Publications

2024

  • Tolga Çukur
    • Abdallah Z. Alkilani, Tolga Cukur, Emine U. Saritas, “FD-Net: An unsupervised deep forward-distortion model for susceptibility artifact correction in EPI,” Magnetic Resonance in Medicine, vol. 91, pp. 280 – 296, 2024. PDF
  • Hacı Hulusi Kafalıgönül
    • A. Karaduman, E.T. Karoglu-Eravsar, M.M. Adams, H. Kafaligonul, “Passive exposure to visual motion leads to short-term changes in the optomotor response of aging zebrafish,” Behavioural Brain Research, vol. 460, pp. 114812 – , 2024. PDF
  • Emine Ülkü Sarıtaş Çukur
    • A. Zaid Alkilani, T. Çukur, E. U. Saritas, “FD-Net: An unsupervised deep forward-distortion model for susceptibility artifact correction in EPI,” Magnetic Resonance in Medicine, vol. 91, pp. 280 – 296, 2024. PDF
    • E. Benassai, …, E.U. Saritas, A. Abou-Hassan, “High-throughput large scale microfluidic assembly of iron oxide nanoflowers@PS-b-PAA polymeric micelles as multimodal nanoplatforms for photothermia and magnetic imaging,” Nanoscale Advances, vol. 6, pp. 126 – 135, 2024. PDF
  • Burcu Ayşen Ürgen
    • Hilal Nizamoğlu, Burcu A. Urgen, “Neural processing of bottom-up perception of biological motion under attentional load,” Vision Research, vol. 214, pp. 108328 – , 2024. PDF
  • Ausaf Ahmed Farooqui
    • Hasan Duymuş, Mohini Verma, Yasemin Güçlütürk, Mesut Öztürk, Ayşe B Varol, Şehmus Kurt, Tamer Gezici, Berhan F Akgür, İrem Giray, Elif E Öksüz, Ausaf A Farooqui, The visual cortex in the blind but not the auditory cortex in the deaf becomes multiple-demand regions, Brain, 2024;, awae187, https://doi.org/10.1093/brain/awae187

2023

  • Michelle Marie Adams
    • A. Karaduman, E.T. Karoglu-Eravsar, U. Kaya, A. Aydin, M.M. Adams, H. Kafaligonul, “Zebrafish optomotor response to second-order motion illustrates that age-related changes in motion detection depend on the activated motion system,” Neurobiology of Aging, vol. 130, pp. 12 – 21, 2023. PDF
    • B. Erbaba, D. Macaroglu, N.I. Ardic-Avci, A. Arslan-Ergul, M.M. Adams, “Caloric restriction reinforces the stem cell pool in the aged brain without affecting overall proliferation status,” Gene, vol. 851, pp. 147026-1–12, 2023. PDF
    • E.T. Karoglu-Eravsar, …, M.M. Adams, “Long-Term Acetylcholinesterase Depletion Alters the Levels of Key Synaptic Proteins while Maintaining Neuronal Markers in the Aging Zebrafish (Danio rerio) Brain,” Gerontology, vol. 69, pp. 1424 – 1436, 2023. PDF
  • Yasemin Afacan
    • A. Santos Nouri, I. Charalampopoulos-, Y.Afacan, A. Matzarakis, “Detection and quantification of seasonal human heat and cold stress frequencies in representative existing and future urban canyons: The case of Ankara,” Theoretical and Applied Climatology, vol. 153, pp. 593 – 620, 2023. PDF
    • B. Gündoğdu, A.Santos Nouri, Y.Afacan, A. Matzarakis, “Investigating the impacts of shaded outdoor spaces on thermal adaptation and cognitive performance of university students in classroom environments,” International Journal of Biometeorology, vol. 67, pp. 1941 – 1955, 2023. PDF
    • Y. Afacan, “Impacts of urban living lab (ULL) on learning to design inclusive, sustainable, and climate-resilient urban environments,” Land Use Policy, vol. 124, pp. 106443-1–10, 2023. PDF
  • Ergin Atalar
    • Ehsan Kazemivalipour, Alireza Sadeghi-Tarakameh, Boris Keil, Yigitcan Eryaman, Ergin Atalar, Laleh Golestanirad, “Effect of field strength on RF power deposition near conductive leads: A simulation study of SAR in DBS lead models during MRI at 1.5 T—10.5 T,” PLoS ONE, vol. 18, pp. 0280655 – , 2023. PDF
    • Manouchehr Takrimi, Ergin Atalar, “Minimization of Eddy Power Loss in the Cryostat for a Z-Gradient Array Coil Driven by an Arbitrary Pulse Sequence: An Electromagnetic Approach,” Magnetic Resonance in Medicine, vol. 91, pp. 1225 – 1238, 2023. PDF
  • Hüseyin Boyacı
    • Amna Malik, Katja Doerschner, Huseyin Boyaci, “Unmet expectations about material properties delay perceptual decisions,” Vision Research, vol. 208, pp. 108223 – , 2023. PDF
    • B.T. Gurbuz, H. Boyaci, “Tilt aftereffect spreads across the visual field,” Vision Research, vol. 205, pp. 108174-1–9, 2023. PDF
  • Tolga Çukur
    • Alper Gungor, …, Tolga Cukur, “Adaptive diffusion priors for accelerated MRI reconstruction,” Medical Image Analysis, vol. 88, pp. 102872 – , 2023. PDF
    • Alper Gungor, Baris Askin, Damla Alptekin Soydan, Can Baris Top, Emine Ulku Saritas, Tolga Cukur, “DEQ-MPI: A Deep Equilibrium Reconstruction with Learned Consistency for Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. , pp. 1 – 13, 2023. PDF
    • E. Ilicak, E.U. Saritas, T. Cukur, “Automated Parameter Selection for Accelerated MRI Reconstruction via Low-Rank Modeling of Local k-Space Neighborhoods,” Zeitschrift Fur Medizinische Physik, vol. 33, pp. 203-219, 2023. PDF
