GUR LABORATORY

Associate Professor, Department of Computational and Systems Biology
Executive Director, Computational Biomedicine and Biotechnology M.S. Program
https://www.csb.pitt.edu/cobb/

Description

Global Academic Experience with Interdisciplinary Roles Across Top Institutions: Associate Professor Mert Gur earned his B.S. degree from the Middle East Technical University Mechanical Engineering (ME) department in 2006, attended the ME M.S. program at Koc University from 2006 to 2007, and completed his Ph.D. degree in Computational Science and Engineering at Koc University in 2010. He began working as a postdoctoral associate in the University of Pittsburgh (Pitt) School of Medicine (SOM) Department of Computational and Systems Biology (CSB), and in 2012, he was jointly appointed as a Lecturer in the Pitt Department of Mechanical Engineering and Materials Science. In 2014, he joined Lawrence Berkeley National Laboratory Joint Center for Artificial Photosynthesis as a postdoctoral fellow. He became a faculty member of ITU ME at the rank of Assistant Professor in 2015, was promoted to Associate Professor in 2021, received his tenure in 2022, and additionally served in Vice Deans roles starting in 2018. Throughout the summers 2016 and 2017, he was a Visiting Faculty Scholar in Pitt SOM and at the University of California Berkeley College of Chemistry. In 2022, he took a sabbatical leave from ITU ME and stepped down from his Vice Dean role to join the Pitt SOM CSB as a Visiting Associate Professor. At Pitt CSB he assumed the role of Executive Director of the CoBB M.S. Program in 2023 and in 2024 further expanded his role at Pitt by becoming the Co-Director of the Training and Experimentation in Computational Biology (TECBiO) REU Program. That same year, he transitioned from a Visiting Associate Professor to an Associate Professor in the at Pitt CSB and resigned from his tenured position at ITU.

Demonstrated Leadership in High-Impact Research on Biological Systems Modeling, Molecular Mechanisms, and Therapeutics: Dr. Gur brings over 16 years of experience and a proven record of innovation in applying molecular dynamics (MD) simulations and coarse-grained elastic network models to address cutting-edge scientific challenges in biology, biotechnology, biomedicine, and pharmaceutical and health sciences. His expertise spans a wide range of protein classes, such as enzymes, motors, and membrane proteins, as well as peptide design, and includes development of novel methods for enhanced sampling and free-energy calculation. Mert excels in conducting MD simulations of large biomolecular systems (up to multimillion-atoms), performing simulations with lengths several orders longer than typical, and handling big data generated by such simulations. His extensive experience in analyzing large datasets, protein-protein interactions, and designing peptide-based drugs has further solidified his standing in the field. To date, Dr. Gur and his research group have performed over 350 M core hours of MD simulations at premier Tier-0 supercomputers, including Anton and Summit (USA), Mahti (Finland), and Marconi100 (Italy). So far, Dr. Gur has published two book chapters and nearly 40 journal papers, including those published in prominent journals such Nature, Science, Nature Communications, Science Advances, and PNAS. Mert was awarded with multiple awards and honors, including, Outstanding Young Scientist Award (Turkish Academy of Sciences) in 2016, Young Scientist Award (Science Academy) and National Outstanding Researcher Fellowship (The Scientific and Technological Research Council of Turkey (TUBITAK) in 2022 and Health Institutes of Türkiye (TUSEB) Aziz Sancar Incentive Award in 2023.   

Proven High Success in Grantsmanship and Adaptation in Global Research Funding: Dr. Gur has demonstrated exceptional success in grantsmanship. As a faculty member at Istanbul Technical University (2015-2024), he secured a total of $871,393 in direct external funding as PI, primarily from TUBITAK, Turkey’s leading science and research agency. His portfolio includes prestigious grants such as the Career Grant, Primary Subjects R&D Funding Program, and the National Outstanding Researchers Program. With the upper funding limit for a standard TUBITAK grant being approximately $48,295 in 2024, and an acceptance rate between 15-17%, Dr. Gur’s achievement—securing 1800% of this limit—significantly outpaces his peers in Turkey. In addition to external funding, Dr. Gur obtained $30,597 in internal funding at ITU. It is important to note that in Turkey, research costs such as graduate stipends, research space, and benefits are considerably lower than in the U.S., providing a clearer context to Dr. Gur’s success in managing research budgets efficiently. In addition to the $904,990 in research funding, he has also secured high-performance computing resources, acquiring 278,233,490 standardized core-hours on Tier-0 supercomputers through competitive EU and US computational resource grants, valued at approximately $1,000,000. This brings his total secured research support during his tenure at ITU to nearly $2 million. Dr. Gur has also contributed as a postdoc, researcher, and collaborator in a range of nationally and internationally funded projects, including those supported by NIH and ANSO.  

