Publications & Patents

Journal
Tags
Liquid Biopsy
A Computational Statistics Approach to Evaluate Blood Biomarkers for Breast Cancer Risk Stratification
K. Oktay, A. Santaliz-Casiano, M. Patel, N. Marino, A.M.V. Storniolo, H. Torun, B. Acar, Z. Madak Erdogan
Hormones & Cancer, vol. 11, pp. 17-33 (2020)
Journal
Tags
Industrial Data Analytics
Anomaly Monitoring Improves Remaining Useful Life Estimation of Industrial Machinery
Gurkan Aydemir, Burak Acar
Journal of Manufacturing Systems, 56, 463-469 (July 2020)
Theses
Tags
Industrial Data Analytics
Machine Health Monitoring for Cyber-Physical Systems
Gurkan Aydemir
PhD Thesis, Bogazici University, EE Dept., Turkey, May 2020
Journal
Tags
Brain Connectomes
B-Tensor: Brain Connectome Tensor Factorization for Alzheimer’s Disease
Goktekin Durusoy, Zerrin Yıldırım, Demet Y. Dal, Cigdem Ulasoglu-Yildiz, Elif Kurt, Gunes Bayır, Erhan Ozacar, Evren Ozarslan, Aslı Demirtas-Tatlıdede, Basar Bilgic, Tamer Demiralp, Hakan Gurvit, Alkan Kabakcıoglu, Burak Acar
IEEE Journal of Biomedical and Health Informatics (2020), doi: 10.1109/JBHI.2020.3023610.
Conference
Tags
Brain Connectomes
Alzheimer Sürekliliğinde Papez Devresinin Fonksiyonel Bağlantısallık Değişiklikleri
Hari E., Eryurek K., Bayram A., Acar B., Demiralp T., Gurvit H.
55. Ulusal Noroloji Kongresi, 15-21 Nov. 2019, Antalya, Turkey
Theses
Tags
Liquid Biopsy
Spectral Analysis of Cancer Biomarkers in Human Serum Using A Custom Portable Analyzer
Kaan Oktay
M.S. Thesis, Boğaziçi University, EE Dept., Turkey, June 2019
Conference
Tags
Brain Connectomes
fMRI Guided Personalization of Cortical Parcellation Maps
Onay M.S., Kucukaslan U., Acar B.
RSNA 2018, Chicago, USA
Conference
Tags
Brain Connectomes
Multi-modal Brain Tensor Factorization: Preliminary Results with AD Patients
Durusoy G., Karaaslanlı A., Yüksel Dal D., Yıldırım Z., Acar B.
In: Wu G., Rekik I., Schirmer M., Chung A., Munsell B. (eds) Connectomics in NeuroImaging. CNI 2018. Lecture Notes in Computer Science, vol 11083. Springer, Cham
Journal
Tags
Simulation
Multi-ray Medical Ultrasound Simulation Without Explicit Speckle Modeling
Tuzer M., Yazici A., Turkay R., Boyman M., Acar B.
Int. Journal of Computer Assisted Radiology and Surgery, 2018, vol. 13(7), pp. 1009-1017
Theses
Tags
Brain Connectomes
Seed-based and Data-driven Analyses of Default Mode Network Connectivity Measures in Dementia
Basak Kilic
MS Thesis, Bogazici University, Systems and Control Eng. Program, Turkey January 2017
Conference
Tags
Brain Connectomes
Differential Resting State Connectivity and Its Relationship with Cognitive Performance among Participants with Subjective Cognitive Impairment (SCI), Mild Cognitive Impairment (MCI), and Early Stage Alzheimer’s Disease (AD)
Yildirim E., Buyukiscan E.S., Kurt E., Yildiz C.U., Tatlidede A.D., Bilgiç B., Hanagasi H., Bayram A., Acar B., Demiralp T, Gurvit H.I.
AAIC 2017, London, England
Journal
Tags
Biomechanics
Magnetic resonance and diffusion tensor imaging analyses indicate heterogeneous strains along human medial gastrocnemius fascicles caused by submaximal plantar-flexion activity
Karakuzu A., Pamuk U., Ozturk C., Acar B., Yucesoy C.A.
Journal of Biomechanics, May 2017, vol. 57, pp. 69-78
Journal
Tags
Biomechanics
Combined Magnetic Resonance And Diffusion Tensor Imaging Analyses Provide A Powerful Tool For In Vivo Assessment Of Deformation Along Human Muscle Fibers
Pamuk U., Karakuzu A., Ozturk C., Acar B., Yucesoy C.A.
Journal of the Mechanical Behavior of Biomedical Materials, October 2016, vol. 63, pp. 207-219
Conference
Tags
Biomechanics
Combined Diffusion Tensor and Magnetic Resonance Imaging for in vivo Assessment of Human Muscle Function
Karakuzu A., Pamuk U., Ozturk C., Acar B., Yucesoy C.A.
