2011 Yılı Yayınları

1.        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.

2.        Rende D.,Baysal N., Kirdar B., “A novel integrative network approach to understand the interplay between cardiovascular disease and other complex disorders”, 7, 2205–2219, 2011.

3.        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, Vol. 27, 2425-2433, 2011.

4.        Fleishman J. Sarel et al., Community-Wide Assessment of Protein-Interface Modeling

Suggests Improvements to Design Methodology, Journal of Molecular Biology, 414(2), 289-  302, 2011.

5.        Ozen Aysegul, Haliloglu Turkan, Schiffer Celia A., Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope, Journal of Molecular Biology, 410(4), Special Issue: SI Pages: 726-744, 2011.

6.        Ma Buyong, Tsai Chung-Jung, Haliloglu Turkan et al., Dynamic Allostery: Linkers Are Not Merely Flexible,  Structure, 19(7), 907-917, 2011.

7.        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.

8.        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(11-12), 986-995, 2011.

9.        Uyar A., Kurkcuoglu O., Nilsson L. Doruker P., The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases, Physical Biology, 8(5),  Special Issue: SI Article Number: 056001, 2011.

10.     Ozaltin T. Furuncuoglu, Degirmenci I., Aviyente V., et al., Controlling the tacticity in the polymerization of N-isopropylacrylamide: A computational study, Polymer, 52(24), 5503-5512, 2011.

11.     Karahan Ozlem, Avci Duygu, Aviyente Viktorya, Structure-Reactivity Relationships of Alkyl alpha-Hydroxymethacrylate Derivatives, Journal of Polymer Science Part A-Polymer Chemistry, 49(14), 3058-3068, 2011.

12.     Karahan Ozlem, Isik Mehtap, Cifci Gulsah et al.,  Cyclization Tendencies in the Free Radical Polymerization of Allyl Acrylate Derivatives: A Computational Study, Journal of Polymer Science Part A-Polymer Chemistry, 49(11), 2474-2483, 2011.

13.     Agopcan Sesil, Celebi-Olcum Nihan, Ucisik Melek Nihan et al., Origins of the diastereoselectivity in hydrogen bonding directed Diels-Alder reactions of chiral dienes with achiral dienophiles: a computational study, Organic&Biomolecular Chemistry, 9(23), 8079-8088, 2011 .

14.     Gonen Mehmet, Alpaydin Ethem, Multiple Kernel Learning Algorithms, Journal of Machine Learning Research, 12, 2211-2268, 2011.

15.     Kursun Olcay, Alpaydin Ethem, Favorov Oleg V.,  Canonical correlation analysis using within-class coupling, Pattern Recognition Letters, 32(2), 134-144, 2011.

16.     Gonen Mehmet, Alpaydin Ethem, Regularizing multiple kernel learning using response surface methodology, Pattern Recognition, 44(1), 159-171, 2011.

17.     Bilgici Zeynep Sarayli, Ordu Oznur Demir, Isik Mehtap et al., Synthesis and Polymerizations of Six Aminophosphonate-Containing Methacrylates, Journal of Polymer Science Part A-Polymer Chemistry, 49(23), 5042-5048, 2011.

18.     Ozer Ali Haydar, Ozturan Can, A direct barter model for course add/drop process,  Discrete Applied Mathematics, 159(8), 812-825, 2011.

19.     Haydar, Ozturan Can, Multi-unit differential auction-barter model for electronic marketplaces, Electronic Commerce Research and Applications, 10(2), 132-143, 2011.

20.     Enünlü, I., Ozansoy, M., Başak, A.N., “Alfaclass prefoldin protein UXT is a novel interacting partner of amyotrophic lateral sclerosis 2 (ALS2) Protein”, Biochemical and Biophysical Research Communications, 413, 3, 471-475, 2011.

21.     Giardine, B., Borg, Başak, A.N., et al., “Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach”, Nature Genetics, 43, 4, 295-302, 2011.