Having recently transitioned his laboratory from ITU to the University of Pittsburgh, Dr. Gur is actively pursuing new grant opportunities and strategically leveraging his startup funding to build upon his strong track record and further elevate his research impact.

Notable Career in Academic Leadership and Administration: Dr. Gur has held multiple leadership positions, showcasing his significant contributions to academic administration. He served as the Vice Dean of the ITU Graduate School of Science, Engineering, and Technology from 2018 to 2020 and as the Vice Dean of the ITU School of Mechanical Engineering (SME), from 2020 to 2022. He simultaneously managed both roles for seven months in 2020, accumulating nearly five years of Vice Dean experience. From 2017 to 2020, he acted as the Coordinator and Vice Coordinator of the ME Minor and Double Major Programs at ITU, demonstrating his dedication to interdisciplinary education. In recognition of his leadership, he was elected by the SME associate professors to serve as their representative on the Faculty Board from 2021 to 2024. Furthermore, Dr. Gur held positions as an Advisory Committee Member of the National High Performance Computing Center and as a Board Member of the Research and Application Center for Critical and Functional Materials. He has also been an active member of 19 different commissions, underscoring his broad engagement in academic governance. Since August 2023, he has been serving as the Executive Director of the Pitt SOM Computational Biomedicine & Biotechnology (CoBB) M.S. Program. Under his leadership, the number of new incoming full-time CoBB students increased from two in 2023 to 11 in 2024, marking a remarkable 450% increase, while the number of incoming part-time students grew from two to three, representing a 50% increase. His extensive experience and impactful leadership have significantly advanced the institutions he has served, exemplifying his commitment to excellence in academic administration and his ability to drive growth and innovation.

Extensive Teaching Experience: From 2015 to 2022, he taught 43 courses to 2,528 students across nine undergraduate and four graduate programs at ITU, including Molecular Biology-Genetics and Biotechnology, ME, and Materials and Manufacture programs, averaging six courses and 361 students per year. At Pitt, he taught at MEMS in 2012 and has been teaching at Pitt CSB since 2023, covering an additional nine courses in the Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology (CPCB), CoBB M.S., Integrative Systems Biology Ph.D (ISB), and Interdisciplinary Biomedical Graduate Programs. This brings his total number of courses taught to 52.

Comprehensive Experience in Course and Curriculum Development with Interdisciplinary Integration: At ITU, Dr. Gur developed and introduced three new courses into the ME undergraduate and graduate programs, including Thermodynamics of Biomolecular Systems, and Fundamentals and Applications of Nanomachines courses, bridging emerging scientific fields with traditional engineering education by integrating interdisciplinary advancements into the established curriculum. As the Vice Dean for Academic Affairs at ITU SME, he led the complete process of designing and implementing new courses and spearheaded the revision and modernization of the existing ME curriculum. This comprehensive effort was based on a thorough analysis of feedback from students, employers, and faculty, as well as evolving ABET accreditation criteria and advancements in the field. Dr. Gur successfully guided the curriculum through all stages—from initial concept to final approval by the faculty and the Office of the Provost. At Pitt, Dr. Gur developed a Spring staggered curriculum for the CoBB M.S. Program, building upon our existing Fall staggered curriculum, and submitted it for review to the SOM Graduate Office and the Provost Office. These combined experiences at both ITU and Pitt further showcase Dr. Gur’s expertise in course and curriculum development, demonstrating my ability to adapt, enhance, and align educational programs to meet institutional needs and standards across diverse academic environments.

