2013 Yılı Yayınları

1.       Mishra, A.K., Tsachaki, M., Rister, J., Ng, J., Çelik, A., ve S.G. Sprecher, "Binary cell fate decisions and fate transformation in the Drosophila larval eye," PLoS Genetics, 9, e1004027 (2013).

2.       Li, X., Erclik, T, Chen, Z., Venkatesh, S., Morante, J., Çelik, A., ve C. Desplan, "Temporal patterning of Drosophila medulla neuroblasts controls neural fates," Nature, 498, 456-62 (2013).

3.       Okamoto Y, Goksungur MT, Pehlivan D, Beck CR, Gonzaga-Jauregui C, Muzny DM, Atik MM, Carvalho CM, Matur Z, Bayraktar S, Boone PM, Akyuz K, Gibbs RA, Battaloglu E, Parman Y, Lupski JR. Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. Genet Med. 2013 Oct 17. doi: 10.1038/gim.2013.155.

4.       Karahan, Ö., Aviyente, V., Avci, D., Zijlstra, H., Bickelhaupt, F. M., ’A ‘Computational   Study on the Reactivity Enhancement in the Free Radical Polymerization of Alkyl Hydroxymethacrylate and Acrylate Derivatives’ Journal of Polymer Science Part A:  Polymer Chemistry,  2013, 51, 880–889.

5.       Degirmenci,I.,  Tugba Furuncuoglu Ozaltın, Ozlem Karahan,Veronique Van Speybroeck, Michel. Waroquier, Viktorya Aviyente ’Origins of the Solvent Effect on the Propagation Kinetics of Acrylic Acid and Methacrylic Acid’ Journal of Polymer Science Part A: Polymer Chemistry,  2013, 51, 2024–2034.

6.       Mehtap Isık, Ozlem Karahan, Duygu Avci, Viktorya Aviyente ‘Computational Approach to the Free Radical Polymerization Kinetics of Alkyl -Hydroxymethacrylate Monomers: A Structure–Reactivity Relationship’ Journal of Polymer Science Part A: Polymer Chemistry,  2013, 51, 2375–2384.

7.       A. Altin, B. Akgun, O. Buyukgumus, Z. Sarayli Bilgici, S. Agopcan, D. Avci, ‘Synthesis and Photopolymerizations of Novel Highly Reactive Phosphonated-urea-methacrylates for Dental Materials’, React. Funct. Polym., 2013, 73, 1319.

8.       Z. Sarayli Bilgici , S. Begum Turker , D. Avci, Novel Bisphosphonated Methacrylates:

Synthesis, Polymerizations, and Interactions with Hydroxyapatite, Macromol. Chem. Phys. 2013, 214, 2324.

9.       Dedeoglu, B  ; Ugur, I ; Degirmenci, I ; Aviyente, V ; Barcin, B ; Cayli, G  ; Acar, HY ’First RAFT polymerization of captodative 2-acetamidoacrylic acid (AAA) monomer: An experimental and theoretical study’ POLYMER  2013, 54, 5122-5132.

10.    C. Özen, A. Yıldırım, N. Ş. Tüzün, P. Haslak, E. Doğan, E. Acar, V. Aviyente

‘Prediction of the 1H NMR spectra of epoxy-fused cyclopentane derivatives by calculations of chemical shifts and spin–spin coupling constants’  Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 2013,111, 3147-3155.

11.    H. Torun, S. Sadeghzadeh, A.D. Yalcinkaya "Tunable overlapping half-ring resonator" Rev Sci Instrum. 2013 Oct, 84(10):106107.

12.    Ozguc, C., Helvacioglu, E., Nugay, N., Nugay, T., "Synthesis and Characterization of Poly(N-isopropylacrylamide) and Poly(vinyl acetate) Diblock Copolymers via MADIX Process", Macromolecular Symposia, 2013, 323, 18-25.

13.    Aydınoğlu, D., Şen, S., Helvacıoğlu, D., Nugay, T., Nugay, N., "Tuning of Heavy Metal Removal Efficiency from Water via Micro Algae/Hydrogel Composites", e-polymers, 2013, 16, 1-17.

14.    Nugay, N., Nugay, T., Kennedy, J. P., "Minute amounts of organically modified montmorillonite improve the properties of polyisobutylene-based polyurethanes", Journal of Polymer Science Part A: Polymer Chemistry, 2013, 51, 4076-4087.