    • Gokberk Elmas, …, Tolga Cukur, “Federated Learning of Generative Image Priors for MRI Reconstruction,” IEEE Transactions on Medical Imaging, vol. 42, pp. 1996 – 2009, 2023. PDF
    • Hasan A. Bedel, Irmak Sivgin, Onat Dalmaz, Salman UH Dar, Tolga Cukur, “BolT: Fused window transformers for fMRI time series analysis,” Medical Image Analysis, vol. 88, pp. 102841 – , 2023. PDF
    • Muzaffer Ozbey, …, Tolga Cukur, “Unsupervised Medical Image Translation with Adversarial Diffusion Models,” IEEE Transactions on Medical Imaging, vol. 42, pp. 3524 – 3539, 2023. PDF
    • Saban Ozturk, Emin Celik, Tolga Cukur, “Content-based medical image retrieval with opponent class adaptive margin loss,” Information Sciences, vol. 637, pp. 118938 – , 2023. PDF
    • Saban Ozturk, Tolga Cukur, “Focal modulation network for lung segmentation in chest X-ray images,” Turkish Journal of Electrical Engineering and Computer Sciences, vol. 31, pp. 1006 – 1020, 2023. PDF
    • Salman UH Dar, Saban Ozturk, Muzaffer Ozbey, Kader K Oguz, Tolga Cukur, “Parallel-stream fusion of scan-specific and scan-general priors for learning deep MRI reconstruction in low-data regimes,” Computers in Biology and Medicine, vol. 167, pp. 107610 – , 2023. PDF
  • Ausaf Ahmed Farooqui
    • Ausaf A. Farooqui, Tamer Gezici, Tom Manly, “Chunking of Control: An Unrecognized Aspect of Cognitive Resource Limits,” Journal of Cognition, vol. 6, pp. 25 – , 2023. PDF
    • Sami Boudelaa, Said Boujraf, Faouzi Belahcen, Mohamed Ben Zagmout, Ausaf Farooqui, “Impaired morphological processing: insights from multiple sclerosis,” Language Cognition and Neuroscience, vol. 38, pp. 1237 – 1250, 2023. PDF
  • Hacı Hulusi Kafalıgönül
    • A. Karaduman, E.T. Karoglu-Eravsar, U. Kaya, A. Aydin, M.M. Adams, H. Kafaligonul, “Zebrafish optomotor response to second-order motion illustrates that age-related changes in motion detection depend on the activated motion system,” Neurobiology of Aging, vol. 130, pp. 12 – 21, 2023. PDF
    • A. Pavan, A. Contillo, S. Koc Yilmaz, H. Kafaligonul, R. Donato, L. O’Hare, “A comparison of equivalent noise methods in investigating local and global form and motion integration,” Attention Perception and Psychophysics, vol. 85, pp. 152-165, 2023. PDF
    • E.T. Karoglu-Eravsar, …, H. Kafaligonul, M.M. Adams, “Long-term acetylcholinesterase depletion alters the levels of key synaptic proteins while maintaining neuronal markers in the aging zebrafish (Danio rerio) brain,” Gerontology, vol. 69, pp. 1424 – 1436, 2023. PDF
  • Özlen Konu Karakayalı
    • Elif Tugce Karoglu-Eravsar, …, Ozlen Konu, …, Michelle M Adams, “Long-Term Acetylcholinesterase Depletion Alters the Levels of Key Synaptic Proteins while Maintaining Neuronal Markers in the Aging Zebrafish (Danio rerio) Brain,” Gerontology, vol. 69, pp. 1424 – 1436, 2023. PDF
    • Fatma Chafra, Felipe Borim Correa, Faith Oni, Ozlen Konu Karakayali, Peter F Stadler, Ulisses Nunes da Rocha, “StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins,” Bioinformatics Advances, vol. 3, pp. vbad069 – , 2023. PDF
    • Gulcin Cakan Akdogan, Abdul Moiz Aftab, Muazzez Celebi Cinar, Khalid A. Abdelhalim, Ozlen Konu, “Zebrafish as a model for drug induced liver injury: state of the art and beyond,” Exploration of Digestive Diseases, vol. 2, pp. 44 – 55, 2023. PDF
  • Zahide Pamir Karatok
    • Lotfi B. Merabet, Claire E. Manley, Zahide Pamir, Corinna M. Bauer, Jan Skerswetat, Peter J. Bex, “Motion and form coherence processing in individuals with cerebral visual impairment,” Developmental Medicine and Child Neurology, vol. 65, pp. 1379 – 1386, 2023. PDF
  • Emine Ülkü Sarıtaş Çukur
    • A. Güngör, B. Askin, D. Alptekin Soydan, C.B. Top, E.U. Saritas, T. Çukur, “DEQ-MPI: A Deep Equilibrium Reconstruction with Learned Consistency for Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. , pp. , 2023. PDF
    • E. Gumeler, E. Aygun, F.I. Tezer, E.U. Saritas, K.K. Oguz, “Assessment of glymphatic function in narcolepsy using DTI-ALPS index,” Sleep Medicine, vol. 101, pp. 522 – 527, 2023. PDF
    • E. Ilicak, E.U. Saritas, T. Cukur, “Automated Parameter Selection for Accelerated MRI Reconstruction via Low-Rank Modeling of Local k-Space Neighborhoods,” Zeitschrift Fur Medizinische Physik, vol. 33, pp. 203-219, 2023. PDF
    • M. Kafali, …, E.U. Saritas, …, B. Ercan, “Antibacterial properties and osteoblast interactions of microfluidically synthesized chitosan – SPION composite nanoparticles,” Journal of Biomedical Materials Research Part A, vol. 111, pp. 1662 – 1677, 2023. PDF
  • Timothea Toulopoulou
    • B. Wang, …, Timothea Toulopoulou , …., E. Bramon, “Psychosis Endophenotypes: A Gene-Set-Specific Polygenic Risk Score Analysis,” Schizophrenia Bulletin, vol. 49, pp. 1625 – 1636, 2023. PDF
