Publications

1. BOOK CHAPTERS:

Urartu O. S. Seker, H. Volkan Demir, “Biomedical and Biochemical Approaches Using Quantum Dot Nanocrystals Enabled Förster Resonance Energy Transfer”, UV-VIS and Photoluminescence Spectroscopy for Nanomaterials Characterization, Chp13 (531-561) Ed. Challa Kumar, Springer Verlag, 2013. ISBN 978-3-642-27593-7 (*Corresponding Author)

UP

 2. ARTICLES

underlines indicate corresponding authorship, * indicates equal contribution

2017

24. Ebuzer Kalyoncu, Recep Erdem Ahan, Tolga Tarkan Olmez, Urartu Ozgur Safak Seker, Genetically Encoded Conductive Protein Nanofibers Secreted by Engineered Cells, RSC Advances, 2017,7, 32543-32551 .

23. Tugce Onur, Esra Yuca, Ebuzer Kalyoncu, Tolga Tarkan Olmez, Urartu Ozgur Safak Seker, Self-Assembled Bacterial Biofilm Proteins Based Nanomaterials, Langmuir, 2017 (in revision)

22. Tarek Abdelwahab, Ebuzer Kalyoncu, Tugce Onur, Mehmet Z. Baykara, Urartu Ozgur Safak Seker, Genetically-Tunable Mechanical Properties of Bacterial Functional Amyloid Nanofibers, Langmuir, 2017 , 33 (17), 4337-4345.


2016

21. Urartu Ozgur Safak Seker, Allen Chen, Timothy K. Lu, Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity,  ACS Synthetic Biology2017, 6 (2), pp 266–275.  (Publicaton date web : 2016.)

20. Gözde Kabay, Gizem Kaleli, Zahida Sultanova, Tolga Tarkan Ölmez, Urartu Özgür Şafak Şeker, Mehmet Mutlu, Biocatalytic protein membranes, Reactive and Functional Polymers, 2016, 6, 26.


Before 2016

19. Allen Y. Chen, D. Zhong, N. Billing, Urartu Ozgur Safak Seker, Michelle Y. Lu, Robert J. Citorik, B. Zakeri, Timothy K. Lu, Synthesizing and Patterning Tunable Multiscale Amyloid Materials with Synthetic Biofilms, Nature Materials, 2014, 13, 515.  NEWS 1, NEWS2

18. Urartu O. S. Seker, Brandon Wilson, John L. Kulp , John S. Evan, Candan Tamerler, Mehmet Sarikaya, Thermodynamics of Engineered Gold Binding Peptides- Establishing Structure-Activity Relationship, Biomacromolecules, 2014, 15 (7), 2369.

17. Urartu O. S. Seker*, Evren Mutlugun*, Pedro Ludwig Hernandez- Martinez, Vijay K. Sharma, Alexander Eychmüller, Hilmi Volkan Demir*, Bio-Nanohybrids of Photoproteins and Quantum Dots Facilitating Energy Transfer for Biosensing, Nanoscale, March 2013, 5, 7034-7040 (*corresponding author ) Impact Factor: 6

16. Urartu O. S. Seker, Vijay Kumar Sharma, Shahab Akhavan, H. V. Demir, Genetically Engineered Peptides for Nano-hybrid Assemblies, Langmuir, 2014, 30 (8), 2137-2143. (*corresponding author). Impact Factor: 4.2

15. Urartu O. S. Seker, Tuncay Ozel, Hilmi V Demir, Peptide-Mediated Constructs of Quantum Dot Nanocomposites for Enzymatic Control of Nonradiative Energy Transfer, Nano Letters, 2011, 11 (4), 1530-1539. Impact Factor: 13

14. Urartu O. S. Seker, G. Zengin, C. Tamerler, M. Sarikaya, H. V. Demir, Assembly Kinetics of Nanocrystals via Peptide Hybridization, Langmuir, 2011, 27 (8), 4867-4872. (*corresponding author) Impact Factor: 4