15.    Ozcan O, Uyar A, Doruker P, Akten ED. “Effect of intracellular loop 3 on intrinsic dynamics of human beta2-adrenergic receptor”, BMC Structural Biology,13(1), (16pp) (2013)

16.    Kurkcuoglu Z. and Doruker P.; “Substrate Effect on Catalytic and Global Dynamics of Triosephosphate Isomerase” Entropy, 15,1085-1099 (2013).

17.    Ozbek P., Soner S., Haliloglu T. “Hot spots in a network of functional sites”, PLoS One, 8(9), e74320, 2013.

18.    Aykac Fas B., 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), e10031412013, 2013.

19.    Kaya C., Armutlulu A., Ekesan S. and Haliloglu T. “MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues”, Nucleic Acids Research, 41, (Web Server Issue), w429-w255, 2013.

20.    Soner S., Özturan C., “Integer Programming Based Heterogeneous CPU-GPU Cluster Schedulers for SLURM Resource Manager”, Journal of Computer and System Sciences, in press.

21.    Begum Alaybeyoglu, Deniz Meneksedag, Berna Sariyar Akbulut, Elif Ozkirimli “A novel antimicrobial peptide” in preparation.

22.    A.U. Cakaci, M.H.M. Kouhani, H.Torun, A.D. Yalcinkaya "An ElectromagneticMEMS Based Resonator Design for Catheter Tracking in MRI" Technical Digest of the 24th Micromechanics and Microsystems Europe Conference (MME 2013), 2013.

23.    RB Erarslan, U Adiyan, SZ Lulec, S Olcer, Y Temiz, Y Leblebici, H Torun, H Urey, "Design and characterization of micromachined sensor array integrated with CMOS based optical readout", accepted for publication, _Sensor Actuat A-Phys, 2013.

24.    M. Tumer, B. Sarioglu, S. Mutlu, A.D. Yalcinkaya, C. Ozturk "LARFET (Low Amplitude RF at Echo Time) for Catheter Tracking" Proceedings of the 21st annual meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), 2013

25.    C. Kasap, M.L. Arslan, “A unified approach to speech enhancement and voice activity detection”, Turkish Journal of Electrical Engineering and Computer Sciences, vol. 21, pp. 527-547, 2013.

26.    Yalcinkaya M, Yüksel Ş. Investigation of LL-37 Mediated siRNA Transfection. Turkish Journal of Biology.37:426-432.(2013)

27.    Topaloğlu N, Gülsoy M, Yüksel Ş. Antimicrobial Photodynamic Therapy of Resistant Bacterial Strains by Indocyanine Green and 809-nm Diode Laser. Photomedicine and Laser Surgery. 31(4):255-162. (2013).

28.    Yüksel, Ş. Eren E, Hatemi G, Sahillioglu A, Gultekin Y, Demiroz D, Akdis C, Fresko I, Özören N.  The Cryopyrin (CIAS1/NALP3) Novel NLRP3/Cryopyrin Mutations and Pro-inflammatory Cytokine Profiles in Behcet’s Syndrome Patients.  International Immunology Journal. DOI: 10.1093/intimm/dxt046. (2013)

29.    Ozansoy Mehmet, Başak A.N, "The Central Theme Of Parkinson Disease: Alpha-Synuclein ”, Mol Neurobiol, 47 (2) :460-5. doi: 10.1007/s12035-012-8369-3 2013 Apr.

30.   Wang S, Chen K, Kayıtmazer AB , Li L, Guo X , tunable adsorptıon of bovıne serum albumın by annealed catıonıc spherıcal polyelectrolyte brushes, colloıds and surfaces b: bıoınterfaces, 107 , 251–256, , 2013

31.    Kayitmazer, A.B.; Seeman, D.; Minsky, B.B., Dubin, P.L., Xu, Y.; Protein-Polyelectrolyte Interactions, Soft Matter , 9 (9), 2553- 2583, 2013

32.    Agim Zeynep Sena, Esendal Melda , Uyan Ozgun, Meschian Mehran, Martinez Luis Antonio Mendoza, Ding Yongmei, Basak AN, Ozcelik Hilmi,"Discovery, Validation And Characterization Of Erbb4 And Nrg1Haplotypes Using Data From Three Genome-Wide Association Studies Of Schizophrenia", PLOS One,10.1371/journal.pone.0053042, January 2013 

