Publications

The full list can also be followed on Google Scholar and PubMed. Code for most of our methods is on GitHub. To receive a copy of any paper, please email cukur[at]ee.bilkent.edu.tr.

2026

Kabas B, Arslan F, Nezhad VA, Oguz KK, Ozturk S, Saritas EU, Çukur T. Physics-Driven Autoregressive State Space Models for Medical Image Reconstruction. IEEE Transactions on Medical Imaging. 2026;1-13. doi:10.1109/TMI.2026.3716153. (Code)
Atli OF, Kabas B, Arslan F, Demirtas AC, Yurt M, Dalmaz O, Çukur T. I2I-Mamba: Multi-modal medical image synthesis via selective state space modeling. IEEE Transactions on Biomedical Engineering. 2026;1-12. doi:10.1109/TBME.2026.3698056. (Code)
Chen Y, Li Z, Wang Y, Li Y, Zheng J, Yang H, Liu M, Çukur T, Fan Q, Li Z, Lu J, Tian Q. MicroKAN: Mapping human brain microstructure using diffusion MRI and adaptive nonlinear modeling. NeuroImage. 2026;337:122032. doi:10.1016/j.neuroimage.2026.122032.
Yurt M, Alkan C, Cao X, Liao C, Zhou Z, Çukur T, Syed A, Pauly J, Vasanawala S, Setsompop K. Semi-supervision for clinical contrast-weighted image synthesis from magnetic resonance fingerprinting. Magnetic Resonance Materials in Physics, Biology and Medicine. 2026; doi:10.1007/s10334-026-01338-7.
Mirza MU, Dalmaz O, Bedel HA, Elmas G, Korkmaz Y, Gungor A, Dar SUH, Oguz KK, Çukur T. Learning Fourier-Constrained Diffusion Bridges for MRI Reconstruction. IEEE Transactions on Medical Imaging. 2026; doi:10.1109/TMI.2026.3673956. (Code)
Yilmaz MB, Ozturk S, Kara M, Koc A, Çukur T. Meta-entity driven triplet mining for aligning medical vision-language models. IEEE Journal of Biomedical and Health Informatics. 2026; doi:10.1109/JBHI.2026.3678306. (Code)
Wang G, Çukur T, Kruger U, Ferrina J, Shan H. Editorial: AI Reviewer (AIR) Trial for Responsible, Secure, and Efficient Peer Review. IEEE Transactions on Medical Imaging. 2026; doi:10.1109/TMI.2026.3658770.
Kulkul E, Çukur T, Koc A. scHyperLink: Revealing Cell-Type-Specific Gene Regulation with Hypergraph Neural Networks. IEEE Journal of Biomedical and Health Informatics. 2026; doi:10.1109/JBHI.2025.3650661. (Supp. Materials, Code)

2025

Ozturk S, Duran OC, Çukur T. DenoMamba: A fused state-space model for low-dose CT denoising. IEEE Journal of Biomedical and Health Informatics. 2025; doi:10.1109/JBHI.2025.3629034. (Supp. Materials, Code)
Baqapuri HI, Terneusen A, Luehrs M, Peters J, Kuijf M, Goebel R, Linden D, Lozano AM, Mana J, Jarraya B, Loução R, Kocher M, Visser-Vandewalle V, Çukur T. Basal ganglia as an fMRI motor neurofeedback target in Parkinson’s disease. Applied Psychophysiology and Biofeedback. 2025 Nov; doi:10.1007/s10484-025-09747-5.
Çukur T, Dar SUH, Nezhad VA, Jun Y, Kim TH, Fujita S, Bilgic B. A Tutorial on MRI Reconstruction: From Modern Methods to Clinical Implications. IEEE Transactions on Biomedical Engineering. 2025; doi:10.1109/TBME.2025.3617575. (Code)
Arslan F, Kabas B, Dalmaz O, Ozbey M, Çukur T. Self-consistent recursive diffusion bridge for medical image translation. Medical Image Analysis. 2025; 106, 103747. (Code)
Loução R, Kocher M, Brandt GA, Petry-Schmelzer JN, Barbe M, Dafsari H, Mana J, Jech R, Wirths J, Visser-Vandewalle V, Andrade P, Baqapuri H, Luehrs M, Linden DEJ, Santyr B, Lozano A, Bongioanni A, Jarraya B, Çukur T. Structural connectivity of the basal ganglia from patient-individual tractography is key for understanding the effects of deep brain stimulation in Parkinson’s Disease. Stereotactic and Functional Neurosurgery. 2025 Jun; doi:10.1159/000546716.
Koc E, Kulkul E, Kaynar G, Çukur T, Acar M, Koc A. scGraPhT: Merging Transformers and Graph Neural Networks for Single-Cell Annotation. IEEE Transactions on Signal and Information Processing over Networks. 2025 May;11:505-519. (Code)
Ozturk S, Gungor A, Çukur T. Diffusion Probabilistic Models for Image Formation in MRI. Generative Machine Learning Models in Medical Image Computing, Springer Nature. 2025.
Ozturk S, Turali MY, Çukur T. HydraViT: Adaptive multi-branch transformer for multi-label disease classification from Chest X-ray images. Biomedical Signal Processing and Control. 2025; 100A:106959.