22.     Agopcan, S., Çelebi-Ölçüm, N., Üçışık, M.N., Sanyal, A., Aviyente, V., “Origins of the diastereoselectivity in hydrogen bonding directed diels alder reactions of chiral dienes with achiral dienophiles: A computational study”, Organic & Biomolecular Chemistry, 9, 23, 8079-8088, 2011.

23.     Billiet, L., Gök, O., Dove, A.P., Sanyal, A., Nguyen, L.T.T., Du, P.R.E.Z.,., “Metal free functionalization of linear polyurethanes by thiol maleimide coupling reactions”, Macromolecules, 44, 20, 7874-7878, 2011.

24.     Hizal, G., Tunca, U., Sanyal, A., “Discrete macromolecular constructs via the Die is alder ‘click’ reaction”, Journal of Polymer Science Part A-Polymer Chemistry, 49, 19, 4103-4120, 2011.

25.     Köse, M.M., Önbulak, S., Yılmaz, I.I., Sanyal, A., “Orthogonally ~clickable~biodegradable dendrons”, Macromolecules, 44, 8, 2707-2714, 2011.

26.     Subramani, C., Cengiz, N., Saha, K., Gevrek, T.N., Yu, X., Jeong, Y., Bajaj, A., Sanyal, A., Rotello, V.M., “Direct fabrication of functional and biofunctional nanostructures through reactive ımprinting”, Advanced Materials, 23, 28, 3165-+, 2011.

27.     Yiğit, S., Sanyal, R., Sanyal, A., “Fabrication and functionalization of hydrogels through ‘click’ chemistry”, Chemistry-An Asian Journal, 6, SI, 2648-2659, 2011.

28.     Aktan, O., Sarıoğlu, B., Cindemir, U., Ünlü, S.O., Dündar, G., Mutlu, S., Yalçınkaya, A.D., “Optoelectronic cmos power supply unit for electrically isolated microscale applications”, IEEE Journal of Selected Topics in Quantum Electronics, 17, 3, 747-756, 2011.

29.     Yalçınkaya, A.D., Gökdel, Y.D., Sarıoğlu, B., “One dimensional led array integrated polymer composite scanner for 2D imaging”, Sensors and Actuators A-Physical, 168, 1, 195-201, 2011.

30.     Kızılay, E., Kayıtmazer, A.B., Dubin, P.L., “Complexation and coacervation of polyelectrolytes with oppositely charged colloids”, Advances in Colloid and Interface Science, 167, SI, 24-37, 2011.

31.     Akgül, C.B., Rubin, D.L., Napel, S., Beaulieu, C.F., Greenspan, H., Acar, B., “Content based image retrieval in radiology: Current status and future directions”, Journal of Digital Imaging, 24, 2, 208-222, 2011.

32.     Işık, S., Dönmez, M.Y., Ersoy, C., “Cross layer load balanced forwarding schemes for video sensor networks”, Ad Hoc Networks, 9, 3, 265-284, 2011.

33.     Koşar, R., Bojaxhiu, I., Onur, E., Ersoy, C., “Lifetime extension for surveillance wireless sensor networks with ıntelligent redeployment”, Journal of Network and Computer Applications, 34, 6, 1784-1793, 2011.

34.     Yiğitel, M.A., İncel, O.D., Ersoy, C., “Design and implementation of A QOS aware mac protocol for wireless multimedia sensor networks”, Computer Communications, 34, 16, 1991-2001, 2011.

35.     Yiğitel, M.A., İncel, O.D., Ersoy, C., “QOS aware MAC protocols for wireless sensor networks: A survey”, Computer Networks, 55, 8, 1982-2004, 2011.

36.     Sin, B.A., Akdiş, M., Zumkehr, J., Bezzine, S., Bekpen, C., Lambeau, G., Akdiş, C.A., “T-cell and antibody responses to phospholipase A(2) from different species show distinct cross reactivity patterns”, Allergy, 66, 12, 1513-1521, 2011.