13. Hilmi V Demir, Urartu O. S. Seker, G. Zengin, E. Mutlugun, E. Sari, C. Tamerler, M. Sarikaya, Spatially Selective Assembly of Quantum Dot Light Emitters in an LED using Engineered Peptides, ACS Nano, 2011, 5 (4), 2735-2741. Impact Factor: 12

12. Esra Yuca, Ayten Karatas, Urartu O. S. Seker, Mustafa Gungormus, Gizem Dinler, Mehmet Sarikaya, Candan Tamerler, In vitro labeling of hydroxyapatite minerals by an engineered protein, Biotechnology and Bioengineering, 108 (5), 1021-1030, 2011. Impact Factor: 4

11. Urartu O.  S.  Seker, H. Volkan Demir, Material Binding Peptides for Nanotechnology, Molecules, (Invited review paper for Special issue of “Phage Display of Combinatorial Libraries” Ed. Brendan P. Orner) 16 (1), 1426-1451, 2011. Impact Factor: 3

10. Urartu O.  S. Şeker, B.Wilson, D. Sahin, C. Tamerler, M. Sarikaya. Quantitative Affinity of Genetically Engineered Repeating Polypeptides to Inorganic Solids, Biomacromolecules, 10 (2), 250-257, (2009). Impact Factor: 5

9. M. Hnilova, E. E. Oren, Urartu O. S. Seker, J. Evans, C. Tamerler, M. Sarikaya, Effect of Conformation on Adsorption Behavior of Gold Binding Peptides, Langmuir, 24 (21), 12440-12445, (2008). Impact Factor: 4

8. Urartu O.  S. Şeker, B. Wilson, S. Dincer, I. W. Kim, E. E. Oren, J. S. Evans, C. Tamerler, M. Sarikaya. Adsorption Behavior of Genetically Engineered Platinum Binding Peptides, Langmuir, 23 (15), 7895-7900, (2007).

7. E. E. Oren, C. Tamerler, D. Sahin, M. Hnillova, Urartu O.  S. Seker, M. Sarikaya, R. Samudrala. A Novel Informatics-Based Approach to Design Inorganic Binding Peptides, Bioinformatics, 24 (21), 2816-2822, (2007). Impact Factor: 6

6. Z. P. Cakar, Urartu O.  S. Seker, C. Tamerler, M. Sonderegger, Uwe Sauer, Evolutionary Engineering of Multiple Stress Resistant Saccharomyces cerevisiae, FEMS Yeast Research, (6-7), 569-578 (2005). Impact Factor: 3

5. B. Erdag, B. K. Balcioglu, A. O. Bahadir, M. Serhatli, O. Kacar, A. Bahar, Urartu O.  S. Seker et al., Identification of Novel Neutralizing Single-Chain Antibodies Against Vegfr-2, Biotechnology and Applied Biochemistry, 58 (16), (2011). Impact Factor: 2

4. I. H. Boyaci, Urartu O.  S. Seker, D. Bas, A. Topcu, C. Tamerler, Statistical Modeling of Product Inhibition Effect on β-Galactosidase Enzyme During Lactose Hydrolysis, Food Biotechnology, 20 (1), 79-91, (2006). Impact Factor: 2

3. Urartu O.  S. Seker, T. Catal, Y. Taptık, C. Tamerler, H. Bermek, Enhanced production of manganese peroxidase by the white rot fungus Bjerkandera adusta using media engineering. Biotechnology and Biotechnological Equipment, 22 (3), 844-848 (2008). Impact Factor: 1.5

1. I. H. Boyaci,Urartu O.  S. Seker and M. Mutlu, Determination of β-glucan content of cereals with amperometric glucose electrode, European Food Research and Technology (15), 538-541 (2002). Impact Factor: 2

UP

 3. SELECTED CONFERENCE PRESENTATIONS

2017.

