Serdar Turkarslan, PhD

Senior Research Scientist

Baliga Lab

Serdar Turkaslan

Dr. Turkarslan is a Research Scientist at Institute for Systems Biology in Seattle, Washington. He got his PhD in Cell and Molecular Biology at University of Pennsylvania. He is interested in understanding how cells respond to changes in the environment by reprogramming their gene regulatory networks (GRN) and delineating the principles underlying the evolution of these complex regulatory programs. Dr. Turkarslan uses systems approaches to build global scale predictive network models for microbial organisms and simple communities to reverse engineer biological circuits. Currently, he is focused on delineating regulatory network readjustments that drive evolution of syntrophic community between sulfate reducing bacteria and methanogenic archaea. He is also interested in developing tools for exploration and visualization of large datasets in the field of systems biology and metagenomics. Dr. Turkarslan recently led development of the Network Portal Framework for storing, analyzing and visualizing biological networks.

Cell and Molecular Biology

PhD, Cell and Molecular Biology, University of Pennsylvania, 2007

Turkarslan, S., D. J. Reiss, G. Gibbins, W. L. Su, M. Pan, J. C. Bare, C. L. Plaisier, and N. S. Baliga. 2011. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7: 554. Cite
Yoon, S. H., S. Turkarslan, D. J. Reiss, M. Pan, J. A. Burn, K. C. Costa, T. J. Lie, et al. 2013. “A Systems Level Predictive Model for Global Gene Regulation of Methanogenesis in a Hydrogenotrophic Methanogen.” Genome Res 23 (11): 1839–51. Cite
Ekici, Seda, Serdar Turkarslan, Grzegorz Pawlik, Andrew Dancis, Nitin S. Baliga, Hans-Georg Koch, and Fevzi Daldal. 2014. “Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production.” MBio 5 (1): e01055-13. Cite
Rustad, Tige R., Kyle J. Minch, Shuyi Ma, Jessica K. Winkler, Samuel Hobbs, Mark Hickey, William Brabant, et al. 2014. “Mapping and Manipulating the Mycobacterium Tuberculosis Transcriptome Using a Transcription Factor Overexpression-Derived Regulatory Network.” Genome Biology 15 (11). Cite
Turkarslan, S., E. J. Wurtmann, W. J. Wu, N. Jiang, J. C. Bare, K. Foley, D. J. Reiss, P. Novichkov, and N. S. Baliga. 2014. “Network Portal: A Database for Storage, Analysis and Visualization of Biological Networks.” Nucleic Acids Res 42 (1): D184-90. Cite
Hillesland, K. L., S. Lim, J. J. Flowers, S. Turkarslan, N. Pinel, G. M. Zane, N. Elliott, et al. 2014. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America, September. Cite
Peterson, Eliza J. R., David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher L. Plaisier, William J. R. Longabaugh, David R. Sherman, and Nitin S. Baliga. 2014. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Research 42 (18): 11291–303. Cite
Lopez Garcia de Lomana, A., S. Schauble, J. Valenzuela, S. Imam, W. Carter, D. D. Bilgin, C. B. Yohn, et al. 2015. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels 8: 207. Cite
Turkarslan, Serdar, Eliza J. R. Peterson, Tige R. Rustad, Kyle J. Minch, David J. Reiss, Robert Morrison, Shuyi Ma, Nathan D. Price, David R. Sherman, and Nitin S. Baliga. 2015. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Scientific Data 2: 150010. Cite
Minch, Kyle J., Tige R. Rustad, Eliza J. R. Peterson, Jessica Winkler, David J. Reiss, Shuyi Ma, Mark Hickey, et al. 2015. “The DNA-Binding Network of Mycobacterium Tuberculosis.” Nature Communications 6. Cite
Yoon, Heeyong, Simon A. B. Knight, Alok Pandey, Jayashree Pain, Serdar Turkarslan, Debkumar Pain, and Andrew Dancis. 2015. “Turning Saccharomyces Cerevisiae into a Frataxin-Independent Organism.” PLoS Genet 11 (May): e1005135. Cite
Thompson, Anne W., Matthew J. Crow, Brian Wadey, Christina Arens, Serdar Turkarslan, Sergey Stolyar, Nicholas Elliott, et al. 2015. “A Method to Analyze, Sort, and Retain Viability of Obligate Anaerobic Microorganisms from Complex Microbial Communities.” Journal of Microbiological Methods 117 (October): 74–77. Cite Download
Ashworth, J., S. Turkarslan, M. Harris, M. V. Orellana, and N. S. Baliga. 2015. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics, November. Cite
