Publications

  • Algin O, Kilin M, Ocakoglu G, Ozmen E (2016). “Assessment of Liliequist membrane by 3D-SPACE technique at 3T.” Neuroradiology 58(7): 637-647.
  • Beşalti Ö, Çalışkan M, Can P, Atalay SV, Algin O, Ahlat O (2016). “Imaging and surgical outcomes of spinal tumors in 18 dogs and one cat.” J Vet Sci. 17(2): 225-234.
  • Dalgic A, Caliskan M, Can P, Alagoz F, Guvenc Y, Ocakcioglu A, Algin O, et al (2016). “Experimental Endoscopic Cordotomy in the Sheep Model.” Turk Neurosurg. 26(2): 286-290.
  • Agaoglu, MN, Clarke, AM, Herzog, MH, & Öğmen, H (2016). “Motion-based nearest vector metric for reference frame selection in the perception of motion.” Journal of vision, 16:7, 14-14.
  • Manassi, M, Lonchampt, S, Clarke, A, & Herzog, MH (2016). “What Crowding Can Tell Us About Object Representations.” Vision Research, 16(3):35, 1-13.
  • Pamir, Z, Boyaci, H (2016). “Context-dependent Lightness Affects Perceived Contrast.” Vision Research 124: 24-33. doi: 10.1016/j.visres.2016.06.003.
  • Turkozer, HB, et al. (2016). “Contrast Affects fMRI Activity in Middle Temporal Cortex Related to Center-Surround Interaction in Motion Perception.” Frontiers in Psychology 7:454, 1-8. doi:10.3389/fpsyg.2016.00454
  • Cukur, T. (2016) “Spectrally selective imaging with wideband balanced steady-state free precession MRI.” Magnetic Resonance in Medicine 75:1132–1141
  • Todd, J. et al. (2016). The effect of threat on cognitive biases and pain outcomes: An eye tracking study. DOI: 10.1002/ejp.887
  • Khatibi, A. (2016). Be precise and suffer less pain! A comment on “A brief intervention utilising visual feedback reduces pain and enhances tactile acuity in CLBP patients.” Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.3233/BMR-160664
  • Akbari, F. et al. (2016). Incorporating Family Function into chronic pain disability: the role of catastrophizing. http://dx.doi.org/10.1155/2016/6838596