    • Helin Yilmaz Kafali, …, Timothea Toulopoulou, “The effect of SARS-CoV-2 virus on resting-state functional connectivity during adolescence: Investigating brain correlates of psychotic-like experiences and SARS-CoV-2 related inflammation response.,” Psychiatry Research-Neuroimaging, vol. 336, pp. 111746 – , 2023. PDF
    • Tuğçe Çabuk, Emre Mutlu, Timothea Toulopoulou, “Thought and language disorder as a possible endophenotype in schizophrenia: Evidence from patients and their unaffected siblings,” Schizophrenia Research, vol. 254, pp. 78 – 80, 2023. PDF
  • Burcu Ayşen Ürgen
    • Büşra Sarıgül, Burcu A. Urgen, “Audio–Visual Predictive Processing in the Perception of Humans and Robots,” International Journal of Social Robotics, vol. 15, pp. 855 – 865, 2023. PDF
    • Gaye Aşkın, İmge Saltık, Tuğçe Elver Boz, Burcu A. Urgen, “Gendered Actions with a Genderless Robot: Gender Attribution to Humanoid Robots in Action,” International Journal of Social Robotics, vol. 15, pp. 1915 – 1931, 2023. PDF
    • Muhammed Ali Koşan, Hacer Karacan, Burcu A. Urgen, “Personality traits prediction model from Turkish contents with semantic structures,” Neural Computing and Applications, vol. 35, pp. 17147 – 17165, 2023. PDF
    • Tuğçe Nur Pekçetin, Şeyda Evsen, Serkan Pekçetin, Cengiz Acatürk, Burcu A. Urgen, “A Naturalistic Setup for Presenting Real People and Live Actions in Experimental Psychology and Cognitive Neuroscience Studies,” Jove-Journal of Visualized Experiments, vol. 198, pp. e65436 – , 2023. PDF

2022

  • Michelle Marie Adams
    • N. Serifoglu, B. Erbaba, M.M. Adams, A. Arslan-Ergul, “TERT distal promoter GC islands are critical for telomerase and together with DNMT3B silencing may serve as a senescence-inducing agent in gliomas,” Journal of Neurogenetics, vol. , pp. 1-10, 2022. PDF
  • Yasemin Afacan
    • Y. Afacan, “Impacts of Biophilic Design on the Development of Gerotranscendence and the Profile of Mood States during the COVID-19 Pandemic,” Ageing and Society, vol. , pp. 1-25, 2022. PDF
  • Ergin Atalar
    • A. Sadeghi-Tarakameh, S. Jungst, M. Lanagan, L. DelaBarre, X. Wu, G. Adriany, G.J. Matzger, P-F. Van de Moortele, K. Ugurbil, E. Atalar, Y. Eryaman, “A nine-channel transmit/receive array for spine imaging at 10.5 T: Introduction to a nonuniform dielectric substrate antenna,” Magnetic Resonance in Medicine, vol. 87, pp. 2074-2088, 2022. PDF
    • A.Sadeghi-Tarakameh, N.I.H. Zulkarnain, X. He, E. Atalar, N. Harel, Y. Eryaman, “A workflow for predicting temperature increase at the electrical contacts of deep brain stimulation electrodes undergoing MRI,” Magnetic Resonance in Medicine, vol. 88, pp. 2311-2325, 2022. PDF
    • M. Takrimi, E. Atalar, “A z-gradient array coil with a dedicated active-shielded array coil for MRI,” Magnetic Resonance in Medicine, vol. 88, pp. 2718-2731, 2022. PDF
    • R. Babaloo, E. Atalar, “Nonlinear droop compensation for current waveforms in MRI gradient systems,” Magnetic Resonance in Medicine, vol. 88, pp. 973-985, 2022. PDF
  • Robert Ian Bowers
    • R.I. Bowers, “Taming the boojum: Being theoretical about peculiarities of learning,” Learning and Behavior, vol. 50, pp. 433-440, 2022. PDF
  • Hüseyin Boyacı
    • M. Kiniklioglu, H. Boyaci, “Increasing the spatial extent of attention strengthens surround suppression,” Vision Research, vol. 199, pp. 108074-1–, 2022. PDF
  • Tolga Çukur
    • A. Gungor, B. Askin, D. Alptekin Soydan, E.U. Saritas, C.B. Top, T. Cukur, “TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. , pp. , 2022. PDF
    • K. Keskin, U. Yilmaz, T. Cukur, “Constrained Ellipse Fitting for Efficient Parameter Mapping with Phase-cycled bSSFP MRI,” IEEE Transactions on Medical Imaging, vol. 41, pp. 14-26, 2022. PDF
    • L.K. Senel, F. Sahinuc, V. Yucesoy, H. Schutze, T. Cukur, A. Koc, “Learning interpretable word embeddings via bidirectional alignment of dimensions with semantic concepts,” Information Processing and Management, vol. 59, pp. 102925-1–17, 2022. PDF
    • M. Shadloo, E. Celik, B.A. Urgen, J.L. Gallant, T. Cukur, “Task-Dependent Warping of Semantic Representations during Search for Visual Action Categories,” Journal of Neuroscience, vol. 42, pp. 6782-6799, 2022. PDF
    • M. Yurt, M. Ozbey, S.U.H. Dar, B. Tinaz, K.K. Oguz, T. Cukur, “Progressively volumetrized deep generative models for data efficient contextual learning of MR image recovery,” Medical Image Analysis, vol. 78, pp. 102429-1–19, 2022. PDF
    • M. Yurt, O. Dalmaz, S. Dar, M. Ozbey, B. Tinaz, K. Oguz, T. Cukur, “Semi-Supervised Learning of MRI Synthesis without Fully Sampled Ground Truths,” IEEE Transactions on Medical Imaging, vol. , pp. , 2022. PDF
