Publications

2019

Kaya, U. & Kafaligonul, H. Cortical processes underlying the effects of static sound timing on perceived visual speed. Neuroimage 199, 194–205 (2019).

Urgen BA*, Pehlivan S*, Saygin AP (2019). Distinct representations in occipito-temporal, parietal, and premotor cortex during action perception revealed by fMRI and computational modeling. Neuropsychologia, 127, 35-47.

Urgen, B.M., Topac, Y., Ustun, F.S., Demirayak, P., Oguz, K.K., Kansu, T., Saygi, S., Ozcelik, T., Boyaci, H. and Doerschner, K. (2019). Homozygous LAMC3 mutation links to structural and functional changes in visual attention networks. NeuroImage190, 242-253.

Celik, E., Dar, S. U. H., Yilmaz, O., Keles, U. & Cukur, T. Spatially informed voxelwise modeling for naturalistic fMRI experiments. Neuroimage 186, 741–757 (2019).

2018

Türközer HB, Hasoğlu T, Chen Y, Norris LA, Brown M, Delaney-Busch N, Kale EH, Pamir Z, Boyacı H, Kuperberg G, Lewandowski KE. (2018). Integrated assessment of visual perception abnormalities in psychotic disorders and relationship with clinical characteristics. Psychological Medicine, 1-9.

Urgen BA, Kutas M, Saygin AP (2018). Uncanny valley as a window into predictive processing in the social brain. Neuropsychologia, 114, 181-185

Schmid, A. C., & Doerschner, K. (2018). Shatter and splatter: The contribution of mechanical and optical properties to the perception of soft and hard breaking materials. Journal of vision18(1), 14-14.

2017

Toscani, M., Gegenfurtner, K.R., Doerschner, K., (2017). Differences in illumination estimation in #thedress. Journal of Vision, 17(1), 1-14. doi:10.1167/17.1.22.

Dövencioğlu, D. N., Ben-Shahar, O., Barla, P., & Doerschner, K. (2017). Specular motion and 3D shape estimation. Journal of Vision17(6), 3-3.

2016

Arslan-Ergul, A. et al., (2016). Short-term dietary restriction in old zebrafish changes cell senescence mechanisms. Neuroscience 334: 64-75.

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, Pamir, Z, Boyaci, H (2016). Contrast Affects fMRI Activity in Middle Temporal Cortex Related to Center-Surround Interaction in Motion Perception. Frontiers in Psychology, 7:454, 1-8, http://journal.frontiersin.org/article/10.3389/fpsyg.2016.00454/full, doi: 10.3389/fpsyg.2016.00454

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

2015

Gulseren, G., et al. (2015). “Alkaline Phosphatase-Mimicking Peptide Nanofibers for Osteogenic Differentiation.” Biomacromolecules 16(7): 2198-2208.

Gulseren, G., et al. (2015). “Alkaline Phosphatase-Mimicking Peptide Nanofibers for Osteogenic Differentiation.” Biomacromolecules 16(7): 2198-2208.

Urgen BA, Miller LE (2015). Towards an empirically grounded predictive coding account of action understanding. Journal of Neuroscience, 35(12), 4789-4791

Hofree G*, Urgen BA*, Winkielman P, Saygin AP (2015). Observation and imitation of actions performed by humans, androids, and robots: an EMG study. Front. Human Neurosci. 9:364

Dövencioğlu, D. N., Wijntjes, M. W., Ben-Shahar, O., & Doerschner, K. (2015). Effects of surface reflectance on local second order shape estimation in dynamic scenes. Vision research, 115, 218-230.

Kam, T.E., Mannion, D. , Lee, S.W., Doerschner, K., Kersten, D. (2015). Human visual cortical responses to specular and matte motion flows. Front. Hum. Neurosci. 9:579.

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.

2014

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.

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.

Boyaci, H, Şimşek, MK, Subaşı, E (2014). Effect of contiguity and figure-ground organization on the area rule of lightness. Journal of Vision, 14(13):26, 1-11, http://www.journalofvision.org/content/14/13/26.full, doi: 10.1167/14.13.26

Yilmaz. O., Doerschner, K. (2014). Detection and Localization of Specular Surfaces using Motion Cues, Machine Vision and Applications. Volume 25, Issue 5, pp 1333-1349. doi: 10.1007/s00138-014-0610-9

Akin, B, Ozdem, C, Eroglu, S, Taslak Keskin, D, Fang, F, Doerschner, K, Kersten, D, Boyaci, H. (2014). Attention modulates neuronal correlates of interhemispheric integration and global motion perception. Journal of Vision, 14(12):30, 1-13, http://www.journalofvision.org/content/14/12/30.full, doi:10.1167/14.12.30

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.

