying knowledge that melds two or more traditional disciplines to solve a problem

• 2-year training program that involves 32 program faculty members and selected pre-doctoral trainees matriculated into 13 degree-granting Ph.D. programs.

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Administrative Structure

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Program co-directors with complementary expertise:•biological sciences (Yana Zavros, Ph.D.)

•computational sciences (Jarek Meller, Ph.D.)

Program co-directors with complementary expertise:•biological sciences (Yana Zavros, Ph.D.)

•computational sciences (Jarek Meller, Ph.D.)

Executive Committee•Bruce Aronow, Ph.D. (Professor, Biomedical Informatics)•Andrew Herr, Ph.D. (Associate Professor, Pediatrics, Divisions of Immunobiology and Infectious Diseases)•Evangelia Kranias, Ph.D. (Professor, Pharmacology and Cell Biophysics)•Mario Medvedovic, Ph.D. (Professor, Environmental Health)•Seongho Song, Ph.D. (Associate Professor, Mathematical Sciences)

Executive Committee•Bruce Aronow, Ph.D. (Professor, Biomedical Informatics)•Andrew Herr, Ph.D. (Associate Professor, Pediatrics, Divisions of Immunobiology and Infectious Diseases)•Evangelia Kranias, Ph.D. (Professor, Pharmacology and Cell Biophysics)•Mario Medvedovic, Ph.D. (Professor, Environmental Health)•Seongho Song, Ph.D. (Associate Professor, Mathematical Sciences)

Internal Advisory Committee•James P. Herman, Ph.D. (Director, Neuroscience Training Program)•Gurjit (Neeru) K. Khurana Hershey, MD, Ph.D. (Director, Medical Scientist Training Program)•Raphael Kopan, Ph.D. (Director, Division of Developmental Biology)•Harinder Singh, Ph.D. (Director, Division of Immunobiology)•Susan Waltz, Ph.D. (Director, Cancer Therapeutics Training Program)•Peter S. White, Ph.D. (Director, Division of Biomedical Informatics)

Internal Advisory Committee•James P. Herman, Ph.D. (Director, Neuroscience Training Program)•Gurjit (Neeru) K. Khurana Hershey, MD, Ph.D. (Director, Medical Scientist Training Program)•Raphael Kopan, Ph.D. (Director, Division of Developmental Biology)•Harinder Singh, Ph.D. (Director, Division of Immunobiology)•Susan Waltz, Ph.D. (Director, Cancer Therapeutics Training Program)•Peter S. White, Ph.D. (Director, Division of Biomedical Informatics)

Administrative Structure

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•Recruitment and Admissions Committee•Nathan Salomonis, Ph.D. (Assistant Professor, Pediatrics – Division of Biomedical Informatics)•Christian Hong, Ph.D. (Professor, Molecular and Cellular Physiology)•David Plas, Ph.D. (Associate Professor, Cancer Biology)•Student representatives – Nina Bertaux-Skeirik (Systems Biology and Physiology) and Alexander Thorman (Molecular Genetics)

•Recruitment and Admissions Committee•Nathan Salomonis, Ph.D. (Assistant Professor, Pediatrics – Division of Biomedical Informatics)•Christian Hong, Ph.D. (Professor, Molecular and Cellular Physiology)•David Plas, Ph.D. (Associate Professor, Cancer Biology)•Student representatives – Nina Bertaux-Skeirik (Systems Biology and Physiology) and Alexander Thorman (Molecular Genetics)

Curriculum Committee•Christy Holland, Ph.D. (Professor, Biological and Medical Engineering)•Sookkyung Lim, Ph.D. (Assistant Professor, Mathematical Sciences)•Matthew Weirauch, Ph.D. (Assistant Professor, Pediatrics – Divisions of Biomedical Informatics and Developmental Biology)•Student representatives - Jacob Bellman (Mathematics) and Christopher Burke (Mathematics)