    • O. Dalmaz, M. Yurt, T. Cukur, “ResViT: Residual Vision Transformers for Multimodal Medical Image Synthesis,” IEEE Transactions on Medical Imaging, vol. 41, pp. 2598-2614, 2022. PDF
    • S. Ozturk, T. Cukur, “Deep Clustering via Center-Oriented Margin Free-Triplet Loss for Skin Lesion Detection in Highly Imbalanced Datasets,” IEEE Journal of Biomedical and Health Informatics, vol. 26, pp. 4679-4690, 2022. PDF
    • Y. Korkmaz, S.U.H. Dar, M. Yurt, M. Ozbey, T. Cukur, “Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers,” IEEE Transactions on Medical Imaging, vol. 41, pp. 1747-1763, 2022. PDF
  • Hacı Hulusi Kafalıgönül
    • A. Duyar, A. Pavan, H. Kafaligonul, “Attentional modulations of audiovisual interactions in apparent motion: temporal ventriloquism effects on perceived visual speed,” Attention Perception and Psychophysics, vol. 84, pp. 2167-2185, 2022. PDF
    • A. Pavan, S. Koc Yilmaz, H. Kafaligonul, L. Battaglini, S.P. Blurton, “Motion processing impaired by transient spatial attention: potential implications for the Magnocellular pathway,” Vision Research, vol. 109, pp. 108080-1–14, 2022. PDF
    • E.N. Catak, M. Ozkan, H. Kafaligonul, G.R. Stoner, “Behavioral and ERP evidence that object-based attention utilizes fine-grained spatial mechanisms,” Cortex, vol. 151, pp. 89-104, 2022. PDF
  • Özlen Konu Karakayalı
    • A.G. Keskus, M. Tombaz, B.I. Arici, F.B. Dincaslan, A. Nabi, H. Shehwana, O. Konu, “Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease,” Genome, vol. 65, pp. 57-74, 2022. PDF
    • I. Cagnan, M. Keles, A.G. Keskus, M. Tombaz, O.B. Sahan, F.Aerts-Kaya, D. Uckan-Cetinkaya, O. Konu, A. Gunel-Ozcan, “Global miRNA expression of bone marrow mesenchymal stem/stromal cells derived from Fanconi anemia patients,” Human Cell, vol. 35, pp. 111-124, 2022. PDF
    • M. Tombaz, C. Yanyatan, A.G. Keskus, O. Konu, “Extraction and Prioritization of a Gene-Cancer-By Survival Network Involved in Homeostasis of Intracellular Calcium Concentrations Using TCGA PANCAN Data,” Bioelectricity, vol. 4, pp. 92-102, 2022. PDF
  • Emine Ülkü Sarıtaş Çukur
    • A. Gungor, B. Askin, D. Alptekin Soydan, E.U. Saritas, C.B. Top, T. Cukur, “TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. , pp. , 2022. PDF
    • B.A Barlas, C.D Bahadir, S.G Kafali, U Yilmaz, E.U Saritas, “Sheared 2D RF Excitation for Off-resonance Robustness and Fat Suppression in Reduced Field-of-View Imaging,” Magnetic Resonance in Medicine, vol. 88, pp. 2504-2519, 2022. PDF
    • M. Utkur, E.U. Saritas, “Simultaneous Temperature and Viscosity Estimation Capability via Magnetic Nanoparticle Relaxation,” Medical Physics, vol. 49, pp. 2590-2601, 2022. PDF
    • M. Yavuz, M. Utkur, E.S. Kehribar, E. Yagiz, E.U. Saritas, U.O.S. Seker, “Engineered Bacteria with Genetic Circuits Accumulating Nanomagnets as MRI Contrast Agents,” Small, vol. 18, pp. 2200537-1–11, 2022. PDF
    • M.T. Arslan, A.A. Ozaslan, S. Kurt, Y. Muslu, E.U. Saritas, “Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. , pp. , 2022. PDF
    • O.C Eren, B.A Barlas, E.U Saritas, “2D RF pulse design for optimized reduced field-of-view imaging at 1.5T and 3T,” Magnetic Resonance Imaging, vol. 85, pp. 210-216, 2022. PDF
  • Timothea Toulopoulou
    • H.Y. Kafali, S. Turan, S. Akpinar, M. Mutlu, A.O. Parlakay, E. Cop, T. Toulopoulou, “Correlates of psychotic like experiences (PLEs) during Pandemic: An online study investigating a possible link between the SARS-CoV-2 infection and PLEs among adolescents,” Schizophrenia Research, vol. 241, pp. 36-43, 2022. PDF
    • N.V. Ribeiro, V. Tavares, E. Bramıon, T. Toulopoulou, I. Valli, S. Shergill, R. Muraay, D. Patra, “Effects of psychosis-associated genetic markers on brain volumetry: a systematic review of replicated findings and an independent validation,” Psychological Medicine, vol. , pp. 1-16, 2022. PDF
  • Burcu Ayşen Ürgen
    • M. Shadloo, E. Celik, B.A. Urgen, J.L. Gallant, T. Cukur, “Task-Dependent Warping of Semantic Representations during Search for Visual Action Categories,” Journal of Neuroscience, vol. 42, pp. 6782-6799, 2022. PDF
    • M.A. Kosan, H. Karacan, B.A. Urgen, “Predicting personality traits with semantic structures and LSTM-based neural networks,” Alexandria Engineering Journal, vol. 61, pp. 8007-8025, 2022. PDF
    • T.E. Boz, H. Demirkan, B.A. Urgen, “Visual perception of the built environment in virtual reality: A systematic characterization of human aesthetic experience in spaces with curved boundaries,” Psychology of Aesthetics Creativity and The Arts, vol. , pp. , 2022. PDF

2021

  • Michelle Marie Adams