2013

Urgen BA, Plank M, Ishiguro H, Poizner H, and Saygin AP (2013) EEG theta and mu oscillations during perception of human and robot actions. Front. Neurorobot. 7:19

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.

Doerschner, K., Yilmaz. O., Kucukoglu, Fleming, R. (2013) Effects of 3D Shape and Surface Reflectance on Perceived Rotation Axis, Journal of Vision, 13(11):8, pp.1-23, doi: 10.1167/13.11.8

Oguz, K. K., Temucin, E., Gocmen, R., Has, A.C., Dolgun, A., Doerschner, K., Alikasifoglu, M. (2013) Assessment of Whole Brain White Matter by DTI in Autosomal Recessive Spastic Ataxia of Charlevoix- Saguenay, AJNR, [Epub ahead of print], doi: 10.3174/ajnr.A3488

Oguz, K. K., Sanverdi, E.,Temucin, C., Turk, S., Haliloglu G., Doerschner, K. (2013) Tract-Based Spatial Statistics of Diffusion Tensor Imaging in Hereditary Spastic Paraplegia with Thin Corpus Callosum Reveals Widespread White Matter Abnormality, Diagnostic and Interventional Radiology, 19(3):181-6. doi: 10.5152/dir.2013.046.

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.

2012

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.

Wijntes, M., Doerschner, K., Kucukoglu, G., Pont, S., (2012) Relative flattening between velvet and matte 3D shapes: evidence for similar shape-from-shading computations. Journal of Vision, 12(1)2, 1-11, http://journalofvision.org/12/1/2/; doi:10.1167/12.1.2.

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.

2011

Behroozi, M., Daliri, M.R., Boyaci, H. (2011). Statistical analysis methods for the fMRI data. Basic and Clinical Neuroscience, 2(4), 67-74.

Gulsuner, S., Tekinay, A.B., Doerschner, K., Boyaci, H., Bilguvar, K., Unal, H., Ors, A., Onat, O.E., Atalar, E., Basak, A.N., Topaloglu, H., Kansu, T., Tan, M., Tan, U., Gunel, M., Ozcelik, T. (2011). Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hy- poplasia and quadrupedal locomotion in a consanguineous kindred. Genome Research, 21, pp. 1995-2003. http://genome.cshlp.org/content/21/12/1995.abstract, doi:10.1101/gr.126110.111

Barak, T. , Kwan, K.Y. , Louvi, A., Demirbilek, V., Saygi, S., Tüysüz, B., Choi, M., Boyaci, H., Doerschner, K., et al. (2011). Recessive LAMC3 mutations cause malformations of occipital cortical development. Nature Genetics, 43, 590-594, http://www.nature.com/ng/journal/v43/n6/full/ng.836.html, doi:10.1038/ng.836.

Doerschner, K., Kersten, D., Schrater, P. (2011). Rapid Classification of Specular and Diffuse Reflection from Image Velocities. Pattern Recognition, 44(9), 1874-1884 http://dx.doi.org/10.1016/j.patcog.2010.09.007

Doerschner, K., Fleming, R., Yilmaz, O., Schrater, P., Hartung, B., Kersten, D., (2011) Visual Motion and the Perception of Surface Material. Current Biology 21(23), 2010-2016; doi:10.1016/j.cub.2011.10.036

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.

2010

Adams, M. M., et al. (2010). “Age-related synapse loss in hippocampal CA3 is not reversed by caloric restriction.” Neuroscience 171(2): 373-382.

Doerschner, K., Maloney, LT, Boyaci, H. (2010). Perceived Glossiness in High Dynamic Range Scenes. Journal of Vision, 10(9):11, 1-11, http://www.journalofvision.org/content/10/9/11.full, doi:10.1167/10.9.11

Boyaci, H., Fang, F., Murray, SO, Kersten, D. (2010). Perceptual grouping-dependent lightness processing in human early visual cortex. Journal of Vision, 10(9):4, 1-12, http://www.journalofvision.org/content/10/9/4.full, doi:10.1167/10.9.4

Doerschner, K., Boyaci, H., Maloney, L.T. (2010). Estimating the glossiness transfer function induced by illumination change and testing its transitivity. Journal of Vision, 10(4):8, 1-9, http://journalofvision.org/10/4/8/, doi:10.1167/10.4.8

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.

2009

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.

Fang, F., Boyaci, H., Kersten, D. (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- 08.200.

Kafaligönül, H., et al. (2009). “Effects of contrast polarity in paracontrast masking.” Attention, Perception, & Psychophysics 71(7): 1576-1587.

2008

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.

Fang, F., Boyaci, H., Kersten, D., and Murray, S.O. (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

2007

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.

2006

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.

2005

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.