Serdar Turkarslan

Senior Research Scientist

401 Terry Ave N
206-732-2102
Serdar.Turkarslan@isbscience.org

Dr. Turkarslan is a Research Scientist at Institute for Systems Biology. 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 studying adaptation of microorganisms and their communities to fluctuating environments and role of regulation through investigation of gene regulatory network models, bioenergetics, modeling and single cell studies. In addition, he develops data management and dissemination tools and portals for visualization and exploration of multi-dimensional systems biology data. Dr. Turkarslan is also pursuing studies related to developing experimental and computational framework for microbial single cell genomics and transcriptomics.

Publications

Wang, Yaxi, Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan, Kevin J. Cutler, et al. 2023. “Genetic Manipulation of Candidate Phyla Radiation Bacteria Provides Functional Insights into Microbial Dark Matter.” BioRxiv: The Preprint Server for Biology, May, 2023.05.02.539146. https://doi.org/10.1101/2023.05.02.539146.
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 8 (2): e0081622. https://doi.org/10.1128/msystems.00816-22.
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. https://doi.org/10.1038/s41698-022-00294-4.
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 29 (11): 1709-1723.e5. https://doi.org/10.1016/j.chom.2021.09.008.
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, August. https://doi.org/10.1111/mec.16064.
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. https://doi.org/10.1038/s41698-021-00185-0.
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). https://doi.org/10.1128/mSystems.00329-20.
Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. 2020. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” Preprint. Systems Biology. https://doi.org/10.1101/2020.04.01.012351.
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, October. https://doi.org/10.1038/ismej.2017.186.
Lopez Garcia de Lomana, Adrian, Amardeep Kaur, Serdar Turkarslan, Karlyn Beer, Fred Mast, Jennifer Smith, John Aitchison, and Nitin Baliga. 2017. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biology and Evolution in press (June).
Thompson, Anne W., Serdar Turkarslan, Christina E. Arens, Adrian Lopez Garcia 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, April. https://doi.org/10.1111/1462-2920.13764.
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.
Ashworth, Justin, Serdar Turkarslan, Micheleen Harris, Monica V. Orellana, and Nitin S. Baliga. 2016. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics 26 (April): 21–28. https://doi.org/10.1016/j.margen.2015.10.011.
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. https://doi.org/10.1016/j.mimet.2015.07.009.
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. https://doi.org/10.1038/sdata.2015.10.
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: 5829. https://doi.org/10.1038/ncomms6829.
Lopez Garcia de Lomana, Adrian, Sascha Schauble, Jacob Valenzuela, Saheed Imam, Warren Carter, Damla D. Bilgin, Christopher B. Yohn, et al. 2015. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels 8: 207. https://doi.org/10.1186/s13068-015-0391-z.
Hillesland, Kristina L., Sujung Lim, Jason J. Flowers, Serdar Turkarslan, Nicolas Pinel, Grant M. Zane, Nicholas 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 111 (41): 14822–27. https://doi.org/10.1073/pnas.1407986111.
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. https://doi.org/10.1093/nar/gku777.
Turkarslan, Serdar, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel Novichkov, and Nitin S. Baliga. 2014. “Network Portal: A Database for Storage, Analysis and Visualization of Biological  Networks.” Nucleic Acids Research 42 (Database issue): D184-190. https://doi.org/10.1093/nar/gkt1190.
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): 502. https://doi.org/10.1186/PREACCEPT-1701638048134699.
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): e01055-01013. https://doi.org/10.1128/mBio.01055-13.
Yoon, Sung Ho, Serdar Turkarslan, David J. Reiss, Min Pan, June A. Burn, Kyle C. Costa, Thomas J. Lie, et al. 2013. “A Systems Level Predictive Model for Global Gene Regulation of Methanogenesis in  a Hydrogenotrophic Methanogen.” Genome Research 23 (11): 1839–51. https://doi.org/10.1101/gr.153916.112.
Brooks, Aaron N., Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, and Nitin S. Baliga. 2011. “Adaptation of Cells to New Environments.” Wiley Interdisciplinary Reviews. Systems Biology and Medicine 3 (5): 544–61. https://doi.org/10.1002/wsbm.136.
Turkarslan, Serdar, David J. Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J. Christopher Bare, Christopher L. Plaisier, and Nitin S. Baliga. 2011. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7: 554. https://doi.org/10.1038/msb.2011.87.