Publications (selected)

Journal Articles (selected)

Selected Publications

Bergamo D, Handjaras G, Picchioni D, Ricciardi E, Legendre G, Özbay PS, de Zwart JA, Duyn JH, Bernardi G, Betta M, Thalamic involvement defines distinct slow-wave subtypes in NREM sleep, Communications Biology (in press, 2026)

Ma F, Özbay PS, Bilgic B, Hedden T, Delman B, Balchandani P, Alipour A., Optimized Quantitative Susceptibility Mapping at 7T MRI for Assessing Iron Deposition in Alzheimer's Disease, NMR Biomed. 2026 Apr;39(4):e70268.

Gold BP, Goodale SE, Zhao C, de Zwart JA, Özbay PS, Bolt TS, Duyn JH, Chen JE, Chang C, The fMRI signal exhibits more autonomic variance as vigilance decreases, Imaging Neuroscience (2024); 2: 1–25.

Picchioni D*, Özbay PS*, Mandelkow H*, de Zwart JA, Wang Y, van Gelderen P, Duyn JH, Autonomic arousals contribute to brain fluid pulsations during sleep. NeuroImage 2022 Apr 1;249:118888 (*indicates equal authorship).

Duyn JH, Özbay PS, Chang C, Picchioni D, Physiological changes in sleep that affect fMRI inference. Current Opinion in Behavioral Sciences 2020 33, 42-50.

Özbay PS, Chang C, Picchioni D, Mandelkow H, Chappel-Farley MG, van Gelderen P, de Zwart JA, Duyn JH, Sympathetic activity contributes to the fMRI signal. Commun. Biol. 2019, 2:421.

Özbay PS, Chang C, Picchioni D, Mandelkow H, Moehlman TM, Chappel-Farley MG, van Gelderen P, de Zwart JA, Duyn JH, Contribution of Systemic Vascular Effects on White Matter BOLD fMRI Signal. NeuroImage 2018 Aug 1;176:541-549.  

Özbay PS, Stieb S, Rossi C, Riesterer O, Boss A, Weiss T, Kuhn FP, Pruessmann KP, Nanz D, Lesion magnetic susceptibility response to hyperoxic challenge: a biomarker for malignant brain tumor microenvironment? Magn Reson Imaging 2018, 47, 147-153.

Özbay PS, Duerst Y, Wilm BJ, Pruessmann KP, Nanz D, Enhanced quantitative susceptibility mapping (QSM) with real-time field control. Magn Reson Med. 2018, 79(2), 770-778.

Özbay PS, Deistung A, Feng X, Nanz D, Reichenbach JR, Schweser F, A comprehensive numerical analysis of background phase correction with SHARP. NMR Biomed. 2016, 30(4).

Özbay PS, Warnock G, Rossi C, Kuhn F, Akin B, Pruessmann KP, Nanz D, Probing neuronal activation by functional quantitative susceptibility mapping under a visual paradigm: a group level comparison with BOLD fMRI and PET. NeuroImage 2016, 15, 137:52-60.

Özbay PS, Rossi C, Kocian R, Redle M, Boss A, Pruessmann KP, Nanz D, Effect of respiratory hyperoxic challenge on magnetic susceptibility in human brain assessed by quantitative susceptibility mapping (QSM). NMR Biomed. 2015, 28(12), 1688-96.

Conference Proceedings (selected)

 

International

2025 ISMRM:

  • Tavashi, B., Hakki, L., Pamuk, U., Hüraydın, O., Öztürk Işık, E., and Özbay, P. S., Quantifying the young rat brain: a cross-sectional region-based analysis of T1, T2, R2*, and quantitative susceptibility maps, ISMRM Annual Meeting 2025, Digital Poster.
  • Hakki, L., Özakçakaya, M., Tavashi, B., Pamuk, U., Hüraydın, O., Öztürk Işık, E., and Özbay, P. S., Automated Brain Extraction for Multi-Contrast MRI in Rat Models Using Enhanced U-Net, ISMRM Annual Meeting 2025, Digital Poster.
  • Eren K., Alqam,L.,Tavashi,B., Yıldırım,K.B., Can,E., Karakuzu,C., Dinçer,A., and Özbay, P.S., Multimodal Analysis of Autonomic Regression on Neuronal and Physiological Correlates, ISMRM Annual Meeting 2025, Digital Poster.
  • Can, E., Öner, B., Özbay, P.S., Effects of Arousal Level and Data-Driven Cardiac Signal Regression on Functional Connectivity, ISMRM Annual Meeting 2025, Digital Poster.
  • Karakuzu, C., Eren K., Can, E., Tavashi, B., Yıldırım, K.B.,  Alqam, L., Dinçer, A., and Özbay, P.S. Group-Level fMRI Analysis of Caffeine Effects: Data-Driven and Connectivity-Based Approaches. ISMRM Annual Meeting 2025, Digital Poster.
  • Alqam, L., Eren, K., Yildirim, K.B., Tawashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Effects of Caffeine during Task and Rest Conditions: EEG-fMRI Study, ISMRM Annual Meeting 2025, Digital Poster.