  • Algin O (2015). “Prediction of endoscopic third ventriculostomy (ETV) success with 3D-SPACE technique.″ Neurosurg Rev. 38(2): 395-397.
  • Atagün MI, Sıkoğlu EM, Can SS, Karakaş-Uğurlu G, Ulusoy-Kaymak S, Algin O, et al (2015). “Investigation of Heschl’s gyrus and planum temporale in patients with schizophrenia and bipolar disorder: A proton magnetic resonance spectroscopy study.″ Schizophr Res. 161(2-3): 202-209.
  • Algin O, Ucar M, Ozmen O, et al (2015). “Assessment of Third Ventriculostomy Patency with 3D-SPACE Technique: A Preliminary Multicenter Research Study.″ The Journal of Neurosurgery 122(6): 1347-1355.
  • Kartal MG, Ocakoglu G, Algin O (2015). “Feasibility of 3D Sampling Perfection with Application Optimized Contrast Sequence in the Evaluation of Patients with Hydrocephalus.″ J Comput Assist Tomogr 39(3): 321-328.
  • Clarke, AM, Friedrich, J, Tartaglia, EM, Marchesotti, S, Senn, W & Herzog, MH (2015). “Human and Machine Learning in Non-Markovian Decision Making.” PLoS One, 10(4): e0123105. doi:10.1371/journal.pone.0123105.
  • Gulseren, G., et al. (2015). “Alkaline Phosphatase-Mimicking Peptide Nanofibers for Osteogenic Differentiation.” Biomacromolecules 16(7): 2198-2208.
  • Uzunalli, G., et al. (2015). “Improving pancreatic islet in vitro functionality and transplantation efficiency by using heparin mimetic peptide nanofiber gels.” Acta biomaterialia.
  • Unal Gulsuner, H., et al. (2015). “Multi-Domain Short Peptide Molecules for In situ Synthesis and Biofunctionalization of Gold Nanoparticles for Integrin-Targeted Cell Uptake.” ACS applied materials & interfaces.
  • Mumcuoglu, D., et al. (2015). “Oligonucleotide Delivery with Cell Surface Binding and Cell Penetrating Peptide Amphiphile Nanospheres.” Molecular pharmaceutics 12(5): 1584-1591.
  • Gulsuner, H. U., et al. (2015). “Reply to Tzoulis et al.: Genetic and clinical heterogeneity of essential tremor.” Proceedings of the National Academy of Sciences 112(18): E2269-E2269.
  • Goktas, M., et al. (2015). “Self-Assembled Peptide Amphiphile Nanofibers and PEG Composite Hydrogels as Tunable ECM Mimetic Microenvironment.” Biomacromolecules 16(4): 1247-1258.
  • Unal Gulsuner, H., et al. (2015). “Osteoselection supported by phase separated polymer blend films.” Journal of Biomedical Materials Research Part A 103(1): 154-161.
  • Kafaligonul, H., et al. (2015). “Feedforward and feedback processes in vision.” Frontiers in psychology 6.
  • Unal Gulsuner, H., et al. (2015). “Osteoselection supported by phase separated polymer blend films.” Journal of Biomedical Materials Research Part A 103(1): 154-161.
  • Kartal MG, Algin O (2014). “Evaluation of hydrocephalus and other cerebrospinal fluid disorders with MRI: An update.″ Insight imaging 5(4): 531-541.
  • Herzog, MH & Clarke, AM (2014). “Why vision is not both hierarchical and feedforward.” Frontiers in Computational Neuroscience, 8:135. doi: 10.3389/fncom.2014.00135.
  • Clarke, AM, Herzog, MH & Francis, G (2014). “Visual crowding illustrates the inadequacy of local versus global and feedforward versus feedback distinctions in modelling visual perception.” Frontiers in Psychology, 5:1193. doi: 10.3389/fpsyg.2014.01193.
  • Cappe, C, Clarke, A M, Mohr, C & Herzog, MH (2014). “Is there a common factor for vision?” Journal of Vision. 14:8, 1-11.
  • Clarke, AM, Grzeczkowski, L, Mast, FW, Gauthier, I., & Herzog, MH (2014). “Deleterious effects of roving on learned tasks.” Vision Research, 99, 88-92.
  • Arslan, E., et al. (2014). “Bioactive supramolecular peptide nanofibers for regenerative medicine.” Advanced healthcare materials 3(9): 1357-1376.
  • Aydın Tekdaş, D., et al. (2014). “Design of a Gd‐DOTA‐Phthalocyanine Conjugate Combining MRI Contrast Imaging and Photosensitization Properties as a Potential Molecular Theranostic.” Photochemistry and photobiology 90(6): 1376-1386.
  • Boyaci, H et al. (2014). “Effect of contiguity and figure-ground organization on the area rule of lightness.” Journal of Vision 14(13):26, 1-11. doi:10.1167/14.13.26
  • Akin, B, et al. (2014). “Attention modulates neuronal correlates of interhemispheric integration and global motion perception.” Journal of Vision, 14(12):30, 1-13. doi:10.1167/14.12.30
  • Ceylan, H., et al. (2014). “Bone-like mineral nucleating peptide nanofibers induce differentiation of human mesenchymal stem cells into mature osteoblasts.” Biomacromolecules 15(7): 2407-2418.
  • Gengec, N. A., et al. (2014). “Selective adsorption of L1210 leukemia cells/human leukocytes on micropatterned surfaces prepared from polystyrene/polypropylene-polyethylene blends.” Colloids and Surfaces B: Biointerfaces 113: 403-411.
  • Gulsuner, H. U., et al. (2014). “Mitochondrial serine protease HTRA2 p. G399S in a kindred with essential tremor and Parkinson disease.” Proceedings of the National Academy of Sciences 111(51): 18285-18290.
  • Mammadov, B., et al. (2014). Extracellular matrix mimetic peptide scaffolds for neural stem cell culture and differentiation. Biomimetics and Stem Cells, Springer: 131-148.
  • Sever, M., et al. (2014). “Tenascin-C mimetic peptide nanofibers direct stem cell differentiation to osteogenic lineage.” Biomacromolecules 15(12): 4480-4487.
  • Uzunalli, G., et al. (2014). “Bioactive self-assembled peptide nanofibers for corneal stroma regeneration.” Acta biomaterialia 10(3): 1156-1166.
  • Arslan-Ergul, A. and M. M. Adams (2014). “Gene expression changes in aging Zebrafish (Danio rerio) brains are sexually dimorphic.” BMC neuroscience 15(1): 29.
    Kafaligonul, H. (2014). “Vision: A Systems Neuroscience Perspective.” The Journal of Neurobehavioral Sciences 1(2): 21-26.

