GUR LABORATORY

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

Description

Global Academic Experience with Interdisciplinary Roles Across Top Institutions: Associate Professor Mert Gur earned his BS degree from the Middle East Technical University Mechanical Engineering (ME) department in 2006, attended the ME MS program at Koc University from 2006 to 2007, and completed his PhD 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). In 2012, he was jointly appointed as a Lecturer in the Pitt Department of Mechanical Engineering and Materials Science (MEMS). In 2014, he joined the Lawrence Berkeley National Laboratory Joint Center for Artificial Photosynthesis as a postdoctoral fellow. He became a faculty member of Istanbul Technical University (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 Dean roles starting in 2018. Throughout the summers of 2016 and 2017, he was a Visiting Faculty Scholar at Pitt SOM and 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 Computational Biomedicine & Biotechnology (CoBB) MS 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 at Pitt CSB and resigned from his tenured position at ITU. He is currently in the process of relocating his laboratory from ITU to Pitt and is establishing a new research lab at CSB.

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 (ENMs) 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 the development of novel methods for enhanced sampling and free-energy calculation. Dr. Gur 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 (US), Mahti (Finland), and Marconi100 (Italy). So far, Dr. Gur has published two book chapters and over 40 journal papers, including those published in prominent journals such as Nature, Science, Nature Communications, Science Advances, and PNAS. He has been invited as a speaker to eight conferences and symposia, including the ACS Annual Meetings and the Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS). Dr. Gur was awarded with multiple awards and honors, including the Outstanding Young Scientist Award (Turkish Academy of Sciences) in 2016, the Young Scientist Award (Science Academy), and the National Outstanding Researcher Fellowship (The Scientific and Technological Research Council of Türkiye (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 ITU (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 $48,300 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 research costs in Turkey, such as graduate stipends, research space, and benefits, are significantly lower than in the US; for instance, a typical graduate student stipend in Turkey is one order of magnitude lower than equivalent US stipends, and no additional fringe benefits or indirect costs are charged on top of these stipends, providing clearer context for Dr. Gur’s success in managing research budgets. 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 the National Institutes of Health (NIH) and Alliance of International Science Organizations (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 CoBB MS Program. Under his leadership, the number of new incoming full-time CoBB students increased from two in 2023 to 10 in 2024, marking a remarkable 400% increase, while the number of incoming part-time students grew from two to three, representing a 50% increase. His impact is equally evident in the surge of total applications. The admission season ends in June, and the program had seven applications by the end of March in the year 2023, before Dr. Gur became director. That figure rose to 24 in March 2024 and then soared to 76 in March 2025, reflecting 243% and 985% increases, respectively, compared to the year prior to his leadership. 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 42 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 11 courses in the Joint Carnegie Mellon University of Pittsburgh PhD Program in Computational Biology (CPCB), CoBB MS, Integrative Systems Biology (ISB) PhD, and Interdisciplinary Biomedical Graduate Programs. In total, he has been involved in teaching 54 courses, most of which he taught fully, while others he co-taught or taught partially.

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 MS 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 two PhD, 10 MS, and 22 undergraduate students across various programs, including Molecular Biology-Genetics and Biotechnology and Mechanical Engineering graduate and undergraduate programs.  He currently mentors one undergraduate, three MS, and three PhD students as well as two postdoctoral associates. 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 SME and member of RPAO, Dr. Gur also contributed to the QS World University Rankings by Subject, helping elevate 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, Dr. Gur has been collaborating on a project focused on sustainably capturing waste atmospheric carbon dioxide, funded by the ANSO.

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 SME’s annual internal evaluation report, quality assurance reports, and administrative activity reports.

Strong commitment to community engagement and outreach. Dr. Gur is the associate director of the TECBio REU program, which provides research opportunities to undergraduate students from diverse backgrounds. 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 has delivered over 20 talks to promote STEM education in Turkey. Additionally, Dr. Gur served on the evaluation committee and advisor for capstone projects in ITU SME’s undergraduate programs, ensuring high standards while promoting inclusive practices. He has been volunteering as a head coach for U-10 youth soccer teams in Pittsburgh, supporting development through sport. Additionally, Dr. Gur participates in the ABRCMS, where Dr. Gur has served as an invited speaker and judge for student posters, and he also promoted CSB’s graduate programs at the Pitt SOM Graduate Studies exhibition booth. Dr. Gur also led our REU and graduate program promotion booth at ABRCMS in 2024.