2024

Bedel HA, Çukur T. DreaMR: Diffusion-driven Counterfactual Explanation for Functional MRI. IEEE Transactions on Medical Imaging. 2024; doi: 10.1109/TMI.2024.3507008. (Code)
Liang D, Rueckert D, Wang G, Çukur T, Yu H. Editorial: Special Issue on Score-based Generative Models for Medical Imaging. IEEE Transactions on Medical Imaging. 2024 Oct;43(10):3393-3397.
Gungor A, Bahceci U, Ergen Y, Sozak A, Yelboga Y, Çukur T. CalibFPA: A Focal Plane Array Imaging System based on Online Deep-Learning Calibration. IEEE Transactions on Computational Imaging. 2024; doi:10.1109/TCI.2024.3477312.
Sivgin I, Bedel HA, Ozturk S, Çukur T. A Plug-In Graph Neural Network to Boost Temporal Sensitivity in fMRI Analysis. IEEE Journal of Biomedical and Health Informatics. 2024; doi: 10.1109/JBHI.2024.3415000. (Code)
Dalmaz O, Mirza MU, Elmas G, Ozbey M, Dar SUH, Ceyani E, Oguz KK, Avestimehr S, Çukur T. One Model to Unite Them All: Personalized Federated Learning of Multi-Contrast MRI Synthesis. Medical Image Analysis. 2024; 94:103121. (Code)
Gungor A, Askin B, Soydan DA, Top CB, Saritas EU, Çukur T. DEQ-MPI: A Deep Equilbrium Reconstruction with Learned Consistency for Magnetic Particle Imaging. IEEE Transactions on Medical Imaging. 2024 Jan;43(1):321-334. (Code)
Alkilani A, Çukur T, Saritas EU. FD-Net: An Unsupervised Deep Forward-Distortion Model for Susceptibility Artifact Correction in EPI. Magnetic Resonance in Medicine. 2024 Jan;91(1):280-296, 2024. (Code)