    • A. Karaduman, E.T. Karoglu-Eravsar, U. Kaya, A. Aydin, M.M. Adams, H. Kafaligonul, “The Optomotor Response of Aging Zebrafish Reveals a Complex Relationship between Visual Motion Characteristics and Cholinergic System,” Neurobiology of Aging, vol. 98, pp. 21-32, 2021. PDF
    • B. Erbaba, A. Arslan-Ergul, M.M. Adams, “Effects of Caloric Restriction on the Antagonistic and Integrative Hallmarks of Aging,” Ageing Research Reviews, vol. 66, pp. 101228-1–23, 2021. PDF
    • E.T. Karoglu-Eravsar, M.U. Tuz-Sasik, M.M. Adams, “Environmental enrichment applied with sensory components prevents age-related decline in synaptic dynamics: Evidence from the zebrafish model organism,” Experimental Gerontology, vol. 149, pp. 111346-1–13, 2021. PDF
    • E.T. Karoglu-Eravsar, M.U. Tuz-Sasik, M.M. Adams, “Short-term dietary restriction maintains synaptic plasticity whereas short-term overfeeding alters cellular dynamics in the aged brain: evidence from the zebrafish model organism,” Neurobiology of Aging, vol. 106, pp. 169-182, 2021. PDF
  • Yasemin Afacan
    • A.S. Nouri, Y. Afacan, O. Caliskan, T-P. Lim, A. Matzarakis, “Approaching environmental human thermophysiological thresholds for the case of Ankara, Turkey,” Theoretical and Applied Climatology, vol. 143, pp. 533-555, 2021. PDF
    • I. Caglayan, Y. Afacan, “Simulation-based Service Walkthrough (SBSW) to Assess Airport Environment Performance,” Archnet-IJAR International Journal of Architectural Research, vol. 15, pp. 905-924, 2021. PDF
    • P. Mahmoudzadeh, Y. Afacan, M.N. Adi, “Analyzing occupants’ control over lighting systems in office settings using immersive virtual environments,” Building and Environment, vol. 196, pp. 107823-1–15, 2021. PDF
  • Ergin Atalar
    • A. Sadeghi-Tarakameh, E. Kazemivalipour, U. Gundogdu, S. Erdogan, E. Atalar, “Accelerating the co-simulation method for the design of transmit array coils for MRI,” Magnetic Resonance Materials In Physics Biology and Medicine, vol. 34, pp. 165-178, 2021. PDF
    • B. Tasdelen, A. Sadeghi-Tarakameh, U. Yilmaz, E. Atalar, “Analysis and mitigation of noise in simultaneous transmission and reception in MRI,” Magnetic Resonance in Medicine, vol. 86, pp. 1746-1758, 2021. PDF
    • C. Ariyurek, B. Tasdelen, Y.Z. Ider, E. Atalar, “SNR Weighting for Shear Wave Speed Reconstruction in Tomoelastography,” NMR in Biomedicine, vol. 34, pp. 4413-1–18, 2021. PDF
    • E. Kazemivalipour, B. Bhusal, J. Vu, S. Lin, B.T. Nguyen, J. Kirsch, E. Nowac, J. Pilitsis, J. Rosenow, E. Atalar, L. Golestanirad, “Vertical open-bore MRI scanners generate significantly less radiofrequency heating around implanted leads: A study of deep brain stimulation implants in 1.2T OASIS scanners versus 1.5T horizontal systems,” Magnetic Resonance in Medicine, vol. 86, pp. 1560-1572, 2021. PDF
  • Hüseyin Boyacı
    • B.M. Urgen, H. Boyaci, “Unmet Expectations Delay Sensory Processes,” Vision Research, vol. 181, pp. 1-9, 2021. PDF
  • Tolga Çukur
    • E. Celik, U. Keles, I. Kirmeitci, J.L. Gallant, T. Cukur, “Cortical networks of dynamic scene category representation in the human brain,” Cortex, vol. 143, pp. 127-147, 2021. PDF
    • I. Kiremitci, O. Yilmaz, E. Celik, M. Shahdloo, A.G. Huth, T. Cukur, “Attentional Modulation of Hierarchical Speech Representations in a Multitalker Environment,” Cerebral Cortex, vol. 31, pp. 4986-5005, 2021. PDF
    • M. Yurt, S.U.H. Dar, A. Erdem, E. Erdem, K.K. Oguz, T. Cukur, “mustGAN: multi-stream Generative Adversarial Networks for MR Image Synthesis,” Medical Image Analysis, vol. 70, pp. 101944-1–13, 2021. PDF
  • Hacı Hulusi Kafalıgönül
    • A. Aydin, H. Ogmen, H. Kafaligonul, “Neural correlates of metacontrast masking across different contrast polarities,” Brain Structure and Function, vol. 226, pp. 3067-3081, 2021. PDF
    • A. Karaduman, E.T. Karoglu-Eravsar, U. Kaya, A. Aydin, M.M. Adams, H. Kafaligonul, “The Optomotor Response of Aging Zebrafish Reveals a Complex Relationship between Visual Motion Characteristics and Cholinergic System,” Neurobiology of Aging, vol. 98, pp. 21-32, 2021. PDF
    • U. Kaya, H. Kafaligonul, “Audiovisual interactions in speeded discrimination of a visual event,” Psychophysiology, vol. 58, pp. 1-15, 2021. PDF
  • Özlen Konu Karakayalı
    • A. Ozhan, M. Tombaz, O. Konu, “Discovery of Cancer-Specific and Independent Prognostic Gene Subsets of the Slit-Robo Family Using TCGA-PANCAN Datasets,” OMICS-A Journal of Integrative Biology, vol. 25, pp. 1-14, 2021. PDF
    • A. Ozhan, M. Tombaz, O. Konu, “SmulTCan: A Shiny application for multivariable survival analysis of TCGA data with gene sets,” Computers in Biology and Medicine, vol. 137, pp. 104793-1–9, 2021. PDF
    • D. Gozen, D.C. Kahraman, K. Narci, H. Shehwana, O. Konu, E. Cetin-Atalay, “Transcriptome profiles associated with selenium deficiency dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells,” Turkish Journal of Biology, vol. 45, pp. 149-161, 2021. PDF