  • Algin O, Turkbey B. (2013). Intrathecal Gadolinium-Enhanced MR Cisternography: A Comprehensive Review. American Journal of Neuroradiology (AJNR) 34(1): 14-22.
  • Algin O, Turkbey B, Ozmen E, et al. (2013). ″Evaluation of spontaneous third ventriculostomy by three-dimensional sampling perfection with application-optimized contrasts using different flip-angle evolutions (3D-SPACE) sequence by 3T MR imaging: Preliminary results with variant flip-angle mode.″ J Neuroradiol. 40: 11-18. Eryaman Y, Turk EA, Oto C, Algin O, Atalar E (2013). “Reduction of the radiofrequency heating of metallic devices using a dual-drive birdcage coil. Magn Reson Med. 69(3): 845-852.
  • Clarke, AM, Repnow, M, Öğmen, H, & Herzog, MH (2013). “Does spatio-temporal filtering account for nonretinotopic motion perception? Comment on Pooresmaeili, Cicchini, Morrone, and Burr (2012).” Journal of Vision, 13(10):19, 1-14.
  • Molina, D. P., et al. (2013). “Growth hormone and insulin-like growth factor-I alter hippocampal excitatory synaptic transmission in young and old rats.” Age 35(5): 1575-1587.
  • Ilay, A., et al. (2013). “Novel object recognition is not affected by age despite age-related brain changes.” World Journal of Neuroscience 2013.
  • Konkle, J. J., et al. (2013). “Twenty-fold acceleration of 3D projection reconstruction MPI.” Biomedizinische Technik/Biomedical Engineering 58(6): 565-576.
  • Karampinos, D. C., et al. (2013). “Diffusion tensor imaging and T2 relaxometry of bilateral lumbar nerve roots: feasibility of in‐plane imaging.” NMR in biomedicine 26(6): 630-637.
  • Saritas, E. U., et al. (2013). “Magnetostimulation limits in magnetic particle imaging.” Medical Imaging, IEEE Transactions on 32(9): 1600-1610.
  • Saritas, E. U., et al. (2013). “Magnetic particle imaging (MPI) for NMR and MRI researchers.” Journal of Magnetic Resonance 229: 116-126.
  • Lu, K., et al. (2013). “Linearity and shift invariance for quantitative magnetic particle imaging.” Medical Imaging, IEEE Transactions on 32(9): 1565-1575.
  • Estrada, V., et al. (2013). “Neural ECM mimetics.” Progress in brain research 214: 391-413.
  • Ayas, S., et al. (2013). “Label-free nanometer-resolution imaging of biological architectures through surface enhanced raman scattering.” Scientific reports 3.
  • Ceylan, H., et al. (2013). “Size-controlled conformal nanofabrication of biotemplated three-dimensional TiO2 and ZnO nanonetworks.” Scientific reports 3.
  • Huri, E., et al. (2013). “Generation of Chimeric “ABS Nanohemostat” Complex and Comparing Its Histomorphological In Vivo Effects to the Traditional Ankaferd Hemostat in Controlled Experimental Partial Nephrectomy Model.” International journal of biomaterials 2013.
  • Kocabey, S., et al. (2013). “Glycosaminoglycan mimetic peptide nanofibers promote mineralization by osteogenic cells.” Acta biomaterialia 9(11): 9075-9085.
  • Mammadov, B., et al. (2013). “Neural differentiation on synthetic scaffold materials.” Biomaterials Science 1(11): 1119-1137.
  • Sardan, M., et al. (2013). “Cell penetrating peptide amphiphile integrated liposomal systems for enhanced delivery of anticancer drugs to tumor cells.” Faraday discussions 166: 269-283.
  • Tekinay, A. B., et al. (2013). “Peptide nanofibers for controlled growth factor release.” Therapeutic delivery 4(6): 651-654.
  • Ustun, S., et al. (2013). Peptide Nanofiber Scaffolds for Multipotent Stromal Cell Culturing. Stem Cell Nanotechnology, Springer: 61-76.Ceylan, H., et al. (2013). “Mussel Inspired Dynamic Cross‐Linking of Self‐Healing Peptide Nanofiber Network.” Advanced Functional Materials 23(16): 2081-2090.