2023

Aytekin I, Dalmaz O, Gonc K, Ankishan H, Saritas EU, Bagci U, Celik H, Çukur T. COVID-19 Detection from Respiratory Sounds with Hierarchical Spectrogram Transformers. IEEE Journal of Biomedical and Health Informatics. 2023; doi: 10.1109/JBHI.2023.3339700. (Code)
Dar SUH, Ozturk S, Ozbey M, Oguz KK, Çukur T. Parallel-Stream Fusion of Scan-Specific and Scan-General Priors for Learning Deep MRI Reconstruction in Low-Data Regimes. Computers in Biology and Medicine. 2023; 167:107610. (Code)
Ozbey M, Dalmaz O, Dar SUH, Bedel HA, Ozturk S, Gungor A, Çukur T. Unsupervised Medical Image Translation with Adversarial Diffusion Models. IEEE Transactions on Medical Imaging. 2023 Dec;42(12):3524-3539. doi: 10.1109/TMI.2023.3290149. (Code)
Gungor A, Dar SUH, Ozturk S, Korkmaz Y, Bedel HA, Elmas G, Ozbey M, Çukur T. Adaptive Diffusion Priors for Accelerated MRI Reconstruction. Medical Image Analysis. 2023; 88:102872. (Code)
Bedel HA, Sivgin I, Dalmaz O, Dar SUH, Çukur T. BolT: Fused Window Transformers for fMRI Time Series Analysis. Medical Image Analysis. 2023; 88:102841. (Code)
Elmas G, Dar SUH, Korkmaz Y, Ceyani E, Susam B, Ozbey M, Avestimehr S, Çukur T. Federated Learning of Generative Image Priors for MRI Reconstruction. IEEE Transactions on Medical Imaging. 2023 Jul;42(7):1996-2009. (Code)
Çukur T, Yurt M, Dar SUH, Chung H, Ye JC. Image Synthesis in Multi-Contrast MRI with Generative Adversarial Networks. Deep Learning for Biomedical Image Reconstruction, Cambridge University Press. 2023; 279-298.
Zhang Q, Çukur T, Greenspan H, Yang G. Editorial: Generative Adversarial Networks in Cardiovascular Research. Frontiers in Cardiovascular Medicine. 2023; 10:1307812.
Bilgic B, Çukur T. Parallel Imaging and Reconstruction Techniques. Advances in Magnetic Resonance Technology and Applications, Academic Press. 2023; 10:139-159.
Ozturk S, Celik E, Çukur T. Content-Based Medical Image Retreival with Opponent Class Adaptive Margin Loss. Information Sciences. 2023;637:118938.
Ilicak E, Saritas EU, Çukur T. Automated Parameter Selection for Accelerated MRI Reconstruction via Low-rank Modeling of Local k-Space Neighborhood. Z Med Phys. 2023. 33:203-219. (Code)
Vural FTY, Newman SD, Çukur T, Ertugrul IO. Machine Learning Mehtods for Human Brain Imaging. Frontiers in Neuroinformatics. 2023;17:1154835.

2022

Yurt M, Dalmaz O, Dar SUH, Ozbey M, Tinaz B, Oguz KK, Çukur T. Semi-Supervised Learning of MRI Synthesis without Fully-Sampled Ground Truths. IEEE Transactions on Medical Imaging. 2022 Dec;41(12):3895-3906. (Code)
Gungor A, Askin B, Soydan DA, Saritas EU, Top CB, Çukur T. TranSMS: Transformers for Super-Resolution Calibration in Magnetic Particle Imaging. IEEE Transactions on Medical Imaging. 2022 Dec;41(12):3562-3574. (Code)
Shahdloo M, Celik E, Urgen BA, Gallant JL, Çukur T. Task-Dependent Warping of Semantic Representations During Search for Visual Action Categories. Journal of Neuroscience. 2022 Aug;42(35):6782-6799. (Brain Viewer)
Ozturk S, Çukur T. Deep Clustering via Center-Oriented Margin Free-Triplet Loss for Skin Lesion Detection in Highly Imbalanced Datasets. IEEE Journal on Biomedical and Health Informatics. 2022 Sep;26(9):4679-4690.
Dalmaz O, Yurt M, Çukur T. ResViT: Residual Vision Transformers for Multi-Modal Medical Image Synthesis. IEEE Transactions on Medical Imaging. 2022 Oct;41(10):2598-2614. (Code)
Korkmaz Y, Dar SUH, Yurt M, Ozbey M, Çukur T. Unsupervised MRI Reconstruction via Zero-Shot Learned Adversarial Transformers. IEEE Transactions on Medical Imaging. 2022 Jul;41(7):1747-1763. (Supp. Materials, Code)
Yurt M, Ozbey M, Dar SUH, Tinaz B, Oguz KK, Çukur T. Progressively volumetrized deep generative models for data-efficient contextual learning of MR image recovery. Medical Image Analysis. 2022;78:102429. (Code)
Keskin K, Yilmaz U, Çukur T. Constrained ellipse fitting for efficient parameter mapping with phase-cycled bSSFP MRI. IEEE Transactions on Medical Imaging. 2022 Jan;41(1):14-26. (Supp. Materials, Code)
Senel LK, Sahinuc F, Yucesoy V, Schutze H, Çukur T, Koc A. Learning interpretable word embeddings via bidirectional alignment of dimensions with semantic concepts. Information Processing and Management. 2022. 59:102295.