37.     Bayram, A., Bayraktaroğlu, Z., Karahan, E., Erdoğan, B., Bilgiç, B., Özker, M., Kaşıkçı, I., Duru, A.D., Ademoğlu, A., Öztürk, C., Arıkan, K., Tarhan, N., Demiralp, T., “Simultaneous EEG/FMRI analysis of the resonance phenomena in steady state visual evoked responses”, Clinical EEG and Neuroscience, 42, SI, 98-106, 2011.

38.     Dinçer, A., Özyurt, O., Kaya, D., Koşak, E., Öztürk, C., Erzen, C., Pamir, M.N., “Diffusion tensor imaging of guillain mollaret triangle in patients with hypertrophic olivary degeneration”, Journal of Neuroimaging, 21, 2, 145-151, 2011.

39.     İşçi, S., Öztürk, C., Jones, J., Otu, H.H., “Pathway analysis of high throughput biological data within a bayesian network framework”, Bioinformatics, 27, 12, 1667-1674, 2011.

40.     Öztürk, C., Küsefoğlu, S.H., “New polymers from epoxidized soybean oil with pyridine derivatives”, Journal of Applied Polymer Science, 121, 5, 2976-2984, 2011.

41.     Öztürk, C., Küsefoğlu, S.H., “New polymers from epoxidized soybean oil with pyridine derivatives”, Journal of Applied Polymer Science, 121, 5, 2976-2984, 2011.

42.     Öztürk, C., Küsefoğlu, S.H., “Polymerization of epoxidized soybean oil with maleinized polybutadiene”, Journal of Applied Polymer Science, 120, 1, 116-123, 2011.

43.     Öztürk, C., Küsefoğlu, S.H., “Polymerization of epoxidized soybean oil with maleinized polybutadiene”, Journal of Applied Polymer Science, 120, 1, 116-123, 2011.

44.     Öztürk, C., Mutlu, H., Meier, M.A.R., Küsefoğlu, S.H., “4-Vinylbenzenesulfonic acid adduct of epoxidized soybean oil: Synthesis, free radical and admet polymerizations”, European Polymer Journal, 47, 7, 1467-1476, 2011.

45.     Baets, J., Deconinck, T., Bilir, B., Battaloğlu E., et al., “Genetic spectrum of hereditary neuropathies with onset in the first year of life”, Brain, 134, , 2664-2676, 2011.

46.     Deymeer, F., Matur, Z., Poyraz, M., Battaloğlu, E., Oflazer-Serdaroğlu, P., Parman, Y., “Nerve conduction studies in Charcot Marie tooth disease in a cohort from Turkey”, Muscle & Nerve, 43, 5, 657-664, 2011.

47.     Aktan, O., Sarıoğlu, B., Cindemir, U., Ünlü, S.O., Dündar, G., Mutlu, S., Yalçınkaya, A.D., “Optoelectronic cmos power supply unit for electrically isolated microscale applications”, IEEE Journal of Selected Topics in Quantum Electronics, 17, 3, 747-756, 2011.

48.     Sönmez, O.S., Dündar, G., “Simulation based analog and RF circuit synthesis using a modified evolutionary strategies algorithm”, Integration the Vlsi Journal, 44, 2, 144-154, 2011.

49.     Torun, H., Torello, D., Değertekin, F.L., “Note: Seesaw actuation of atomic force microscope probes for improved imaging bandwidth and displacement range”, Review of Scientific Instruments, 82, 8, 2011.

50.     Gubili, C., Bilgin, R., Kalkan, E., Karhan, S.U., Jones, C.S., Sims, D.W., Kabasakal, H., Martin, A.P., Noble, L.R., “Antipodean white sharks on a mediterranean walkabout? Historical dispersal leads to genetic discontinuity and an endangered anomalous population”, Proceedings of the Royal Society B-Biological Sciences, 278, 1712, 1679-1686, 2011.

51.      Bilgin, R., “Back to the suture: The distribution of ıntraspecific genetic diversity ın and around Anatolia”, International Journal of Molecular Sciences, 12, 6, 4080-4103, 2011.

52.     Özbayraktar, F.B.K., Ülgen, K.Ö., “Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of Hydroxylation”, Biosystems, 104, 1, 63-75, 2011.

