2013

Caglayan B. S., Aksoylu A. E., CO2 adsorption on chemically modified activated carbon, Journal of Hazardous Materials, 252, 19-28, 2013.

 

Ozkara-Aydinoglu S., Aksoylu A. E., A comparative study on the kinetics of carbon dioxide reforming of methane over Pt-Ni/Al2O3 catalyst: Effect of Pt/Ni Ratio, Chemical Engineering Journal, 215, 542-549, 2013.

 

Tekir S. D., Cakir T., Ardic E., et al., PHISTO: pathogen-host interaction search tool, Bioinformatics, 29, 10, 1357-1358, 2013.

 

Kaya C., Armutlulu A., Ekesan S., et al., MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues, Nucleic Acids Research, 41, W1, W249-W255, 2013.

 

Ozbek P., Soner S., Haliloglu T., Hot Spots in a Network of Functional Sites, Plos One, 8, 9, e74320, 2013.

 

Simsek E., Karakaya M., Avci A. K., et al., Oxidative steam reforming of methane to synthesis gas in microchannel reactors, International Journal of Hydrogen Energy, 38, 2, 870-878, 2013.

 

Cankorur-Cetinkaya A., Eraslan S., Kirdar B., Transcriptional remodelling in response to changing copper levels in the Wilson and Menkes disease model of Saccharomyces cerevisiae, Molecular Biosystems, 9, 11, 2889-2908. 2013.

 

Tekir S. D., Ulgen K. O., Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era, Biotechnology Journal, 8, 1, SI, 85-+, 2013.

 

Gunay, M. E., Yildirim R., Knowledge Extraction from Catalysis of the Past: A Case of Selective CO Oxidation over Noble Metal Catalysts between 2000 and 2012, ChemCatChem, 5, 6, 1395-1406, 2013.

 

Gunay, M. E., Yildirim R., Modeling preferential CO oxidation over promoted Au/Al2O3 catalysts using decision trees and modular neural networks, Chemical Engineering Research & Design, 91, 5, 874-882, 2013.

 

Ozcan O., Uyar A., Doruker P., et al., Effect of intracellular loop 3 on intrinsic dynamics of human beta(2)-adrenergic receptor, BMC Structural Biology, 13, 29, 2013.

 

Fas B. A., Tutar Y., Haliloglu, T., Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein, Plos Computational Biology, 9, 7, e1003141, 2013.

 

Akman U., Okay E., Okay N., Current snapshot of the Turkish ESCO market, Energy Policy, 60, 106-115, 2013.

 

Ozcan A., Olmez E. O., Alakent B., Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B, Proteins-Structure Function and Bioinformatics, 81, 5, 788-804, 2013.

 

Eren D., Alakent B., Frequency Response of a Protein to Local Conformational Perturbations, Plos Computational Biology, 9, 9, e1003238, 2013.

 

Akdag I. O., Ozkirimli E., The Uptake Mechanism of the Cell-Penetrating pVEC Peptide, Journal of Chemıstry, 851915, 2013.

 

Karakaya M., Onsan Z. I., Avci A. K., Microchannel Autothermal Reforming of Methane to Synthesis Gas, Topics in Catalysis, 56, 18-20, SI, 1716-1723, 2013.

 

Gokaliler F., Onsan Z. I., Aksoylu A. E., Power-law type rate expression for WGS reaction over Au-Re/CeO2 catalyst under realistic fuel processor conditions, Catalysis Communicatıons, 39, 70-73, 2013.

 

Rende D., Baysal N., Kirdar B.,Complex Disease Interventions from a Network Model for Type 2 Diabetes, Plos One, 8, 6, e65854, 2013.

 

Yucel E. B., Ulgen K. O., Assessment of crosstalks between the Snf1 kinase complex and sphingolipid metabolism in S. cerevisiae via systems biology approaches, Molecular Biosystems, 9, 11, 2914-2931, 2013.

 

Kurkcuoglu Z., Doruker P., Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase, Entropy, 15, 3, 1085-1099, 2013.