2021

Celik E, Keles E, Kiremitci I, Gallant JL, Çukur T. Cortical networks of dynamic scene category representations in the human brain. Cortex. 2021. doi:10.1016/j.cortex.2021.07.008.
Kiremitci I, Yilmaz O, Celik E, Shahdloo M, Huth AG, Çukur T. Attentional modulations of hierarchical speech representations in a multitalker environment. Cerebral Cortex. 2021 Jun; bhab136.
Yurt M, Dar SUH, Erdem A, Erdem E, Oguz KK, Çukur T. mustGAN: Multi-stream generative adversarial networks for MR image synthesis Medical Image Analysis, 2021, 101944.
Zhang T, Gao JS, Çukur T, Gallant JL. Voxel-based state space modeling recovers task-related cognitive states in naturalistic fMRI experiments Frontiers in Neuroscience. 2021 May;14:1103.

2020

Dar SUH, Yurt M, Ildiz ME, Shahdloo M, Tinaz B, Çukur T. Prior-Guided image reconstruction for accelerated multi-contrast MRI via generative adversarial networks IEEE Journal of Selected Topics in Signal Processing, 2020 Oct;14(6):1072-1087.
Yilmaz O, Celik E, Çukur T. Informed feature regularization in voxelwise modeling for naturalistic fMRI experiments European Journal of Neuroscience. 2020 Sep;52(5):3394-3410.
Dar SUH, Ozbey M, Catli AB, Çukur T. A transfer-learning approach for accelerated MRI using deep neural networks. Magnetic Resonance in Medicine. 2020 Aug;84(2):663–685.
Shahdloo M, Celik E, Çukur T. Biased competition in semantic representation during natural visual search. Neuroimage. 2020 Aug; 216:116383.
Tokgoz S, Aydogdu D, Ilhan B, Sahin Y, Bariseri N, Ozturkler BM, Çukur T. Musical mirror-symmetrical movement tasks: comparison of rhythm versus melody-playing. NeuroReport. 2020 May;31(7):523-529.
Biyik E, Keskin K, Dar SUH, Koc A, Çukur T. Factorized sensitivity estimation for artifact suppression in phase-cycled bSSFP MRI. NMR in Biomedicine. 2020 Apr;33(4):e4228.
Kopanoglu E, Gungor A, Kilic T, Saritas EU, Oguz KK, Çukur T, Guven HE. Simultaneous use of individual and joint regularization terms in compressive sensing: Joint reconstruction of multi-channel multi-contrast MRI acquisitions. NMR in Biomedicine. 2020 Apr;33(4):e4247.
Demirel OB, Kilic T, Çukur T, Saritas EU. Anatomical measurements correlate with individual magnetostimulation thresholds for kHz-range homogeneous magnetic fields. Medical Physics. 2020 Apr;47(4):1836-1844.

2019

Dar SUH, Yurt M, Karacan L, Erdem A, Erdem E, Çukur T. Image synthesis in multi-contrast MRI with conditional generative adversarial networks. IEEE Transaction on Medical Imaging. 2019 Oct;38(10):2375-2388. (https://github.com/icon-lab/pGAN-cGAN)
Ilbey S, Top CB, Gungor A, Çukur T, Saritas EU, Guven HE. Fast system calibration with coded calibration scenes for magnetic particle imaging. IEEE Transaction on Medical Imaging. 2019 Sep;38(9):2070-2080.
Ozaslan AA, Alacaoglu A, Demirel OB, Çukur T, Saritas EU. Fully automated gridding reconstruction for non-cartesian x-space magnetic particle imaging. Physics in Medicine and Biology. 2019 Aug 21;64(16):165018.
Senel LK, Kilic T, Gungor A, Kopanoglu E, Guven HE, Saritas EU, Koc A, Çukur T. Statistically segregated k-Space sampling for accelerating multiple-acquisition MRI. IEEE Transaction on Medical Imaging. 2019 Jul;38(7):1701-1714. (https://github.com/icon-lab/segSampling)
Shahdloo M, Ilicak E, Tofighi M, Saritas EU, Cetin AE, Çukur T. Projections onto epigraphs sets for rapid self-tuning compressed sensing MRI. IEEE Transaction on Medical Imaging. 2019 Jul;38(7):1677-1689. (https://github.com/icon-lab/PESCaT)
Celik E, Dar SUH, Yilmaz O, Keles U, Çukur T. Spatially informed voxel-wise modeling for naturalistic fMRI experiments. Neuroimage. 2019 Feb;186:741-57. (https://github.com/icon-lab/SPIN-VM)