53.     Toku, A.E., Tekir, S.D., Özbayraktar, F.B.K., Ülgen, K.Ö., “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.

54.     Bilici, T., Mutlu, Ş., Kalaycıoğlu, H., Kurt, A., Sennaroğlu, A., Gülsoy, M., “Development of a thulium (TM:YAP) laser system for brain tissue ablation”, Lasers in Medical Science, 26, 5, 699-706, 2011.

55.      Bilici, T., Mutlu, Ş., Kalaycıoğlu, H., Kurt, A., Sennaroğlu, A., Gülsoy, M., “Development of a thulium (TM:YAP) laser system for brain tissue ablation”, Lasers in Medical Science, 26, 5, 699-706, 2011.

56.     Sarp, A.S.K., Gülsoy, M., “Ceramic bracket debonding with ytterbium fiber laser”, Lasers in Medical Science, 26, 5, 577-584, 2011.

57.     Sarp, A.S.K., Gülsoy, M., “Etching of enamel for direct bonding with a thulium fiber laser”, Lasers in Dentistry XVII, 7884, 2011.

58.     Sayar-Türet, M., Dreisigacker, S., Braun, H.J., Hede, A., Maccormack, R., Boyd, L.A., “Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan and Europe as determined by nucleotide binding site profiling”, Genome, 54, 5, 419-430, 2011.

59.     Bilici, T., Mutlu, Ş., Kalaycıoğlu, H., Kurt, A., Sennaroğlu, A., Gülsoy, M., “Development of a thulium (TM:YAP) laser system for brain tissue ablation”, Lasers in Medical Science, 26, 5, 699-706, 2011.

60.     Bilici, T., Mutlu, Ş., Kalaycıoğlu, H., Kurt, A., Sennaroğlu, A., Gülsoy, M., “Development of a thulium (TM:YAP) laser system for brain tissue ablation”, Lasers in Medical Science, 26, 5, 699-706, 2011.

61.     Mutlu, Ş., Haydaroğlu, I., Sevim, A.O., “Realization of polymer charge pump circuits using polymer semiconductors”, Organic Electronics, 12, 2, 312-321, 2011.

62.     Arzu Temizyürek  “A Holistic Approach To Laboratory Animal Science:”One Health Concept”.                             3rd East Mediterranean ICLAS  International Council for Laboratory Animal Science. Symposium and 15 th ICLAS General Assembly.” Laboratory Animal Science: New trends and perspectives”.  Doç.Dr.Siyami Karahan, Prof.Dr. Tuncay Altuğ, Prof.Dr.Cemal Aygıt, Prof.Dr. Bayram Yılmaz, Dr.Tayfun İde ,Sf: 129,  İstanbul, 2011

63.     Dereli E., Dikicioglu D., Kirdar B., “A Systems Biology Based Approach to Reveal the Effect of Rapamycin and Caffeine on the Lifespan and Life Quality of Yeast”, SYSINBIO Workshop, Frankfurt am Main, 2011.

64.     Dereli E., Dikicioglu D., Eraslan S., Oliver S. G., Kirdar B. “Transcriptional Responses of Yeast to Two Drug Effectors: Rapamycin and Caffeine”, International Conference on System Biology, Mannheim, Germany, 2011.

65.     Cankorur Cetinkaya A., Eraslan S, Kirdar B., “A System Based Approach to Understand Wilson and Menkes Diseases Using Saccharomyces cerevisiae as a Model Organism”, International Conference on System Biology, Mannheim, Germany, 2011.

66.     Karabekmez M.E., Dikicioglu D., Oliver S. G., Kirdar B., “Comparison of TEAFS and NP Analysis: Integration of Interactome and Time Course Transcriptome Data to Reveal Dynamic Response to C-pulse in S.cerevisiae”, Joint 4th FEBS & Systems X Advanced Lecture Course, Innsbruck, Austria, 2011.