33.    Uyan Özgün, Omur Ozgur , Agım Zeynep Sena , Ozoguz  Aslıhan, Li Hong, Parman Yesim , Deymeer Feza, Oflazer Piraye , Koc Filiz, Tan Ersin, Ozcelik Hilmi , Basak AN, “Genome-Wide Copy Number Variation in Sporadic Amyotrophic Lateral Sclerosis in the Turkish Population: Deletion of EPHA3 Is a Possible Protective Factor”, PLoS ONE 8(8): e72381, Ağustos, 2013

34.    Gultekin Yetiş, Eren Elif and Özören Nesrin, NLRC3 Acts as an Anti-Inflammatory Cytosolic Receptor, (accepted J of Innate Immunity), 2014

35.    Y. Bakış, H. H. Otu, N. Taşcı, C. Meydan, N. Bilgin, S. Yüzbaşıoğlu, U. Sezerman Testing robustness of relative complexity measure method                 constructing robust phylogenetic trees for Galanthus L. using the relative complexity     measure. BMC Bioinformatics 14, 20-37, 2013

36.    N. Taşçı Margoz, İ. S. Yüzbaşıoğlu, Z. Çelen, T. Ekim, A. N. Bilgin Molecular phylogeny of Galanthus (Amaryllidaceae) of Anatolia inferred from multiple nuclear and chloroplast DNA regions. Turkish Journal of Botany 37: 993-1007, 2013

37.    Kempe, K.; Onbulak, S.; Schubert, U. S.; Sanyal, A.; Hoogenboom, R. “pH Degradable Dendron-functionalized poly(2-ethyl-2-oxazoline) Prepared by a Cascade 'Double-Click' Reaction” Polymer Chemistry 2013, 4, 3236-3244.

38.    Topaloglu, Nermin ; Gulsoy, Murat; Yuksel, Sahru, Antimicrobial Photodynamic Therapy of Resistant Bacterial Strains by Indocyanine Green and 809-nm Diode Laser, Photomedıcıne And Laser Surgery, v31, 155-162,2013

39.    Dikici, Erinc; Semerci, Murat ; Saraclar, Murat ; Alpaydin, Ethem ; Classification and Ranking Approaches to Discriminative Language Modeling for ASR, IEEE Transactıons On Audıo Speech And Language Processıng, v21, 291-300, 2013

40.    Tunc, Burcu; Gulsoy, Murat, Tm:Fiber laser ablation with real-time temperature monitoring for minimizing collateral thermal damage: ex vivo dosimetry for ovine brain, Lasers In Surgery And Medıcıne, v45, 48-56,2013

41.    Gurol, Omer C, Sankur, Acar, Burak; Guney, Mehmet, Efficient estimation of disparity statistics and their use as a predictor for perceived 3d video scene quality, eurasıp journal on ımage and vıdeo processıng,  1-12,2013

42.    Aydin, Cagatay, Oktay, Oytun, Gunebakan, Adem Umut, Ademoglu, Ahmet , Ciftci, Rifat, Role of Alpha Oscillations During Short Time Memory Task Investigated by Graph Based Partitioning, Radıoengıneerıng, v22, 123-131, 2013

43.    Devecioglu, Ismail, Devecioglu, Ismail Guclu, Burak Asymmetric response properties of rapidly adapting mechanoreceptive fibers in the rat glabrous skin, Somatosensory And Motor Research, v30, 16-29, 2013

44.    Guclu, Burak, Dincer, S. Mete, Neural coding in the Non-Pacinian I tactile channel: A psychophysical and simulation study of magnitude, Somatosensory And Motor Research, v30, 1-15, 2013

45.    Yildiz, Mustafa Zahid,Guclu, Burak, Relationship between vibrotactile detection threshold in the Pacinian channel and complex mechanical modulus of the human glabrous skin, Somatosensory And Motor Research, v30, 37-47,2013

46.    Goksel-Duru, Dilek; Ozkan, Mehmed, Application of Self-Organizing Artificial Neural Networks on Simulated Diffusion Tensor Images, Mathematıcal Problems In Engıneerıng, 2013

47.    Kiziloz, Burcu Kaya, Tekcan, Ali I., Canonical Categories in Flashbulb Memories, Applıed Cognıtıve Psychology, v27, 352-359, 2013