2018

Senel LK, Utlu I, Yucesoy V, Koc A, Çukur T. Semantic structure and interpretability of word embeddings. IEEE/ACM Transactions on Audio, Language and Speech Processing. 2018 Oct;26(10):1769-79.
Kafali SG, Çukur T, Saritas EU. Phase-correcting non-local means filtering for diffusion-weighted imaging of the spinal cord. Magnetic Resonance in Medicine. 2018 Sep;80(3):1020-35.
Gozcu B, Mahabadi RK, Li YH, Ilicak E, Çukur T, Scarlett J, Cevher V. Learning-based compressive MRI. IEEE Transactions on Medical Imaging. 2018 Jun;37(6):1394-1406.
Biyik E, Ilicak E, Çukur T. Reconstruction by calibration over tensors for multi-coil multi-acquisition balanced SSFP imaging. Magnetic Resonance in Medicine. 2018 May;79(5):2542-54. (https://github.com/icon-lab/ReCaT)

2017

Ilicak E, Senel LK, Biyik E, Çukur T. Profile-encoding reconstruction for multiple-acquisition balanced steady-state free precession imaging. Magnetic Resonance in Medicine. 2017 Oct;78(4):1319-29.
Ilbey S, Top CB, Gungor A, Çukur T, Saritas EU, Guven HE. Comparison of system-matrix-based and projection-based reconstructions for field free line magnetic particle imaging. International Journal on Magnetic Particle Imaging. 2017, Mar;3:1-8.
Koc A, Bartan B, Gundogdu E, Çukur T, Ozaktas H. Sparse representation of two- and three-dimensional images with fractional Fourier, Hartley, linear canonical, and Haar wavelet transforms. Expert Systems with Applications. 2017 Feb;77:247-255.

2016

Çukur T, Huth AG, Nishimoto S, Gallant JL. Functional subdomains within scene-selective cortex: Parahippocampal Place Area, Retrosplenial Complex, and Occipital Place Area. Journal of Neuroscience. 2016 Oct;36(40):10257-73.
Yilmaz O, Saritas EU, Çukur T. Enhanced phase-sensitive SSFP reconstruction for fat-water separation in phased-array acquisitions. Journal of Magnetic Resonance Imaging. 2016 Jul;44(1):148-57.
Ilicak E, Cetin S, Bulut E, Oguz KK, Saritas EU, Unal G, Çukur T. Targeted vessel reconstruction in non-contrast-enhanced steady-state free precession angiography. NMR in Biomedicine. 2016 May;29(5):532-44.
Çukur T. Spectrally selective imaging with wideband balanced steady-state free precession MRI. Magnetic Resonance in Medicine. 2016 Mar;75(3):1132-41.

2015

Çukur T. Accelerated phase-cycled SSFP imaging with compressed sensing. IEEE Transaction on Medical Imaging. 2015 Jan;34(1):107-15.