In Congress of the European College of Sport Science, 2016
Conference
Tags
Simulation
A Multiray Approach To Phased Array US Simulation From CT Images
M. Tuzer, A. Yazici, B. Acar, M. Boyman
Proc. of Computer Assisted Radiology and Surgery (CARS 2015), Barcelona, Spain, 2015
Theses
Tags
Simulation
Ultrasound Simulations Using Computed Tomography Images as Priors
Mert Tuzer
MS Thesis, Bogazici University, Department of Physics, Turkey, July 2015
Conference
Tags
Biomechanics
Using Advanced MRI Techniques for Estimating Strain Distributions Along Muscle Fibers During Isometric Plantar-Flexion Activity of Human Medial Gastrocnemius, In Vivo
Karakuzu A., Pamuk U., Acar B., Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK
Conference
Tags
Biomechanics
MRI analyses Indicate Non-uniform Human Muscle Tissue Deformations and Confirm Theoretically Anticipated Sarcomere Length Heterogeneity, In Vivo
U Pamuk, A Karakuzu, P Akyazi, B Acar, C Ozturk, CA Yucesoy
18th National Biomedical Engineering Meeting (BIYOMUT), 2014, Istanbul
Theses
Tags
Biomechanics
Skeletal Muscle Deformation Analysis Using Diffusion Tensor Magnetic Resonance Imaging
Pinar Akyazi
MS thesis, Bogazici University, Electrical & Electronics Eng. Dept., Turkey August 2013
Journal
Tags
Brain Connectomes, Brain Imaging
SMT: A Reliability Based Interactive DTI Tractography Algorithm
Yoldemir B., Acar B., Firat Z., Kilickesmez O.
IEEE Transactions on Medical Imaging, October 2012, Vol. 31-10, pp. 1929-1940.
Theses
Tags
CT Colonography
Liver Segmentation in 3D CT Data
Serkan Cimen
MS Thesis, Bogazici University, Electrical and Electronics Engineering, Turkey, September 2011
Theses
Tags
Brain Connectomes, Brain Imaging
Assessing DT-MRI Tractography Results via Sampling The Fiber Tract Space
A. Burak Yoldemir
MS Thesis, Bogazici University, Electrical & Electronics Eng. Dept., Turkey June 2011
Conference
Tags
Brain Connectomes, Brain Imaging
bootSMT:Bootstrap Split/Merge Fiber Tractography for DT-MRI Data
Yoldemir A.B., Acar B.
RSNA 2011, Chicago, USA
Patent
Tags
CT Colonography
Heat diffusion based detection of structures of interest in medical images.
Acar B., Konukoglu E., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7729739 10/06/2010
Conference
Tags
Brain Connectomes, Brain Imaging
A Pointwise Correspondence Based DT-MRI Fiber Similarity Measure
Berkiten S., Acar B.
Proc. 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2010), Buenos Aires, Argentina, IEEE, 2010
Book Chapter/Section
Tags
Brain Connectomes, Brain Imaging
Similar Tensor Arrays: A Framework for Storage of Tensor Array Data
Brun, A., Martin-Fernandez, M., Acar, B., Munoz-Moreno, E., Cammoun, L., Sigfridsson, A., Sosa-Cabrera, D., Svensson, B., Herberthson, M., Knutsson, H.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de Luis García, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern Recognition, ISBN: 978-1-84882-298-6, Springer, 2009
Book Chapter/Section
Tags
Brain Imaging
DT-MRI Connectivity and/or Tractography?: Two New Algorithms
Acar B., Yoruk E.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de Luis García, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern Recognition, ISBN: 978-1-84882-298-6, Springer, 2009
Theses
Tags
Brain Imaging
Diffusion Tensor Field Visualization
Sila Girgin
MS Thesis, Bogazici University, Computer Engineering, Turkey January 2008
Patent
Tags
CT Colonography
Three-dimensional pattern recognition method to detect shapes in medical images.
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7346209 18/03/2008
Journal
Tags
CT Colonography
Polyp Enhancing Level Set Evolution of Colon Wall: Method and Pilot Study
Konukoglu E., Acar B., Paik D.S.,Beaulieu CF,Rosenberg J., Napel S.
IEEE Transactions on Medical Imaging, December 2007, Vol. 26-12, pp.1649-1656.
