Senior Research Scientist

Serdar Turkarslan

Senior Research Scientist

401 Terry Ave N
206-732-2102

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

Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” Preprint. Systems Biology, April 1, 2020. https://doi.org/10.1101/2020.04.01.012351. Cite
Qin, Wei, Shady A. Amin, Rachel A. Lundeen, Katherine R. Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, et al. “Stress Response of a Marine Ammonia-Oxidizing Archaeon Informs Physiological Status of Environmental Populations.” The ISME Journal, October 20, 2017. https://doi.org/10.1038/ismej.2017.186. Cite
Lopez Garcia de Lomana, Adrian, Amardeep Kaur, Serdar Turkarslan, Karlyn Beer, Fred Mast, Jennifer Smith, John Aitchison, and Nitin Baliga. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biology and Evolution in press (June 2017). Cite
Turkarslan, Serdar, Arjun V. Raman, Anne W. Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, et al. “Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment.” Molecular Systems Biology 13, no. 3 (March 20, 2017): 919. Cite
Thompson, Anne W., Serdar Turkarslan, Christina E. Arens, Adrian Lopez Garcia de Lomana, Arjun V. Raman, David A. Stahl, and Nitin S. Baliga. “Robustness of a Model Microbial Community Emerges from Population Structure among Single Cells of a Clonal Population.” Environmental Microbiology, April 17, 2017. https://doi.org/10.1111/1462-2920.13764. Cite
Brooks, Aaron N., Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, and Nitin S. Baliga. “Adaptation of Cells to New Environments.” Wiley Interdisciplinary Reviews. Systems Biology and Medicine 3, no. 5 (October 2011): 544–61. https://doi.org/10.1002/wsbm.136. Cite
Turkarslan, Serdar, David J. Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J. Christopher Bare, Christopher L. Plaisier, and Nitin S. Baliga. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7 (2011): 554. https://doi.org/10.1038/msb.2011.87. Cite
Yoon, Sung Ho, Serdar Turkarslan, David J. Reiss, Min Pan, June A. Burn, Kyle C. Costa, Thomas J. Lie, et al. “A Systems Level Predictive Model for Global Gene Regulation of Methanogenesis in  a Hydrogenotrophic Methanogen.” Genome Research 23, no. 11 (November 2013): 1839–51. https://doi.org/10.1101/gr.153916.112. Cite
Turkarslan, Serdar, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel Novichkov, and Nitin S. Baliga. “Network Portal: A Database for Storage, Analysis and Visualization of Biological  Networks.” Nucleic Acids Research 42, no. Database issue (January 2014): D184-190. https://doi.org/10.1093/nar/gkt1190. Cite
Rustad, Tige R., Kyle J. Minch, Shuyi Ma, Jessica K. Winkler, Samuel Hobbs, Mark Hickey, William Brabant, et al. “Mapping and Manipulating the Mycobacterium Tuberculosis Transcriptome Using a Transcription Factor Overexpression-Derived Regulatory Network.” Genome Biology 15, no. 11 (2014): 502. https://doi.org/10.1186/PREACCEPT-1701638048134699. 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. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Research 42, no. 18 (October 2014): 11291–303. https://doi.org/10.1093/nar/gku777. Cite
Hillesland, Kristina L., Sujung Lim, Jason J. Flowers, Serdar Turkarslan, Nicolas Pinel, Grant M. Zane, Nicholas Elliott, et al. “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, no. 41 (October 14, 2014): 14822–27. https://doi.org/10.1073/pnas.1407986111. Cite
Thompson, Anne W., Matthew J. Crow, Brian Wadey, Christina Arens, Serdar Turkarslan, Sergey Stolyar, Nicholas Elliott, et al. “A Method to Analyze, Sort, and Retain Viability of Obligate Anaerobic Microorganisms from Complex Microbial Communities.” Journal of Microbiological Methods 117 (October 2015): 74–77. https://doi.org/10.1016/j.mimet.2015.07.009. Cite
Ekici, Seda, Serdar Turkarslan, Grzegorz Pawlik, Andrew Dancis, Nitin S. Baliga, Hans-Georg Koch, and Fevzi Daldal. “Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production.” MBio 5, no. 1 (2014): e01055-01013. https://doi.org/10.1128/mBio.01055-13. 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. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Scientific Data 2 (2015): 150010. https://doi.org/10.1038/sdata.2015.10. Cite
Lopez Garcia de Lomana, Adrian, Sascha Schauble, Jacob Valenzuela, Saheed Imam, Warren Carter, Damla D. Bilgin, Christopher B. Yohn, et al. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels 8 (2015): 207. https://doi.org/10.1186/s13068-015-0391-z. Cite
Minch, Kyle J., Tige R. Rustad, Eliza J. R. Peterson, Jessica Winkler, David J. Reiss, Shuyi Ma, Mark Hickey, et al. “The DNA-Binding Network of Mycobacterium Tuberculosis.” Nature Communications 6 (2015): 5829. https://doi.org/10.1038/ncomms6829. Cite
Ashworth, Justin, Serdar Turkarslan, Micheleen Harris, Monica V. Orellana, and Nitin S. Baliga. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics 26 (April 2016): 21–28. https://doi.org/10.1016/j.margen.2015.10.011. Cite