Experienced Mentor Across Academic and Community Settings: Dr. Gur has mentored 10 M.S. and 23 undergraduate students across various programs. He currently mentors one undergraduate, two M.S., and four Ph.D. students, two of whom will graduate in the coming months and join his lab as postdoctoral researchers in December 2024 and January 2025. As a volunteer coach for a U-10 team, Dr. Gur’s mentoring experience also includes individuals outside of the academic environment.

Driving Academic Global Ranking Success: During Dr. Gur’s tenure as a member of ITU’s Rankings and Performance Assessment Office (RPAO) from 2021 to 2024, and as a member of the two committees that preceded and led to the formation of RPAO (2018-2021), ITU’s QS World University Ranking rose from 751-800 in 2021 to an impressive 326 globally in 2024. The university’s position in the Shanghai Ranking (ARWU) improved from 901-1000 to 701-800, while in the Times Higher Education (THE) World University Rankings, ITU advanced from 801-1000 to 501-600. As Vice Dean of the School of ME and member of RPAO, Dr. Gur also contributed to the QS World University Rankings by Subject, elevating ITU’s ME program from 161st to 134th globally, further enhancing the international prestige of this historically leading program at ITU. His contributions included preparing comprehensive data sets and reports, analyzing performance metrics, and recommending strategic initiatives to enhance the university’s academic ranking performance.

Expert in Sustainability Strategies: As a core member of ITU’s Rankings and Performance Assessment Office, Dr. Gur played a pivotal role in ITU’s remarkable rise in the Times Higher Education Impact Rankings, which assesses universities’ contributions to the United Nations’ Sustainable Development Goals (SDGs). With Dr. Gur and the team’s efforts, ITU advanced from 601+ in 2020 to 101-200 in 2021, 58th in 2023, and 34th globally in the 2024 rankings. His contributions included gathering and preparing data for ranking, developing sustainability initiatives and data-driven strategies that elevated our performance. Dr. Gur also served as an expert on a multiyear project funded by Turkey’s Ministry of Environment and Urbanization, focusing on green usage and solutions for housing, industry, and transportation. Additionally, Gr. Gur has been collaborating on a project focused on sustainably capturing waste atmospheric carbon dioxide, funded by the Alliance of International Science Organizations.

Leadership in Academic Quality Assurance and Accreditation at University and Departmental Levels: Dr. Gur served as a core member of the University Quality Commission (2020-2022), in Vice Dean roles (2018-2022), and on the ME Department Quality Assurance and ABET Committees (2015-2022)at ITU, where he played a pivotal role in driving quality improvement and ensuring that academic programs and administrative processes at both the departmental and university levels adhered to national and international standards. His efforts were instrumental in securing successful ABET accreditations and Turkish Higher Education Quality Council Institutional Accreditations, as well as in leading the ME Department’s and School of ME’s annual internal evaluation report, quality assurance reports, and administrative activity reports.

Strong commitment to community engagement and outreach. Dr. Gur co-directs the TECBio REU program, providing research opportunities to undergraduate students from diverse backgrounds, with a focus on historically underrepresented groups in computational biology. As Vice Dean for Education at ITU SME, Dr. Gur led professional development courses, connecting students with executives and professionals from various fields to broaden career pathways. He has also engaged in community outreach, judging middle and high school science fairs in the US and Turkey, and have delivered over 20 talks to promote STEM education in Turkey. Additionally, Dr. Gur served on the evaluation committee for capstone projects in ITU SME’s undergraduate programs, ensuring high standards while promoting inclusive practices. Currently, he volunteers as a head coach for a U-10 youth soccer team in Pittsburgh, supporting development through sport. Additionally, I actively participate in the Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS), where I have served as an invited speaker and judge for student posters. I also lead our REU and graduate program promotion booth at this year’s ABRCMS, advocating for diversity and supporting the professional development of minoritized scientists. My extensive academic leadership roles have promoted broad engagement, enriching STEM fields by expanding accessibility and opportunities for individuals from varied geographic regions and backgrounds