2025 OHBM:

  • Tavashi, B., Hakki, L., Pamuk, U., Hüraydın, O., Öztürk Işık, E., and Özbay, P. S., Quantitative MRI Analysis of the Young Wistar Rat Brain Including Relaxometry and Susceptibility, OHBM Annual Meeting 2025, Poster.
  • Hakki, L., Özakçakaya, M., Tavashi, B., Pamuk, U., Hüraydın, O., Işık, E., and Özbay, P. S., Deep Learning-Based Brain Extraction and Segmentation Pipeline for Rat MRI, OHBM Annual Meeting 2025, Poster.
  • Eren K., Alqam,L.,Tavashi,B., Yıldırım,K.B., Can,E., Karakuzu,C., Dinçer,A., and Özbay, P.S.,Characterizing Autonomic Contributions to fMRI BOLD and fMRI-EEG Dynamics in a Mental Arithmetic Task, OHBM Annual Meeting 2025, Poster.
  • Karakuzu, C., Eren K., Can, E., Tavashi, B., Yıldırım, K.B.,  Alqam, L., Dinçer, A., and Özbay, P.S.The Effects of Caffeine on Brain Networks during Rest and Task. OHBM Annual Meeting 2025, Poster.
  • Neşe, H., Harı, E., Kurt E., Gürvit H., Ademoğlu, A., Demiralp, T., Frequency-Specific and Across-Frequency Network Disruptions in the Alzheimer’s Continuum, OHBM 2025, Poster.
  • Alqam, L., Yildirim, K.B., Eren, K., Tavashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Effects of Caffeine during Alert and Rest Conditions: EEG-fMRI Study, OHBM Annual Meeting 2025, Poster.

2025 ESMRMB:

  •  Hakki, L., Tavashi, B., Pamuk, U., Hüraydın, O., Öztürk Işık, E., and Özbay, P. S., Volumetric MRI Analysis in 3-Month-Old Wistar Rats: A Baseline for Longitudinal Studies, ESMRMB 2025, Poster.
  • Hakki, L., Yeşiloğlu, Ö., Tavashi, B., Pamuk, U., Hüraydın, O., Öztürk Işık, E., and Özbay, P. S., Investigating Cortical Malformation in a 71-Day-Old Rat Using Quantitative MRI, ESMRMB 2025, Poster.
  • Eren K., Alqam,L.,Tavashi,B., Yıldırım,K.B., Can,E., Karakuzu,C., Dinçer,A., and Özbay, P.S., Task-Evoked Dynamics and EEG–fMRI Coupling Under Autonomic Nuisance Regression, ESMRMB 2025, Oral Presentation.
  • Abacı, Ş.Y, Eren, K., Uçal, F., Alqam, L., Karakuzu, C., Dinçer, A., and Özbay, P.S., Leveraging Pupil and Heart Rate Signals to Understand Attention-Related Effects during Cognitive Tasks, ESMRMB 2025, Lightening Talk and Poster.
  • Neşe, H., Ademoğlu, A., Demiralp, T., Decomposing Brain State Dynamics: A Spectral and Temporal Characterization of Resting fMRI, ESMRMB 2025, Oral Presentation.