    • F. Zengin-Karadayi, M. Yaman, M.M. Kisla, O. Konu, Z. Ates-Alagoz, “Design, synthesis, anticancer activity, molecular docking and ADME studies of novel methylsulfonyl indole-benzimidazoles in comparison with ethylsulfonyl counterparts,” New Journal of Chemistry, vol. 45, pp. 9010-9019, 2021. PDF
    • H. Shehwana, A.G. Keskus, S.E. Ozdemir, A.A. Acikgoz, R. Biyik-Sit, I. Cagnan, D. Gunes, E. Jahja, S. Cingir-Koker, G. Olmezer, C. Sucularli, O. Konu, “CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer,” Cellular Oncology, vol. 44, pp. 453-472, 2021. PDF
    • J.C. Fernandez-Checa, P. Bagnaninchi, H. Ye, …, O. Konu, …., F.J. Cubero, L.J. Nelson, “Advanced preclinical models for evaluation of drug-induced liver injury – consensus statement by the European Drug-Induced Liver Injury Network [PRO-EURO-DILI-NET],” Journal of Hepatology, vol. 75, pp. 935-959, 2021. PDF
    • M. Vural-Ozdeniz, A. Akturk, M. Demirdizen, R. Leka, R. Acar, O. Konu, “CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers,” Genomics, vol. 113, pp. 3174-3184, 2021. PDF
    • S. Targen, O. Konu, “Zebrafish Xenotransplantation Models for Studying Gene Function and Drug Treatment in Hepatocellular Carcinoma,” Journal of Gastrointestinal Cancer, vol. 52, pp. 1248-1265, 2021. PDF
  • Timothea Toulopoulou
    • J.H. Thygesen, … , T. Toulopoulou, …, E. Bramon, “Genetic Copy Number Variants, Cognition and Psychosis: A Meta-analysis and a Family Study,” Molecular Psychiatry, vol. 26, pp. 1-13, 2021. PDF

2020

  • Michelle Marie Adams
    • B. Erbaba, O.P. Burhan, N.Serifoglu, B. Muratoglu, F. Kahveci, M.M. Adams, A. Arslan-Ergul, “Zebrafish Brain RNA Sequencing Reveals that Cell Adhesion Molecules are Critical in Brain Aging,” Neurobiology of Aging, vol. 94, pp. 164-175, 2020. PDF
    • D. Celebi-Birand, N.I. Ardic, E.T. Karoglu-Eravsar, G.F. Sengul, H. Kafaligonul, M.M. Adams, “Dietary and Pharmacological Interventions That Inhibit Mammalian Target of Rapamycin Activity Alter the Brain Expression Levels of Neurogenic and Glial Markers in an Age-and Treatment-Dependent Manner,” Rejuvenation Research, vol. 23, pp. 485-497, 2020. PDF
    • M.U. Tuz-Saslik, E.T. Karoglu-Eravsar, M. Kinali, A. Arslan-Ergul, M.M. Adams, “Expression Levels of SMAD Specific E3 Ubiquitin Protein Ligase 2 (Smurf2) and its Interacting Partners Show Region-specific Alterations During Brain Aging,” Neuroscience, vol. 436, pp. 46-73, 2020. PDF
  • Yasemin Afacan
    • S.M. Tasoz, Y. Afacan, “Simulated physical ageing: A prioritized persona-based model for accessible interiors in senior housing environments,” Indoor and Built Environment, vol. , pp. 1-16, 2020. PDF
  • Ergin Atalar
    • A. Sadeghi-Tarakameh, G. Adriany, G.J. Metzger, R.L. Lagore, S. Jungst, L. DelaBarre, P-F. van de Moortele, K. Ugurbil, E. Atalar, Y. Eryaman, “Improving radiofrequency power and specific absorption rate management with bumped transmit elements in ultra‐high field MRI,” Magnetic Resonance in Medicine, vol. 84, pp. 3485-3493, 2020. PDF
    • A. Sadeghi-Tarakameh, L. DelaBarre, R.L. Lagore, A. Torrado-Carvajal, X. Wu, A. Grant, G. Adriany, G.J. Metzger, P-F. Van de Moortele, K. Ugurbil, E. Atalar, Y. Eryaman, “In vivo human head MRI at 10.5T: A radiofrequency safety study and preliminary imaging results,” Magnetic Resonance in Medicine, vol. 84, pp. 484-496, 2020. PDF
    • A.C. Ozen, B. Silemek, T. Lottner, E. Atalar, M. Bock, “MR safety watchdog for active catheters: Wireless impedance control with real‐time feedback,” Magnetic Resonance in Medicine, vol. 84, pp. 1048-1060, 2020. PDF
    • E. Kazemivalipour, A. Sadeghi-Tarakameh, E. Atalar, “Eigenmode analysis of the scattering matrix for the design of MRI transmit array coils,” Magnetic Resonance in Medicine, vol. 85, pp. 1727-1741, 2020. PDF
    • L. Golestanirad, E. Kazemivalipour, D. Lampman, H. Habara, E. Atalar, J. Rosenow, J. Pilitsis, J. Kirsch, “RF heating of deep brain stimulation implants in open‐bore vertical MRI systems: A simulation study with realistic device configurations,” Magnetic Resonance in Medicine, vol. 83, pp. 2284-2292, 2020. PDF
    • V. Acikel, B. Silemek, E. Atalar, “Wireless control of induced radiofrequency currents in active implantable medical devices during MRI,” Magnetic Resonance in Medicine, vol. 83, pp. 2370-2381, 2020. PDF
  • Hüseyin Boyacı
    • E. Altan, H. Boyaci, “Size aftereffect is non-local,” Vision Research, vol. 176, pp. 40-47, 2020. PDF
    • G. Er, Z. Pamir, H. Boyaci, “Distinct patterns of surround modulation in V1 and hMT+,” NeuroImage, vol. 220, pp. 117084-1–10, 2020. PDF
  • Tolga Çukur