 

  • Algin O, Turkbey B. (2012). Evaluation of aqueductal stenosis by three-dimensional sampling perfection with application optimized contrasts using different flip-angle evolutions (3D-SPACE) sequence: Preliminary results with 3 Tesla MRI. American Journal of Neuroradiology (AJNR) 33(4): 740-746.
  • Aberg, KC, Clarke, AM, Sandi, C, & Herzog, MH (2012). “Trait anxiety and post-learning stress do not affect perceptual learning.” Neurobiology of learning and memory. 98:3, 246-253.
  • Ustun, S., et al. (2012). “Growth and differentiation of prechondrogenic cells on bioactive self-assembled peptide nanofibers.” Biomacromolecules 14(1): 17-26.
  • Ceylan, H., et al. (2012). “Surface-adhesive and osteogenic self-assembled peptide nanofibers for bioinspired functionalization of titanium surfaces.” Soft Matter 8(14): 3929-3937.
  • Cinar, G., et al. (2012). “Amyloid inspired self-assembled Peptide nanofibers.” Biomacromolecules 13(10): 3377-3387.
  • Mammadov, B., et al. (2012). “Cooperative effect of heparan sulfate and laminin mimetic peptide nanofibers on the promotion of neurite outgrowth.” Acta biomaterialia 8(6): 2077-2086.
  • Mammadov, R., et al. (2012). “Growth factor binding on heparin mimetic peptide nanofibers.” Biomacromolecules 13(10): 3311-3319.
  • Tombuloglu, A., et al. (2012). “Materials for Articular Cartilage Regeneration.” Recent Patents on Biomedical Engineering 5(3): 187-199.
  • Molina, D. P., et al. (2012). “Growth hormone modulates hippocampal excitatory synaptic transmission and plasticity in old rats.” Neurobiology of aging 33(9): 1938-1949.
  • Goodwill, P. W., et al. (2012). “Projection x-space magnetic particle imaging.” Medical Imaging, IEEE Transactions on 31(5): 1076-1085.
  • Kafaligonul, H. and G. R. Stoner (2012). “Static sound timing alters sensitivity to low-level visual motion.” Journal of vision 12(11): 2.
  • Goodwill, P. W., et al. (2012). “X‐space MPI: magnetic nanoparticles for safe medical imaging.” Advanced materials 24(28): 3870-3877.
  • Mammadov, R., et al. (2012). “Microscopic characterization of peptide nanostructures.” Micron 43(2): 69-84.
  • Sosa, Y, Clarke, AM & McCourt, ME (2011). “Hemifield asymmetry in the potency of exogenous auditory and visual cues.” Vision Research, 51:11, 1207-1215.
  • Behroozi, M. et al. (2011). “Statistical analysis methods for the fMRI data.” Basic and Clinical Neuroscience, 2(4):67-74.
  • Gulsuner, S et al. (2011). “Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred.” Genome Research 21:1995-2003. doi:10.1101/gr.126110.111.
  • Barak, T et al. (2011). “Recessive LAMC3 mutations cause malformations of occipital cortical development.” Nature Genetics 43:590-594. doi:10.1038/ng.836.
  • Bulut, S., et al. (2011). “Slow release and delivery of antisense oligonucleotide drug by self-assembled peptide amphiphile nanofibers.” Biomacromolecules 12(8): 3007-3014.
  • Ceylan, H., et al. (2011). “Selective adhesion and growth of vascular endothelial cells on bioactive peptide nanofiber functionalized stainless steel surface.” Biomaterials 32(34): 8797-8805.
  • Mammadov, R., et al. (2011). “Heparin mimetic peptide nanofibers promote angiogenesis.” Biomacromolecules 12(10): 3508-3519.
  • Bulut, S., et al. (2011). “Slow release and delivery of antisense oligonucleotide drug by self-assembled peptide amphiphile nanofibers.” Biomacromolecules 12(8): 3007-3014.
    Dagdas, Y. S., et al. (2011). “Nanomechanical characterization by double-pass force–distance mapping.” Nanotechnology 22(29): 295704.
  • Mammadov, R., et al. (2011). “Heparin mimetic peptide nanofibers promote angiogenesis.” Biomacromolecules 12(10): 3508-3519.
    Zaharchuk, G., et al. (2011). “Reduced field-of-view diffusion imaging of the human spinal cord: comparison with conventional single-shot echo-planar imaging.” American Journal of Neuroradiology 32(5): 813-820.
  • Saritas, E. U., et al. (2011). “SNR dependence of optimal parameters for apparent diffusion coefficient measurements.” Medical Imaging, IEEE Transactions on 30(2): 424-437.
  • Zaharchuk, G., et al. (2011). “Reduced field-of-view diffusion imaging of the human spinal cord: comparison with conventional single-shot echo-planar imaging.” American Journal of Neuroradiology 32(5): 813-820.