2024 ISMRM:

  • Yildirim, K.B., Alqam, L., Eren, K., Tavashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Effects of Caffeine Intake on Brain, CSF, and Autonomic Signals: An EEG-fMRI Study, ISMRM Annual Conference 2024.
  • Eren, K., Tavashi, B., Yildirim, K.B., Elif Can, Karakuzu, C., Alqam, L., Dincer, A., and Ozbay, P. S., Autonomic Regression in fMRI during Alertness: Insights from Respiration, Pupil Size, and PPG Amplitude, ISMRM Annual Conference 2024

2024 OHBM:

  • Alqam, L., Yildirim, K.B., Eren, K., Tavashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Impacts of Caffeine Consumption on Brain and CSF Dynamics:An EEG-fMRI Study, OHBM Annual Conference 2024
  • Karakuzu, C., Eren, K., Can, E., Tavashi, B., Yildirim, K.B., Alqam, L., Dincer, A. and Ozbay, P. S., Effects of Caffeine Intake as a Sympathetic Stimulant on Brain Dynamics during Cognitive Tasks, OHBM Annual Conference 2024
  • Can, E., Ozbay P.S., Classification of Vigilance Level Based on Sympathetic Biomarkers: An fMRI-Pupillometry Study, OHBM Annual Conference 2024.
  • Tavashi, B., Eren, K., Yildirim, K.B., Can, E., Karakuzu, C., Alqam, L., Dinçer, A., and Özbay, P. S., Incorporation of PPG-AMP and Pupil Diameter into Autonomic Correction of fMRI Signal, OHBM Annual Meeting 2024, Poster.

2024 ESMRMB:

  • Tavashi, B., Hakki, L., Kula Yeşilot, F. B., Ertaş, N., Hüraydın, O., Arpak, A., Pamuk, U., Öztürk, C., Yücesoy, C., Öztürk Işık, E., and Özbay, P. S., Exploring Aging Related Changes through Multiparametric Mapping in Preclinical Imaging: Preliminary Findings, ESMRMB Annual Meeting 2024, Poster.
  • Can, E., Öner, B., Özbay, P.S., Integrating functional Magnetic Resonance Imaging (fMRI) and Pupillometry: Arousal Classification through Spatiotemporal Patterns. ESMRMB Annual Meeting 2024, Lightning Talk

 