2014 and earlier

Saritas EU, Lee D, Çukur T, Shankaranarayanan A, Nishimura DG. Hadamard slice encoding for reduced-FOV diffusion-weighted imaging. Magnetic Resonance in Medicine. 2014 Nov;72(5):1277-90.
Kwon KT, Wu HH, Shin T, Çukur T, Lustig M, Nishimura DG. Three-dimensional magnetization-prepared imaging using a concentric cylinders trajectory. Magnetic Resonance in Medicine. 2014 May;71(5):1700-10.
Çukur T, Huth AG, Nishimoto S, Gallant JL. Functional subdomains within human FFA. Journal of Neuroscience. 2013 Oct;33(42):16748-66.
Çukur T, Nishimoto S, Huth AG, Gallant JL. Attention during natural vision warps semantic representation across the human brain. Nature Neuroscience. 2013 Jun;16(6):763-70.
Quist B, Hargreaves BA, Çukur T, Morrell GR, Gold GE, Bangerter NK. Simultaneous fat suppression and band reduction with large-angle multiple-acquisition balanced steady-state free precession. Magnetic Resonance in Medicine. 2012 Apr;67(4):1004-12.
Ingle RR, Çukur T, Nishimura DG. The central signal singularity phenomenon in balanced SSFP and its application to positive-contrast imaging. Magnetic Resonance in Medicine. 2012 Jun;67(6):1673-83.
Aksoy M, Forman C, Straka M, Çukur T, Hornegger J, Bammer R. Hybrid prospective and retrospective head motion correction to mitigate cross-calibration errors. Magnetic Resonance in Medicine. 2012 May;67(5)1237-51.
Bangerter NK, Çukur T, Hargreaves BA, Hu BS, Brittain JH, Park D, Gold GE, Nishimura DG. Three-dimensional fluid-suppressed T2-prep flow-independent peripheral angiography using balanced SSFP. Magnetic Resonance Imaging. 2011 Oct;29(8):1119-24.
Çukur T, Shimakawa A, Yu H, Hargreaves BA, Hu BS, Nishimura DG, Brittain JH. Magnetization-prepared IDEAL bSSFP: a flow-independent technique for noncontrast-enhanced peripheral angiography. Journal of Magnetic Resonance Imaging. 2011 Apr;33(2):931-9.
Çukur T, Lustig M, Saritas EU, Nishimura DG. Signal compensation and compressed sensing for magnetization-prepared MR angiography. IEEE Transactions on Medical Imaging. 2011 May;30(5):1017-27.
Çukur T, Santos JM, Pauly JM, Nishimura DG. Variable-density parallel imaging with partially localized coil sensitivities. IEEE Transactions on Medical Imaging. 2010 May;29(5):1173-81.
Çukur T, Yamada M, Overall WR, Yang P, Nishimura DG. Positive contrast with alternating repetition time SSFP (PARTS): a fast imaging technique for SPIO-labeled cells. Magnetic Resonance in Medicine. 2010 Feb;63(2):427-37.
Çukur T, Nishimura DG. Multiple repetition time balanced steady-state free precession imaging. Magnetic Resonance in Medicine. 2009 Jul;62(1):193-204.
Çukur T, Lee JH, Bangerter NK, Hargreaves BA, Nishimura DG. Non-contrast-enhanced flow-independent peripheral MR angiography with balanced SSFP. Magnetic Resonance in Medicine. 2009 Jun;61(6):1533-9.
Çukur T, Lustig M, Nishimura DG. Improving non-contrast-enhanced steady-state free precession angiography with compressed sensing. Magnetic Resonance in Medicine. 2009 May;61(5):1122-31.
Çukur T, Lustig M, Nishimura DG. Multiple-profile homogeneous image combination: application to phase-cycled SSFP and multicoil imaging. Magnetic Resonance in Medicine. 2008 Sep;60(3):732-8.
Çukur T, Nishimura DG. Fat-water separation with alternating repetition time balanced SSFP. Magnetic Resonance in Medicine. 2008 Aug;60(2):479-84.
Çukur T, Santos JM, Nishimura DG, Pauly JM. Varying kernel-extent gridding reconstruction for undersampled variable-density spirals. Magnetic Resonance in Medicine. 2008 Jan;59(1):196-201.
Çukur T, Bangerter NK, Nishimura DG. Enhanced spectral shaping in steady-state free precession imaging. Magnetic Resonance in Medicine. 2007 Dec;58(6):1216-23.