  • Doerschner, K et al. (2010). “Perceived Glossiness in High Dynamic Range Scenes.” Journal of Vision 10(9):11, 1-11. doi:10.1167/10.9.11.
  • Boyaci, H et al. (2010). “Perceptual grouping-dependent lightness processing in human early visual cortex.” Journal of Vision 10(9):4, 1-12. doi:10.1167/10.9.4
  • Doerschner, K et al. (2010). “Estimating the glossiness transfer function induced by illumination change and testing its transitivity.” Journal of Vision 10(4):8, 1-9. doi:10.1167/10.4.8
  • Adams, M. M., et al. (2010). “Age-related synapse loss in hippocampal CA3 is not reversed by caloric restriction.” Neuroscience 171(2): 373-382.
  • Saritas, E., et al. (2010). “Hadamard slice-encoding for reduced-FOV single-shot diffusion-weighted EPI.” Proceedings of the International Society of Magnetic Resonance in Medicine. Stockholm, Sweden: International Society of Magnetic Resonance in Medicine: 189.
  • Kafaligonul, H. and G. R. Stoner (2010). “Auditory modulation of visual apparent motion with short spatial and temporal intervals.” Journal of vision 10(12): 31.
  • Bedell, H. E. and G. Purushothaman (2010). “Perceptual asynchronies and the dual-channel differential latency hypothesis.” Space and Time in Perception and Action: 379.

  • Adams, M. M., et al. (2009). “Stability of local brain levels of insulin-like growth factor-I in two well-characterized models of decreased plasma IGF-I.” Growth Factors 27(3): 181-188.
  • Kafaligönül, H., et al. (2009). “Effects of contrast polarity in paracontrast masking.”
    Attention, Perception, & Psychophysics 71(7): 1576-1587.
  • Fang, F. et al. (2009). “Border ownership selectivity in human early visual cortex and its modulation by attention.” Journal of Neuroscience, 29(2):460-465. doi:10.1523/JNEUROSCI.4628-08.2009.

  • Rainville, S., & Clarke, A. (2008). “Distinct perceptual grouping pathways revealed by temporal carriers and envelopes.” Journal Of Vision, 8(15):9, http://journalofvision.org/8/15/9/, doi:10.1167/8.15.9.
  • Fang, F et al. (2008). “Attention-dependent representation of a size illusion in human V1.” Current Biology 18(21):1707-1712. doi:10.1016/j.cub.2008.09.025
  • Breitmeyer, B. G., et al. (2008). “Metacontrast masking and stimulus contrast polarity.” Vision research 48(23): 2433-2438.
  • Lee, J. H., et al. (2008). “Full‐brain coverage and high‐resolution imaging capabilities of passband b‐SSFP fMRI at 3T.” Magnetic Resonance in Medicine 59(5): 1099-1110.
  • Yildirim, M., et al. (2008). “Estrogen and aging affect synaptic distribution of phosphorylated LIM kinase (pLIMK) in CA1 region of female rat hippocampus.” Neuroscience 152(2): 360-370.

  • Shi, L., et al. (2007). “Caloric restriction eliminates the aging-related decline in NMDA and AMPA receptor subunits in the rat hippocampus and induces homeostasis.” Experimental neurology 206(1): 70-79.

  • Shi, L., et al. (2006). “Spatial learning and memory deficits after whole-brain irradiation are associated with changes in NMDA receptor subunits in the hippocampus.” Radiation research 166(6): 892-899.
  • Breitmeyer, B. G., et al. (2006). “Meta-and paracontrast reveal differences between contour-and brightness-processing mechanisms.” Vision research 46(17): 2645-2658.

  • Ramsey, M. M., et al. (2005). “Functional characterization of des-IGF-1 action at excitatory synapses in the CA1 region of rat hippocampus.” Journal of neurophysiology 94(1): 247-254.