    • E. Biyik, K. Keskin, S.U.H. Dar, A. Koc, T. Cukur, “Factorized sensitivity estimation for artifact suppression in phase-cycled bSSFP MRI,” NMR in Biomedicine, vol. 33, pp. 4228-1–14, 2020. PDF
    • E. Kopanoglu, A. Gungor, E.U. Saritas, K.K. Oguz, T. Cukur, H.E. Guven, “Simultaneous use of Individual and Joint Regularization Terms in Compressive Sensing: Joint Reconstruction of Multi-Channel Multi-Contrast MRI Acquisitions,” NMR in Biomedicine, vol. 33, pp. 4247-1–16, 2020. PDF
    • M. Shahdloo, E. Celik, T. Cukur, “Biased competition in semantic representation during natural visual search,” NeuroImage, vol. 216, pp. 116383-1–10, 2020. PDF
    • O. Yilmaz, E. Celik, T. Cukur, “Informed Feature Regularization in Voxelwise Modeling for Naturalistic fMRI Experiments,” European Journal of Neuroscience, vol. 52, pp. 3394-3410, 2020. PDF
    • O.B Demirel, T. Kilic , T. Cukur, E.U. Saritas, “Anatomical Measurements Correlate with Individual Magnetostimulation Thresholds for kHz‐range Homogeneous Magnetic Fields,” Medical Physics, vol. 47, pp. 1836-1844, 2020. PDF
    • S. Tokgoz, D. Aydogdu, B. Ilhan, Y. Sahin, N. Bariseri, B.M. Ozturkler, T. Cukur, “Musical mirror-symmetrical movement tasks: comparison of rhythm versus melody-playing,” NeuroReport, vol. 31, pp. 523-529, 2020. PDF
    • S. Ul Hasan Dar, M. Ozbey, A.B. Catli, T. Cukur, “A Transfer-Learning Approach for Accelerated MRI Using Deep Neural Networks,” Magnetic Resonance in Medicine, vol. 84, pp. 663-685, 2020. PDF
    • S.U.H. Dar, M. Yurt, M. Shahdloo, M.E. Ildiz, B. Tinaz, T. Cukur, “Prior-Guided Image Reconstruction for Accelerated Multi Contrast MRI via Generative Adversarial Networks,” IEEE Journal of Selected Topics In Signal Processing, vol. 14, pp. 1071-1087, 2020. PDF
  • Hacı Hulusi Kafalıgönül
    • D. Celebi-Birand, N.I. Ardic, E.T. Karoglu-Eravsar, G.F. Sengul, H. Kafaligonul, M.M. Adams, “Dietary and Pharmacological Interventions That Inhibit Mammalian Target of Rapamycin Activity Alter the Brain Expression Levels of Neurogenic and Glial Markers in an Age-and Treatment-Dependent Manner,” Rejuvenation Research, vol. 23, pp. 485-497, 2020. PDF
    • S. Akyuz, A. Pavan, U. Kaya, H. Kafaligonul, “Short- and long-term forms of neural adaptation: an ERP investigation of dynamic motion aftereffects,” Cortex, vol. 125, pp. 122-134, 2020. PDF
  • Özlen Konu Karakayalı
    • F.Z. Karadayi, M. Yaman, M.M. Kisla, A.G. Keskus, O. Konu, Z. Ates-Alagoz, “Design, synthesis and anticancer/antiestrogenic activities of novel indole-benzimidazoles,” Bioorganic Chemistry, vol. 100, pp. 103929-1–20, 2020. PDF
    • S. Targen, T. Kaya, M.E. Avci, D. Gunes, A.G. Keskus, O. Konu, “ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish,” Zebrafish, vol. 17, pp. 305-318, 2020. PDF
  • Emine Ülkü Sarıtaş Çukur
    • E. Kopanoglu, A. Gungor, E.U. Saritas, K.K. Oguz, T. Cukur, H.E. Guven, “Simultaneous use of Individual and Joint Regularization Terms in Compressive Sensing: Joint Reconstruction of Multi-Channel Multi-Contrast MRI Acquisitions,” NMR in Biomedicine, vol. 33, pp. 4247-1–16, 2020. PDF
    • E. Yagiz, A.R. Cagil, E.U. Saritas, “Non-ideal Selection Field Induced Artifacts in X-Space MPI,” International Journal on Magnetic Particle Imaging, vol. 6, pp. 2006001-1–10, 2020. PDF
    • M.S. Aporvari, M. Utkur, E.U. Saritas, G. Volpe, J. Stenhammer, “Anisotropic dynamics of a self-assembled colloidal chain in an active bath,” Soft Matter, vol. 16, pp. 5609-5614, 2020. PDF
    • O.B Demirel, T. Kilic , T. Cukur, E.U. Saritas, “Anatomical Measurements Correlate with Individual Magnetostimulation Thresholds for kHz‐range Homogeneous Magnetic Fields,” Medical Physics, vol. 47, pp. 1836-1844, 2020. PDF
    • S. Kurt, Y. Muslu, E.U. Saritas, “Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. 30, pp. 3441-3450, 2020. PDF
  • Timothea Toulopoulou
    • B. Simoes, E. Vassos, S. Shergill, C. McDonald, T. Toulopoulou, S. Kalidindi, K. Kane, R. Murray, E. Bramon, H. Ferreira, D. Prata, “Schizophrenia polygenic risk score influence on white matter microstructure,” Journal of Psychiatric Research, vol. 121, pp. 62-67, 2020. PDF
  • Burcu Ayşen Ürgen
    • B.A. Urgen, A.P. Saygin, “Predictive processing account of action perception: Evidence from effective connectivity in the action observation network,” Cortex, vol. 128, pp. 132-142, 2020. PDF
    • H. Sawamura, B.A. Urgen, D. Corbo, G.A. Orban, “A parietal region processing numerosity of observed actions: An fMRI study,” European Journal of Neuroscience, vol. 52, pp. 4732-4750, 2020. PDF

2019

  • Yasemin Afacan
    • D.S. Ozgen, Y. Afacan, E. Surer, “Usability of Virtual Reality for Basic Design Education: A Comparative Study with Paper-Based Design,” International Journal of Technology and Design Education, vol. , pp. , 2019.