48.    Yaman, Ozturk, Cengizhan, Huijing, Peter A. (VRIJE UNIV AMSTERDAM); Yucesoy, Can A., Magnetic Resonance Imaging Assessment of Mechanical Interactions Between Human Lower Leg Muscles in Vivo, Journal Of Bıomechanıcal Engıneerıng-Transactıons Of The Asm, v135, 2013

49.    Sen, Ipek, Saraclar, Murat,  Kahya, Yasemin P., Exploring an optimal vector autoregressive model for multi-channel pulmonary sound data, Computer Methods And Programs In Bıomedıcıne, v 111, 550-560,2013

50.    Ates, F., Özdeşlik, R.N., Huijing, P.A. and Yucesoy, C.A., Muscle lengthening surgery causes differential acute mechanical effects in both targeted and non-targeted synergistic muscles. Journal of Electromyography and Kinesiology, 23, 1198-1205, 2013.

51.    Yaman A., Ozturk, C., Huijing, P.A. and Yucesoy, C.A., MRI Assessment of Mechanical Interactions Between Human Lower Leg Muscles in vivo. Journal of Biomechanical Engineering, 135, 091003 1-9, 2013

52.    Demir, Cemil, Demir, Cemil, Saraclar, Murat, Cemgil, Ali Taylan, Single-Channel Speech-Music Separation for Robust ASR With Mixture Models, IEEE Transactıons On Audıo Speech And Language Processıng, v21, 725-736, 2013

53.    Mermer, Coskun (TUBITAK); Mermer, Coskun, Saraclar, Murat, Sarikaya, Ruhi, Improving Statistical Machine Translation Using Bayesian Word Alignment and Gibbs Sampling, Ieee Transactıons On Audıo Speech And Language Processıng, v 21, 1090-1101, 2013

54.    Ates, F. and Yucesoy, C.A, Effects of BTX-A on non-injected bi-articular muscle include a narrower length range of force exertion and increased passive force. Muscle and Nerve, in press, 2013.

55.    Meneksedag, Deniz, Dogan, Asligul, Kanlikilicer, Pinar, Ozkirimli, Elif, Communication between the active site and the allosteric site in class A beta-lactamases, Computatıonal Bıology And Chemıstry, v 43, 1-10, 2013

56.    Ates, F., Temelli, Y. and Yucesoy, C.A, Human spastic Gracilis muscle isometric forces measured intraoperatively as a function of knee angle show no abnormal muscular mechanics. Clinical Biomechanics, 28, 48-54., 2013.

57.    Yucesoy, C.A., Seref, Z. and Huijing, P.A., In muscle lengthening surgery multiple aponeurotomy does not improve intended acute effects and may counter-indicated: an assessment by finite element modeling.

58.    Computer Methods in Biomechanics and Biomedical Engineering, 16, 12-25, 2013.

59.    Gonen, Mehmet, Alpaydin, Ethem , Localized algorithms for multiple kernel learning, Pattern Recognıtıon, v 46, 795-807, 2013

60.    Kabas, Ayse, Ersoy, Tansu, Gulsoy, Murat, Akturk, Selcuk , Femtosecond laser etching of dental enamel for bracket bonding, Journal Of Bıomedıcal Optıcs, v 18, 2013

61.    Jeong, Youngdo, Patra, Debabrata, Sanyal, Amitav, Rotello, Vincent M., Fabrication of Stable Nanoparticle-Based Colloidal Microcapsules, Current Organıc Chemıstry, v 17, 49-57, 2013

62.    Tonga, M.; Yesilbag, G.; Seber, G.; Sanyal, A. “Dendronized Polystyrene via Orthogonal Double-Click Reactions” Journal of Polymer Science Part A: Polymer Chemistry, 51, 5029-5037, 2013.

63.    Gok, O.; Yigit, S.; Kose, M. M.; Sanyal, R.; Sanyal, A. “Dendron-Polymer Conjugates via the Diels-Alder 'Click' Reaction of Novel Anthracene-based Dendrons” Journal of Polymer Science Part A: Polymer Chemistry , 4, 3191-3201, 2013.

64.    Baradel, N.; Gok, O.; Zamfir, M.; Sanyal, A.; Lutz, J.-F. “Sequence-controlled Polymerizations Using Dendritic Macromonomers: Precise Chain-Positioning of Bulky Functional Clusters” Chemical Communications, 49, 7280-7282, 2013.