Curriculum Committee•Christy Holland, Ph.D. (Professor, Biological and Medical Engineering)•Sookkyung Lim, Ph.D. (Assistant Professor, Mathematical Sciences)•Matthew Weirauch, Ph.D. (Assistant Professor, Pediatrics – Divisions of Biomedical Informatics and Developmental Biology)•Student representatives - Jacob Bellman (Mathematics) and Christopher Burke (Mathematics)

Program Faculty• The 32 participating program mentors are identified as:

– Biological-oriented scientists: applies the broad spectrum of tools found in the wet lab environment of biomedical research

– Theoretical-oriented scientists: uses concepts and modeling to generate an experimentally testable theory or model

– Interdisciplinary-oriented scientists: synthesizes approaches and theory from different disciplines with an integrative approach (e.g. computational chemistry applied to answer a biological question)

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Trainees and Training Program• We recruit trainees into the program from matriculated graduate

students in the 13 participating Ph.D. degree-granting programs:

1. Biomedical Engineering

2. Cancer and Cell Biology

3. Environmental Health Biostatistics

4. Immunology

5. Mathematical Sciences

6. Medical Scientist Training Program

7. Molecular, Cellular and Biochemical Pharmacology

8. Molecular and Developmental Biology

9. Molecular Genetics, Biochemistry and Microbiology

10.Neuroscience

11.Pathobiology and Molecular Medicine

12.Systems Biology and Physiology

13.Biomedical Informatics

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Trainees and Training Program• The objective will be achieved by implementation of a training plan

that incorporates the following features:

1. Didactic and experiential training in interdisciplinary research concepts and approaches,

2. A student-centered and flexible curriculum custom tailored to meet the needs of each student via computational and biology elective courses,

3. A research project that will require the student to use interdisciplinary approaches under the mentorship of a multi-disciplinary set of faculty co-mentors, and

4. Students engaged in a community that encourages interaction between students and mentors through seminars, data and journal clubs, and an annual retreat.

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Trainees and Training Program

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Current Trainees• Based on the success of receiving the training grant, the University provided additional

funds to allow us to provide support for another two trainees to join the the training program. This gives us a critical mass of 6 students in the training program in the first year. The awardees supported by the training grant are:

• Jacob Bellman (T32)

Ph.D. candidate in Mathematics, Mentors: Sookyung Lim and Christian Hong• Nina Bertaux-Skeirik (T32)

Ph.D. candidate in Systems Biology and Physiology, Mentors: Yana Zavros and Mario Medvedovic

• Christopher Burke (T32)

Ph.D. candidate in Mathematics, Mentors: Christian Hong and Seongho Song• Alexander Thorman (T32)

Ph.D. candidate in Molecular Genetics, Mentors: Jarek Meller and Andrew Herr• Mokryun (Lily) Baek (COM funds)

Ph.D. candidate in Systems Biology and Physiology, Mentors Christian Hong and Sookkyung Lim

• Jeremy Riddell (COM funds)

Ph.D. candidate in Systems Biology and Physiology, Mentors Matthew and Harinder Singh

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Opportunities and Challenges

• Increasing applicant pool• Attracting minority candidates• Time commitment of program faculty• Infrastructure support

– Program management, renewal application

– Tracking trainees

• Trainees for Fall 2015 (6 slots available)– Deadline for applications: August 9th 2015

– http://www.med2.uc.edu/physiology/tgadmit.htm

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• Program co-director Jarek Meller, Ph.D. (Associate Professor of Environmental Health)

• Ms. Cheryl Holly (Department of Molecular and Cellular Physiology)• Program faculty• Trainees

Supported by:• 5T32GM105526• Institutional support:

– Dean Ball of the College of Medicine– Graduate School enhancement funding for the doctoral Systems Biology and

Physiology Graduate Program, Dr. Chip Montrose, Vice Provost and Dean, The Graduate School

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Acknowledgements