Qin, Wei, Shady A. Amin, Rachel A. Lundeen, Katherine R. Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, et al. 2017. “Stress Response of a Marine Ammonia-Oxidizing Archaeon Informs Physiological Status of Environmental Populations.” The ISME Journal. Cite
López García de Lomana, Adrián, Amardeep Kaur, Serdar Turkarslan, Karlyn D. Beer, Fred D. Mast, Jennifer J. Smith, John D. Aitchison, and Nitin S. Baliga. 2017. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biology and Evolution. Cite Download
Thompson, Anne W., Serdar Turkarslan, Christina E. Arens, Adrián López García de Lomana, Arjun V. Raman, David A. Stahl, and Nitin S. Baliga. 2017. “Robustness of a Model Microbial Community Emerges from Population Structure among Single Cells of a Clonal Population.” Environmental Microbiology. Cite
Turkarslan, Serdar, Arjun V. Raman, Anne W. Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, et al. 2017. “Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment.” Molecular Systems Biology 13 (3): 919. Cite
López García de Lomana, Adrián, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan P. R. Lorenzetti, Robert L. Moritz, and Nitin S. Baliga. 2020. “Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium Salinarum.” MSystems 5 (4). Cite Download
Otwell, Anne E., Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, et al. 2021. “Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.” MSystems 6 (1). Cite Download
Turkarslan, Serdar, Nejc Stopnisek, Anne W. Thompson, Christina E. Arens, Jacob J. Valenzuela, James Wilson, Kristopher A. Hunt, et al. 2021. “Synergistic Epistasis Enhances the Co-Operativity of Mutualistic Interspecies Interactions.” The ISME Journal. Cite Download
Voolstra, Christian R., Jacob J. Valenzuela, Serdar Turkarslan, Anny Cárdenas, Benjamin C. C. Hume, Gabriela Perna, Carol Buitrago-López, et al. 2021. “Contrasting Heat Stress Response Patterns of Coral Holobionts across the Red Sea Suggest Distinct Mechanisms of Thermal Tolerance.” Molecular Ecology 30 (18): 4466–80. Cite Download
Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. 2021. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” NPJ Precision Oncology 5 (1): 60. Cite Download
Arrieta-Ortiz, Mario L., Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, et al. 2021. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe, S1931-3128(21)00424-8. Cite
Park, James H., Abdullah H. Feroze, Samuel N. Emerson, Anca B. Mihalas, C. Dirk Keene, Patrick J. Cimino, Adrian Lopez Garcia de Lomana, et al. 2022. “A Single-Cell Based Precision Medicine Approach Using Glioblastoma Patient-Specific Models.” NPJ Precision Oncology 6 (1): 55. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L. G. de Lomana, et al. 2022. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” bioRxiv. Cite Download
Hughes, Laura D., Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, Tor C. Savidge, Thomas Stoeger, et al. 2023. “Addressing Barriers in FAIR Data Practices for Biomedical Data.” Scientific Data 10 (1): 98. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. 2023. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, e0081622. Cite Download
Wang, Yaxi, Hannah E. Ledvina, Catherine A. Tower, Stanimir Kambarev, Elizabeth Liu, James C. Charity, Lieselotte S. M. Kreuk, et al. 2023. “Discovery of a Glutathione Utilization Pathway in Francisella That Shows Functional Divergence between Environmental and Pathogenic Species.” Cell Host & Microbe, S1931-3128(23)00261-5. Cite
Wang, Yaxi, Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan, Kevin J. Cutler, et al. 2023. “Genetic Manipulation of Patescibacteria Provides Mechanistic Insights into Microbial Dark Matter and the Epibiotic Lifestyle.” Cell, S0092-8674(23)00906-6. Cite Download
Park, James H., Parvinder Hothi, Adrian Lopez Garcia de Lomana, Min Pan, Rachel Calder, Serdar Turkarslan, Wei-Ju Wu, et al. 2024. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” BioRxiv: The Preprint Server for Biology, February, 2024.02.02.578510. Cite Download