67.     Kasavi C., Toksoy Oner E., Kirdar B., “Genomic Comparison of Ethanol Tolerance Genes of Industrial Saccaharomyces cerevisiae Strains”, Comparative Genomics of Eukaryotic Microorganisms: Understanding the Complexity of Diversity, Sant Feliu de Guixols, Spain, 2011.

68.     Kasavi C., Toksoy Oner E., Kirdar B., “Systems Based Modular Approach to Analyze Ethanol Tolerance in Saccaharomyces cerevisiae”, International Conference on System Biology, Mannheim, Germany, 2011.

69.     Durmus Tekir S.,  Sayılırbas A. S., Cakir T., Ulgen K., “PHISTO: PATHOGEN-HOST INTERACTION SEARCH TOOL”, International Conference on System Biology, Mannheim, Germany, 2011.

70.     Yucel E., Ulgen K., “Reconstruction and Analysis of Chronological Aging Network in Saccharomyces cerevisiae”, International Conference on System Biology, Mannheim, Germany, 2011.

71.     Yıldırım, Y., Orhan, E.K., İşeri, S.A.U., Serdaroglu-Oflazer, P., Kara, B., Solakoğlu, S., Tolun, A., “A frameshift mutation of ERLIN2 in recessive intellectual disability, motor dysfunction and multiple joint contractures”, Human Molecular Genetics, 20, 10, 1886-1892, 2011.

72.     Yıldırım, Y., Tolun, A., Tüysüz, B., “The phenotype caused by pycr1 mutations corresponds to geroderma osteodysplasticum rather than autosomal recessive cutis laxa type 2”, American Journal of Medical Genetics Part A, 155A, 1, 134-140, 2011.

73.     Tüysüz, B., Tolun, A., Yıldırım, Y., “Response to Kouwenberg et al. ~Recognizable phenotype with common occurrence of microcephaly, psychomotor retardation, but no spontaneous bone fractures in arcl2b due to pycr1 mutations~”, American Journal of Medical Genetics Part A, 155A, 9, 2333-2334, 2011.

74.     Güçlü, B., Sevinç, E., Canbeyli, R., “Duration discrimination by musicians and nonmusicians”, Psychological Reports, 108, 3, 675-687, 2011.

75.     Battaloğlu, E., Dağlıkoca, E.D., Yıldırım, K., Kılınç, M., Parman, Y., Svenningsen, A.F., Buğra, K., “Expression of FGF1 and FGFR1 in mouse sciatic nerve”, Journal of the Peripheral Nervous System, 16, S9-S9, 2011

76.     Alakent, B., Başkan, S., Doruker, P., “Effect of ligand binding on the intraminimum dynamics of proteins”, Journal of Computational Chemistry, 32, 3, 483-496, 2011.

77.     Uyar, A., Kürkçüoğlu, O., Nilsson, L., Doruker, P., “The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases”, Physical Biology, 8, SI, 2011

78.     Aydemir, N., Özkara, C., Ünsal, P., Canbeyli, R., “A comparative study of health related quality of life, psychological well being, İmpact of illness and stigma in epilepsy and migraine”, Seizure European Journal of Epilepsy, 20, 9, 679-685, 2011

79.     A. Dinçer, O. Özyurt, D. Kaya, E. Koşak, C. Ozturk, C. Erzen, M. N. Pamir, “Diffusion Tensor Imaging of Guillain-Mollaret Triangle in Patients with Hypertrophic Olivary Degeneration”, Journal of Neuroimaging, 21:145-151, 2011.

80.     S. Isci, C. Ozturk, J. Jones, H. H. Otu, “Pathway Analysis of High-Throughput Biological Data within a Bayesian Network Framework”,    Bioinformatics, 27(12): 1667-1674, 2011.

81.     Vasiliauskas, D., Mazzoni, E.O., Sprecher, S.G., Johnston, R.J. Jr, Lidder, P., Vogt, N., Çelik, A., Desplan, C., “Feedback from Rhodopsin controls Rhodopsin exclusion in Drosophila R8 photoreceptors”, Nature, 479, 7371, 108-12, 2011.