 

Gunay M. E., Yildirim R., Developing global reaction rate model for CO oxidation over Au catalysts from past data in literature using artificial neural networks, Applied Catalysis A-General, 468, 395-402, 2013.

 

Meneksedag D., Dogan A., Kanlikilicer P., et al., Communication between the active site and the allosteric site in class A beta-lactamases, Computational Biology and Chemistry, 43, 1-10, 2013.

 

Tekir S. D., Cakir T., Ardic E., et al., PHISTO: A New Web Platform for Pathogen-Human Interactions, Computational Methods in Systems Biology, Book Series: Lecture Notes in Bioinformatics, 8130, 268-269, 2013.



2012

Ozen A., Haliloglu T. and Schiffer C.A. , HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern, Journal of Chemical Theory and Computation​, 8​, 2​, 703-714​, 2012.

 

​Günay ME, Akpınar F, Önsan Zİ, Yıldırım R, Investigation of water gas-shift activity of Pt-MOX-CeO2/Al2O3 (M = K, Ni, Co) using modular artificial neural networks, International Journal of Hydrogen Energy​, 37​, 3​, 2094-2102​, 2012.

 

​Özdemir S, Önsan Zİ, Yıldırım R , Selective CO oxidation over monolithic Au-MgO/Al2O3 catalysts, Journal of Chemical Technology & Biotechnology​, 87​​, 58-64​, 2012.

 

​Gümüşlü G, Avcı AK, Parametric analysis of Fischer-Tropsch synthesis in a catalytic microchannel reactor, AIChE Journal​, 58​​, 227-235​, 2012.

 

​Ozdemir S, Onsan ZI, Yildirim R, , Selective CO oxidation over monolithic Au-MgO/Al2O3 catalysts, J. Chem. Technol. Biotechnol.​, 87​​, 58–64​, 2012.

 

​Karakaya M, Keskin S, Avcı AK, Parametric study of methane steam reforming to syngas in a catalytic microchannel reactor, Applied Catalysis A: General​, 411-412​​, 114-122​, 2012.

 

​Korkmaz N, Nussinov R, Haliloglu T, Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB, PLoS Computational Biology​, 8​, 3​, 1-9​, 2012.

 

​Günay ME, Akpinar F, Onsan Zi, Yildirim R, Investigation of water-gas shift activity of Pt-MOx-CeO2/Al2O3 (M=K, Ni, Co) using modular artificial neural networks, Int. J. Hydrogen Energy​, 37​​, 2094-2102 ​, 2012.



2011

​Alakent B., Baskan S., Doruker P., Effect of Ligand Binding on the Intraminimum Dynamics of Proteins, Journal of Computational Chemistry​, 32​, 3​, 483-496​, 2010.

 

​Olmez EO, Alakent B, Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B, Journal of Biomolecular Structure and Dynamics​, 28​, 5​, 675-693 ​, 2011.

 

​Ma B., Tsai C.J., Haliloglu T., Nussinov R. , Dynamic allostery: linkers are not merely flexible, Structure​, 19​, 7​, 907-917​, 2011.

 

​Ozen A., Haliloglu T., Schiffer C.A., Dynamics of Preferential Substrate Recognition in HIV-1 Protease : Redefining the Substrate Envelope, Journal of Molecular Biology​, 410​, 4​, 726-744​, 2011.

 

​Özbayraktar Kavun, F. B., Ülgen, K., , Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation, BioSystems​, 104​, 1​, 63-75​, 2011.

 

​Acuner Özbabacan S.E., Durmuş Tekir S., Ülgen K.Ö., , Crucial components in toll-like receptor signalling network as key regulators for immunological disorders, International Journal of Physical Sciences​, 6​, 8​, 2016-2026​, 2011.

 

​Eren Toku A., Durmuş Tekir S., Kavun Özbayraktar F.B., Ülgen K., , Reconstruction and Crosstalk of Protein-Protein Interaction Networks of Wnt and Hedgehog Signaling in Drosophila Melanogaster, Computational Biology and Chemistry​, 35​, 5​, 282-292​, 2011.

 

​Uyar A., Kurkcuoglu O., Nilsson L., Doruker P. , The elastic network model reveals a consistent picture on the intrinsic functional dynamics of type II restriction endonucleases, Physical Biology​, 8​, 5​, 13 pp​, 2011.