National

  • Eren K., Alqam,L.,Tavashi,B., Yıldırım,K.B., Can,E., Karakuzu,C., Dinçer,A., and Özbay, P.S., Bilişsel Görev Sırasında Fizyolojik Sinyallerin BOLD fMRI Yanıtları ve EEG-fMRI Dinamiklerine Etkisi, 2. Ulusal Nörogörüntüleme Kongresi (UNK) 2025, Sözlü Sunum.
  • Karakuzu, C., Eren K., Can, E., Tavashi, B., Yıldırım, K.B.,  Alqam, L., Dinçer, A., and Özbay, P.S. Investigating caffeine effects in resting state networks by independent component analysis and dual regression. 2. Ulusal Nörogörüntüleme Kongresi (UNK) 2025, Sözlü Sunum.
  • Neşe, H., Ademoğlu, A., Demiralp, T. Dinlenim durumu fMRI’da beyin durumu dinamiklerinin spektral ve zamansal karakterizasyonu. 2. Ulusal Nörogörüntüleme Kongresi (UNK) 2025, Sözlü Sunum.
  • Alqam, L., Eren, K., Yildirim, K.B., Tavashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Effects of Caffeine on Brain and Autonomic Function during Rest and Cognitive Tasks, 2nd National Neuroimaging Congress (UNK) 2025, Oral Presentation.
  • Yildirim, K.B., Alqam, L., Eren, K., Tawashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Dinlenme Durumunda Eszamanli EEG-fMRG Yontemi ile Kafeinin Beyin ve Otonom Sinyaller Uzerindeki Degisimlerinin Analizi - Analysis of Changes in Brain and Autonomic Signals with Caffeine Using Simultaneous EEG-fMRI in Resting State, 22. Ulusal Sinirbilim Kongresi 2024, Oral Presentation.
  • Tavashi, B., Hakki, L., Kula Yeşilot, F. B., Ertaş, N., Hüraydın, O., Arpak, A., Pamuk, U., Öztürk, C., Yücesoy, C., Öztürk Işık, E., and Özbay, P. S., Preklinik görüntülemede yaşlanmaya bağlı multiparametrik MR haritalama analizi - Exploring Aging Related Changes through Multiparametric Mapping in Preclinical Imaging: Preliminary Findings, 22. Ulusal Sinirbilim Kongresi 2024, Oral Presentation.
  • Eren K., Tavashi,B., Yıldırım,K.B., Can,E., Karakuzu,C., Alqam,L., Dinçer,A., and Özbay, P.S, Bilişsel Görev Sırasında fMRG KOSB Sinyali Üzerindeki Otonomik Etkiler: Otonomik Belirteç Olarak Solunum Hacmi, Parmak Derisi Damar Tonusu ve Göz Bebeği Çapı, 22. Ulusal Sinirbilim Kongresi 2024, Oral Presentation.
  • Karakuzu, C., Eren, K., Can, E., Tawashi, B., Yildirim, K.B., Alqam, L., Dincer, A. and Ozbay, P. S., Sempatik Bir Uyarıcı Olarak Kafeinin Görev ve Dinlenme Sırasında Beyin Dinamikleri Üzerindeki Etkileri, 22. Ulusal Sinirbilim Kongresi, 2024, Poster.
  • Can, E., Öner, B., Özbay, P.S., fMRG ve Goz Bebegi Capi Kullanilarak Sempatik Sistem Belirtecleri ile Uyaniklik Duzeyi Siniflandirmasi - Classifying Arousal Level with Sympathetic Biomarkers Using fMRI-Pupillometry. 22. Ulusal Sinirbilim Kongresi 2024, Oral Presentation.
  • Can, E., Özbay, P.S., Classification of Arousal Level Based on Sympathetic Biomarkers: An fMRI-Pupillometry Study, 3rd International Graduate Research Symposium 2024, Poster Presentation.
  • Alqam, L., Yildirim, K.B., Eren, K., Tawashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Caffeine-Induced Changes in CSF Dynamics and Brain Connectivity: Insights from 4th Ventricle to DMN Regions and EEG Power Modulations, 3rd International Graduate Research Symposium 2024, Oral Presentation.
  • Alqam, L., Yildirim, K.B., Eren, K., Tawashi, B., Can, E., Karakuzu, C., Dincer, A., and Ozbay, P. S., Caffeine's Impact on CSF Flow and Spatiotemporal Brain Dynamics in Arithmetic Tasks: A Multimodal Imaging Study, 22nd Turkish Neuroscience Congress 2024, Oral Presentation.
  • Karakuzu, C., Eren, K., Can, E., Tawashi, B., Yildirim, K.B., Alqam, L., Dincer, A. and Ozbay, P. S., Effects of Caffeine on Brain Networks during Cognitive Tasks and Resting, 10th International Symposium on Brain and Cognitive Science (ISBCS), 2024, Poster
Invited Talks (selected)
  • Understanding Brain States and Dynamics Through Multimodal Imaging and Physiology
    Department of Psychology, Özyeğin University, Istanbul, Türkiye, 2026
  • Understanding Brain Dynamics Through Multimodal Imaging and Physiology, Neuroscience Days, Boğaziçi University Science Club - Biology Subcommittee, North Campus, Istanbul, Türkiye
  • Uyku ve Uyanıklıkta Multimodal Nörogörüntüleme ve Fizyoloji ile Beyin Dinamiklerinin İncelenmesi (Investigating Brain Dynamics through Multimodal Imaging and Physiology in Sleep and Wakefulness), Technology in Medicine, Ankara University Neuroscience Society, Ankara, Türkiye, 2026
  • Biology of CSF Flow During Sleep Measured With MRI, ISMRM Workshop on Fluids, Flows, and Clearance in the Brain: What Can We Image and How Should It Be Interpreted?, Yale University, Orange, CT, USA, 2026
  • Physiological signals in fMRI, Joint ISMRM Workshop on Brain Function and Ultra High Field MRI, Annapolis, MD, USA, 2025
  • Contributions of the Autonomic Nervous System to Brain Dynamics During Sleep and Wake, OHBM, Seoul, South Korea, 2024
  • Susceptibility Imaging at High Field, ISMRM, Singapore, 2024
  • Spatiotemporal fMRI signatures of systemic physiology, OHBM, Montreal, Canada, 2023
  • Novel/Alternative Contrast Mechanisms for Functional MRI - fQSM, ISMRM, Toronto, Canada, 2023
  • Neuronal Oscillations & Neurovascular Coupling, ISMRM, London, UK, 2022
  • Variations in systemic physiology and fMRI signal during sleep and wake, ISMRM Turkish Chapter First Virtual Workshop, 2020
  • Functional QSM, 5th International Workshop on MRI Phase Contrast and QSM, Seoul, South Korea, 2019
  • Contribution of Systemic Vascular Effects on White Matter BOLD fMRI Signal, Martinos Center, MGH, 2017