28. Synthetic Genetic Circuits at the Bio-Nano Interface, Urartu Seker, IEEE-Nano/Micro Engineered and Molecular Systems (NEMS) 2017 Conference at UCLA (April 2017)  (Invited talk)

29. Bacterial functional amyloids based supramolecular assemblies,  Ebuzer Kalyoncu, Ebru Şahin Kehribar, Tolga Tarkan Olmez , Tugce Onur , Esra Yuca1 , Urartu Seker, Systems Chemistry in Paris, 2-3 February 2017 (Invited talk)

 2016

27. Tugce Onur, Tolga Tarkan Olmez, Ebuzer Kalyoncu, Urartu Seker, Self-Assembled Bacterial Biofilm Proteins As Functional Biomaterials”, SysChem 2016, 119, Valtice, Czech Republic, May 5-12 2016 (Invited talk)

26. Tugce Onur, Tolga Tarkan Olmez, Urartu Şeker, Engineered Bacterial Functional Amyloids as Bionanomaterials, Materials Research Society (MRS) Spring Meeting, Phoenix, Arizona, USA, 28 March-1 April 2016. (Oral Presentation)

25. Ebuzer Kalyoncu, Tolga Tarkan Olmez, Urartu  Seker. Genetically Programmed Functional Bacterial Biofilms. American Chemical Society (ACS) Fall Meeting at Pennsylvania Convention Center, Philadelphia, PA, USA, 24 August 2016 (Oral Presentation)

24. Probing the Nano-Bio Interface Using Synthetic Biology, 3rd Applied Synthetic Biology Conference. Urartu Seker. 22-24 February, 2016, Lisbon Portugal. (Oral Presentation)

UP

2015

23.Engineered Bacterial Functional Amyloids. Tugce Onur, Ebru Şahin Kehribar, Tolga Tarkan Olmez, Urartu Özgür Şafak Şeker. IV. International Congress of Molecular Biology Association of Turkey, Ankara, 27-29 November 2015

22. Synthetic Biology Enabled Biomedical Sensors. Side Selin Su Yirmibesoglu, Urartu O. S. Seker. IV. International Congress of Molecular Biology Association of Turkey, Ankara, 27-29 November 2015

21. Nano-Toxicity Sensing Through Synthetic Biology. Behide Saltepe, Urartu O. S. Seker. IV. International Congress of Molecular Biology Association of Turkey, Ankara, 27 – 29 November 2015

20. Synthesis of Functional Curli Fibers as Biotemplates for Nanomaterial Growth. Tolga Tarkan Ölmez, Ebuzer Kalyoncu, Hazal Beril Çatalak, Urartu Ö. Ş. Şeker. IV. International Congress of the Molecular Biology Association of Turkey, Ankara, 27-29 November 2015

19. Living Cellular Sensors to Monitor Nanotoxicity Using Synthetic Biology. Behide Saltepe, Urartu Seker. Computational Nanotoxicology Conference, 4-6 November 2015, Malaga, Spain. (Oral Presentation)

18. Synthetic Biology Enabled Nanotoxicity Monitoring in Real-Time. Behide Saltepe, Urartu O. S. Seker. 21st International Biomedical Science and Technology Symposium, Antalya, 22 – 24 October 2015. (Oral Presentation)

17. Nanotoxicity sensing through synthetic biology. Behide Saltepe, Urartu O. S. Seker. ACS Fall 2015, Boston, 14-20 August 2015.

UP

Before 2015

16. Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces , Urartu O. S. Seker, Allen Y. Chen, Timothy K. Lu, MRS Fall 2015 Meeting, Boston  November 30 – December 5, 2014.

15. Nanophotonics of Quantum Dot-Protein Composites, Urartu O. S. Seker, IEEE Photonics Conference 2013, Seattle USA, 8 – 12 September 2013, Invited Talk.

14. Functional quantum dot-protein nano bio-assembly for superior light harvesting applications, Evren Mutlugun, Urartu O. S. Seker, Pedro Ludwig Hernandez-Martinez, Vijay Kumar Sharma, Vladimir Lesnyak, Nikolai Gaponik, Alexander Eychmuller, Hilmi Volkan Demir, American Physical Society Meeting, ; Baltimore, Maryland, USA March 2013

13. Peptide-Mediated Constructs of Quantum Dot Nanocomposites for Enzymatic Control of Nonradiative Energy Transfer, Urartu O. S. Seker, Hilmi Volkan Demir, 7th International Conference on Quantum Dots, Santa Fe, New Mexico, USA, May 2012

12. Hydroxyapatite Binding Peptide Genetically Fused to Green Fluorescent Protein for Monitoring Mineralization, Esra Yuca, Urartu O. S. Seker, Mustafa Gungormus, Ayten Yazgan Karatas, Mehmet Sarikaya and Candan Tamerler, Society for Biomaterials, 2010 Annual Meeting, Seattle, USA.