65.    Jeong, Y.; Patra, D.; Sanyal, A.; Rotello, V. M. "Fabrication of Stable Nanoparticle-Based Colloidal Microcapsules" Current Organic Chemistry, 49-57, , 2013.

66.    Cengiz, N.; Rao, J.; Sanyal, A.; Khan, A. “Designing functionalizable hydrogels through thiol-epoxy coupling chemistry” Chemical Communications, 49, 11191-11193, 2013.

67.    Meral, Cihan, Caglayan, Hande S.…, De Novo Loss-of-Function Mutations in CHD2 Cause a Fever-Sensitive Myoclonic Epileptic Encephalopathy, Amerıcan Journal Of Human Genetıcs, v 93, 967-975, 2013

68.    Akdag, Ihsan Omur, Ozkirimli, Elif, The Uptake Mechanism of the Cell-Penetrating pVEC Peptide, Journal Of Chemıstry, 2013

69.    Topaloglu, Nermin, Yuksel, Sahru; Gulsoy, Murat, Influence of different output powers on the efficacy of photodynamic therapy with 809-nm diode laser and indocyanine green, Optıcal Interactıons Wıth Tıssue And Cells XXIV, v 8579, 2013

70.    Tunc, Burcu , Gulsoy, Murat, Determination of the ablation efficiencies of the laser irradiated tissues via rate of temperature change over time, Energy-Based Treatment Of Tıssue And Assessment VII, v 8584, 2013

71.    Marvasti, Neda B., Acar, Burak , Assessment of MRF Based Joint Scale Selection and Segmentation for 3D Liver Vessel Segmentation Task,  21st Sıgnal Processıng And Communıcatıons Applıcatıons, 2013

72.    Dikici, Erinc , Saraclar, Murat, Curriculum Based Discriminative Language Model Training, 2013 21st Sıgnal Processıng And Communıcatıons Applıcatıons, 2013

73.    Aysan, Nuray, Topaloglu, Nermin, Yuksel, Sahru; Gulsoy, Murat, Biostimulative effect of 809-nm diode laser and indocyanine green on p.aeruginosa instead of photodynamic therapy, Mechanısms For Low-Lıght Therapy VIII, v8569,2013

74.    C Praetorius, C Grill, SN Stacey, AM Metcalf, DU Gorkin, KC Robinson, EV Otterloo, RSQ Kim, K Bergsteinsdottir, MH Ogmundsdottir, E Magnusdottir, PJ Mishra, SR Davis, T Guo, MR Zaidi, AS Helgason, MI Sigurdsson, PS Melzer, G Merlino, V Petit, L Larue, SK Loftus, DR Adams, U Sobhiafshar, NCT Emre, WJ Pavan, R Cornell, AG Smith, AS McCallion, DE Fisher, K Stefansson, RA Sturm, E Steingrímsson, IRF4 affects human pigmentation by regulating expression of Tyrosinase through a MITF/TFAP2A-dependent pathway. CELL, 155:1022-1033, 2013.

75.    L Lamy, VN Ngo, NCT Emre, AL Shaffer, Y Yang, T Tian, V Nair, MJ Kruhlak, A Zingone, O Landgren, LM Staudt  Control of autophagic cell death by caspase-10 in multiple myeloma.Cancer Cell, 23:435-449, 2013.

76.    Misiti T., Tandukar M., Tezel U., and Pavlostathis S. G. Inhibition and biotransformation potential of naphthenic acids under different electron accepting conditions. Water Research 47(1): 406-418, 2013.

77.    Misiti T., Tezel U., and Pavlostathis S. G, Fate and effect of naphthenic acids on oil refinery activated sludge wastewater treatment systems. Water Research 47(1): 449-460, 2013.

78.    Misiti T., Tezel U., Tandukar M. and Pavlostathis S. G. Aerobic biotransformation potential of a commercial mixture of naphthenic acids. Water Research 47(15): 5520-5534, 2013.

79.    Tandukar M., Oh S., Tezel U., Konstantinidis K. T., and Pavlostathis S. G. Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance. Environmental Science and Technology 47(17): 9730-9738, 2013.

80.    Hong J., Tezel U., Okutman Tas D., Pavlostathis S. G. Influence of quaternary ammonium compounds on the microbial reductive dechlorination of pentachloroaniline. Water Research 47(17): 6780-6789, 2013.

81.    Padhye L. P., Tezel U., Fate of environmental pollutants. Water Environment Research 85(10): 1734-1785, 2013.