    • E. Seles, Y. Afacan, “The Role of healthy urban performance on walkability: Broadening the theory of planned behaviour,” Open House International, vol. 44, pp. 44-52, 2019. PDF
    • Y. Afacan, “Extending Importance-Performance Analysis (IPA) Approach to Turkish Older People’s Self-Rated Home Accessibility,” Journal of Housing and the Built Environment, vol. 34, pp. 619-642, 2019. PDF
  • Ergin Atalar
    • E. Kazemivalipour, B. Keil, A. Vali, S. Rajan, B. Elahi, E. Atalar, L.L. Wald, J. Rosenow, J. Pilitsis, L. Golestanirad, “Reconfigurable MRI technology for low-SAR imaging of deep brain stimulation at 3T: Application in bilateral leads, fully-implanted systems, and surgically modified lead trajectories,” NeuroImage, vol. 199, pp. 18-29, 2019. PDF
    • K. Ertan, S. Taraghinia, E. Atalar, “Driving mutually coupled gradient array coils in magnetic resonance imaging,” Magnetic Resonance in Medicine, vol. 82, pp. 1187-1198, 2019. PDF
  • Hüseyin Boyacı
    • B.M. Urgen, Y. Topac, F.S. Ustun, P. Demirayak, K.K. Oguz, T. Kansu, S. Saygi, T. Ozcelik, H. Boyaci, K. Doerschner, “Homozygous LAMC3 mutation links to structural and functional changes in visual attention networks,” NeuroImage, vol. 190, pp. 242-253, 2019. PDF
    • H.B. Turkozer, T. Hasoglu, Y. Chen, L.A. Norris, M. Brown, N. Delaney-Busch, E.H. Kale, Z. Pamir, H. Boyaci, G. Kuperberg, K.E. Lewandowski, V. Topcuoglu, D. Ongur, “Integrated assessment of visual perception abnormalities in psychotic disorders and relationship with clinical characteristics,” Psychological Medicine, vol. 49, pp. 1740-1748, 2019. PDF
  • Tolga Çukur
    • A.A. Ozaslan, A. Alacaoglu, O.B. Demirel, T. Cukur, E.U. Saritas, “Fully automated gridding reconstruction for non-Cartesian x-space magnetic particle imaging,” Physics in Medicine and Biology, vol. 64, pp. 165018-1–18, 2019. PDF
    • E. Celik, SUH. Dar, O. Yilmaz, T. Cukur, “Spatially Informed Voxelwise Modeling for Naturalistic fMRI Experiments,” NeuroImage, vol. 186, pp. 741-757, 2019. PDF
    • L.K. Senel, T. Kilic, A. Gungor, E. Kopanoglu, H.E. Guven, E.U. Saritas, A. Koc, T. Cukur, “Statistically Segregated k-Space Sampling for Accelerating Multiple-Acquisition MRI,” IEEE Transactions on Medical Imaging, vol. 38, pp. 1701-1714, 2019. PDF
    • M. Shahdloo, E. Ilicak, M. Tofighi, E.U. Saritas, A.E. Cetin, T. Cukur, “Projection onto Epigraph Sets for Rapid Self-Tuning Compressed Sensing MRI,” IEEE Transactions on Medical Imaging, vol. 38, pp. 1677-1689, 2019. PDF
    • S. Ilbey, C.B. Top, A. Gungor, T. Cukur, E.U. Saritas, H.E. Guven, “Fast System Calibration with Coded Calibration Scenes for Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. 38, pp. 2070-2080, 2019. PDF
    • U.H. Salman, M. Yurt, L. Karacan, A. Erdem, E. Erdem, T. Cukur, “Image Synthesis in Multi-Contrast MRI with Conditional Generative Adversarial Networks,” IEEE Transactions on Medical Imaging, vol. 38, pp. 2375-2388, 2019. PDF
  • Hacı Hulusi Kafalıgönül
    • U. Kaya, H. Kafaligonul, “Cortical processes underlying the effects of static sound timing on perceived visual speed,” NeuroImage, vol. 199, pp. 194-205, 2019. PDF
  • Özlen Konu Karakayalı
    • I. Cagnan, E. Cosgun, O. Konu, D. Uckan, A. Gunel-Ozcan, “PKNOX2 expression and regulation in the bone marrow mesenchymal stem cells of Fanconi anemia patients and healthy donors,” Molecular Biology Reports, vol. 46, pp. 667-678, 2019. PDF
  • Emine Ülkü Sarıtaş Çukur
    • A.A. Ozaslan, A. Alacaoglu, O.B. Demirel, T. Cukur, E.U. Saritas, “Fully automated gridding reconstruction for non-Cartesian x-space magnetic particle imaging,” Physics in Medicine and Biology, vol. 64, pp. 165018-1–18, 2019.
    • E.U. Saritas, “Novel Techniques in Instrumentation, Image Reconstruction, and Applications in Magnetic Particle Imaging,” International Journal on Magnetic Particle Imaging, vol. 4, pp. 1903001-1–2, 2019. PDF
    • L.K. Senel, T. Kilic, A. Gungor, E. Kopanoglu, H.E. Guven, E.U. Saritas, A. Koc, T. Cukur, “Statistically Segregated k-Space Sampling for Accelerating Multiple-Acquisition MRI,” IEEE Transactions on Medical Imaging, vol. 38, pp. 1701-1714, 2019.
    • M. Shahdloo, E. Ilicak, M. Tofighi, E.U. Saritas, A.E. Cetin, T. Cukur, “Projection onto Epigraph Sets for Rapid Self-Tuning Compressed Sensing MRI,” IEEE Transactions on Medical Imaging, vol. 38, pp. 1677-1689, 2019. PDF
    • M. Utkur, Y. Muslu, E.U. Saritas, “Relaxation-Based Color Magnetic Particle Imaging for Viscosity Mapping,” Applied Physics Letters, vol. 115, pp. 15240-1–5, 2019. PDF
    • S. Ilbey, C.B. Top, A. Gungor, T. Cukur, E.U. Saritas, H.E. Guven, “Fast System Calibration with Coded Calibration Scenes for Magnetic Particle Imaging,” IEEE Transactions on Medical Imaging, vol. 38, pp. 2070-2080, 2019. PDF
  • Timothea Toulopoulou
    • M.C.Sonja, R.M. Bouwer, I. Agartz, …, T. Toulopoulou, …., N.E.M. van Haren, “The Association Between Familial Risk and Brain Abnormalities Is Disease Specific: An ENIGMA-Relatives Study of Schizophrenia and Bipolar Disorder,” Biological Psychiatry, vol. 86, pp. 545-556, 2019. PDF
    • T. Toulopoulou, X. Zhang, S.S: Cherny, D. Dickinson, K. Berman, R. Straub, P. Sham, D. Weinberger, “Polygenic risk score increases schizophrenia liability through cognition-relevant pathways,” Brain, vol. 142, pp. 471-485, 2019.
  • Burcu Ayşen Ürgen
    • B.A. Urgen, S. Pehlivan, A.P. Saygin, “Distinct representations in occipito-temporal, parietal, and premotor cortex during action perception revealed by fMRI and computational modeling,” Neuropsychologia, vol. 127, pp. 35-47, 2019. PDF