11. SPR Investigation of Fibrillation Kinetics of Huntington Protein Immobilized using Solid Binding Peptides, S. Cetinel, Urartu O S. Seker, C. So, Elvan Arslan, C Tamerler, P. Muchowski and M. Sarikaya, Materials Research Society, MRS 2009 Spring Meeting, Boston, USA.-(Poster Presentation)

10. Material Selectivity of Genetically Engineered Peptides for Inorganics, Brandon R. Wilson, Urartu O. S. Seker, Candan Tamerler and Mehmet Sarikaya, Materials Research Society, MRS 2009 Fall Meeting, Boston, USA.-(Oral Presentation)

9. Supramolecular Self-Assembly of a Metal-binding Polypeptide and Implications for Molecular Recognition, C. So, E. E. Oren, Urartu.Ö. Ş. Şeker, B. R. Wilson, J. Kulp, C. Tamerler , J. S. Evans and M. Sarikaya, Materials Research Society, MRS 2007 Fall Meeting, Boston, USA.-(Oral Presentation)

8. Adsorption Behavior of Linear and Cyclic Genetically Engineered Platinum Binding Peptides, Urartu O. S. Şeker, B. R. Wilson, C. Tamerler and M. Sarikaya, Materials Research Society, MRS 2007 Fall Meeting, Boston, USA.-(Oral Presentation)

7. Molecular Structures of Engineered Inorganic-Binding Peptides. J. S. Evans, W. Kim, J. L. Kulp, S. Collino, K. Delak, Urartu O. S. Seker, C. So, E. E. Oren, C. Tamerler and M. Sarikaya, Materials Research Society, MRS 2007 Fall Meeting, Boston, USA.-(Oral Presentation)

6. Thermodynamic Analysis of the Gold Surface Recognition by a Gold Binding Peptide, Urartu O. S. Şeker, B. R. Wilson, C. Tamerler and M. Sarikaya, American Chemical Society, ACS 2007 Spring Meeting, Chicago, USA.-(Oral Presentattion)

5. Molecular Erectors: Directed Enzyme Immobilization via Genetically Engineered Peptides, Urartu O. S. Şeker, B. R. Wilson, C. Tamerler and M.Sarikaya, Materials Research Society, MRS 2007 Spring Meeting, San Francisco, USA.-(Poster Presentation)

4. Selectivity and Binding Kinetics of Genetically Engineered Peptides on Metals and Oxides. B. R. Wilson, Urartu O. S. Şeker, C. Tamerler, M. Sarikaya, Materials Research Society, MRS 2007 Spring Meeting, San Francisco, USA. –(Poster presentation)

3. Selection of Specific Gold-Binding Peptides via Cell Surface Display, M. Hnilova, E. E. Oren, Urartu.Ö. Ş. Şeker, B. Wilson, X. Xiorong, C. Tamerler, M. Sarikaya, Materials Research Society, MRS 2007 Spring Meeting, San Francisco, USA.-(Poster presentation)

2. Directed Evolution of Ophiostoma piliferum for lipase production, B. Toktay, Urartu Ö. Ş. Şeker, B. Turanli, H. Asimgil, T. Keshavarz, C. Tamerler and Z. P. Çakar, , 3rd International Conference on Analysis of Microbial Cells at the Single-Cell Level, 26-29 May 2005, Semmering, Austria.-(Poster presentation)

1. Improvement of lipase production in Ophiostoma piliferum via evolutionary engineering and media optimization B. Toktay, Urartu .O. S Şeker, B. Turanli, T. Keshavarz, C. Tamerler, Z. P. Cakar, 11th European Congress on Biotechnology, Basel, Switzerland, August 24 – 29, 2003, 267.-(Poster presentation)