 

​Kurkcuoglu Z, Ural G, Akten E.D., Doruker P, , Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human, Molecular Informatics, 30, 986-995 (2011)​, 30​, 11-12​, 986-995​, 2011.

 

​Borklu Yucel E, Ulgen KO, A Network-Based Approach on Elucidating the Multi-Faceted Nature of Chronological Aging in S. cerevisiae, PlosONE​, 6​, 12​, e29284​, 2011.

 

​Fleishman J. Sarel, ...Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T. , Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, Journal of Molecular Biology​, 414​, 2​, 289-302​, 2011.

 

​Karaca E., Tozluoglu M., Nussinov R., Haliloglu, T., Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation , Journal of Molecular Biology​, 406​, 4​, 620-630​, 2011.

 

​Finore I., Kasavi C., Poli A., Romano I., Toksoy Oner E., Kirdar B., Dipasquale L., Nicolaus B., Lama L., Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting α-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov., World J Microbiol Biotechnol​, 27​​​, 2011.

 

Rende D., Baysal N., Kırdar B., A Novel Integrative Network Approach to Understand the Interplay between Cardiovascular Disease and Other Complex Disorders, Biosystems​, 7​​​, 2011.

 

​Dikicioglu D., Karabekmez E., Rash B., Pir P., Kirdar B., Oliver S.G., How yeast re-programmes its transcriptional profile in response to different nutrient impulses, BMC Systems Biology​, 5:148​​​, 2011.

 

​Özkara-Aydınoğlu, Ş., Aksoylu, A. E., CO2 reforming of methane over Pt-Ni/Al2O3 catalysts: Effects of catalyst composition, and water and oxygen addition to the feed, International Journal of Hydrogen Energy​, 36​​, 2950-2959​, 2011.

 

​Ölmez EÖ, Alakent B, Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B , Journal of Biomolecular Structure and Dynamics​, 28​, 5​, 675-693​, 2011.

 

​Şimşek E, Avcı AK, Önsan Zİ, Investigation of catalyst performance and microstructured reactor configuration for syngas production by methane steam reforming, Catalysis Today​, 178 ​, 1​, 157-163​, 2011.

 

​Karakaya M, Avcı AK, Microchannel reactor modeling for combustion driven reforming of iso-octane, International Journal of Hydrogen Energy​, 36​​, 6569-6577​, 2011.

 

​Davran-Candan T, . Tezcanli ST, Yildirim R, , Selective CO oxidation over promoted Au/γ-Al2O3 catalysts in the presence of CO2 and H2O in the feed, Catal. Comm., ​, 12​​, 1149-1152​, 2011.

 

​Davran-Candan T., Demir M, Yildirim R, , Analysis of reaction mechanisms and kinetics of preferential CO oxidation, Reac. Kinet. Mech. Catal.​, 104​​, 389–398​, 2011.

 

​Günay ME, Yildirim R, , Neural network analysis of selective CO oxidation over copper-based catalysts for knowledge extraction for published data in the literature, Ind. Eng. Chem. Res.​, 50​​, 12488–12500​, 2011.

 

​Şimşek E, Avcı AK, Önsan ZI, nvestigation of catalyst performance and microstructured reactor configuration for syngas production by methane steam reforming, Catalysis Today​, 178​​, 157-163​, 2011.

 

​S. Murat Sen, E. Zerrin Bagci, Mehmet C. Camurdan, Bistability analysis of an apoptosis model in the presence of nitric oxide, bulletin of mathematical biology​, 73​​, 1952-1968​, 2011.

 

Selen Çağlayan, B., Aksoylu, AE, Water-gas shift activity of ceria supported Au-Re catalysts, Catalysis Communications​, 12​​, 1206-1211​, 2011.

 

​Selen Caglayan, B, Soykal, İI, Aksoylu, AE, Preferential oxidation of CO over Pt–Sn/AC catalyst: Adsorption, performance and DRIFTS studies, Applied Catalysis B: Environmental​, 106​​, 540-549​, 2011.