Conference
Tags
Human-Computer Interaction, Brain Imaging
DTI Application with Haptic Interfaces
M. Aksoy, N. Avcu, S. Merino-Caviedes, D. Diktas, M.A. Martin-Fernandez, S. Girgin, I. Marras, E. Munoz-Moreno, E. Tekeli, B. Acar, R. Bammer, M. Martin-Fernandez, A.V. Sahiner, S. Uskudarli
Proceedings of Enterface 2007 Workshop, EU 6th Framework Programme SIMILAR NoE, Istanbul, Turkey, July-August 2007
Journal
Tags
CT Colonography
HDF: Heat Diffusion Fields for Polyp Detection in CT Colonography
Konukoglu E., Acar B.
Signal Processing (Elsevier), October 2007, Vol. 87, Issue: 10, pp. 2407-2416.
Conference
Tags
Human-Computer Interaction
A Stereo Tracking System For Arbitrary Slicing Of Volumetric Radiological Data
Yagci E., Acar B.
Sinyal Isleme ve Uygulamalari Kurultayi, SIU 2007, Eskisehir, Turkey, June 2007
Theses
Tags
Human-Computer Interaction
3D Stylus: A Human Computer Interface For 3D Environment
Enver Yagci
MS Thesis, Bogazici University, System & Control Engineering, Turkey June 2007
Patent
Tags
CT Colonography
Method for detecting and classifying a structure of interest in medical images.
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey R.B.Jr., Napel S.A.
US Patent Office: US7272251 18/09/2007
Patent
Tags
CT Colonography
Method for matching and registering medical image data.
Acar B., Beaulieu C.F., Paik D.S., Napel S.A., Jeffrey R.B.Jr.
US Patent Office: US7224827 29/05/2007
Conference
Tags
Brain Imaging, Brain Connectomes
SMT: Split & Merge Fiber Tractography for DT-MRI
Bozkaya U., Acar B.
Lecture Notes in Computer Science, Vol. 4792, pp.153-160 ; Springer, 2007 (MICCAI 2007, Brisbane, Australia)
Journal
Tags
Human-Computer Interaction
Masterpiece: Physical Interaction and 3D Content-Based Search in VR Applications
Moustakas K., Tzovaras D., Strintzis M. G., Carbini S., Bernier O., Viallet J.E., Raidt S., Mancas M., Dimiccoli M., Yagci E., Balci S., Leon E.I.
IEEE Multimedia Magazine, Vol 13/3, pp. 92-100, June 2006
Theses
Tags
Brain Connectomes, Brain Imaging
SMT: Split/Merge Fiber Tractography
Ugur Bozkaya
MS Thesis, Bogazici University, Institute of Biomedical Engineering, Turkey May 2006
Conference
Tags
Brain Imaging
DT-MRI Connectivity And/Or Tractography?: Two New Algorithms
Acar B.
EU FP7 SIMILAR NoE, WP10, Workshop on Tensor Toolboxes, 15-17 November, 2006, Las Palmas, Gran Canaria, Spain.
Conference
Tags
Brain Imaging
Structure Preserving Regularization Of DT-MRI Vector Fields by Nonlinear Anisotropic Diffusion Filtering
Yoruk E., Acar B.
Proceedings of EUSIPCO 2005, European Signal Processing Conference, Antalya, Turkey
Conference
Tags
Brain Imaging
SNR Dependence of DTI Fiber Tracking Protocols
Aksoy M., Acar B., Bammer R.
ISMRM Workshop on Methods for Quantitative Diffusion MRI of Human Brain, 13-16 March 2005, Lake Louise, Alberta, Canada
Conference
Tags
Software Platform
VAVframe: A New Concept in Platform Design
Durusut E., Bozkaya U., Yagci E., Acar B.
EUROCON 2005, Serbia & Montenegro, Belgrade, November 22-24, 2005
Conference
Tags
Software Platform, Human-Computer Interaction
VAVframe: A New Concept in Platform Design
EUROCON 2005, Serbia & Montenegro, Belgrade, November 22-24, 2005
Theses
Tags
CT Colonography
PELS: Polyp Enhancing Level-Sets for CT Colonography
Ender Konukoglu
MS Thesis, Bogazici University, Electrical and Electronics Engineering, Turkey, June 2005
Theses
Tags
Software Platform
VAVframe: Volumetric Analysis and Visualization Framework
Erhan Durusut
MS Thesis, Bogazici University, Dept. of Computer Engineering, Turkey April 2005
Conference
Tags
CT Colonography
Polyp Enhancement Scheme for Improved Detection of Colonic Polyps in CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
Conference
Tags
CT Colonography
Registration of Supine and Prone CT Colonography Data Using Dynamic Time Warping: Method and Evaluation
Balci S.K., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
Conference
Tags
CT Colonography
Polyp Enhancement Scheme for Improved Detection of Colonic Polyps in CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
Conference
Tags
CT Colonography
Heat Diffusion Based Detection Of Colonic Polyps In CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of EUSIPCO 2005, European Signal Processing Conference, Antalya, Turkey (3rd place in EUSIPCO2005 student paper contest)
Conference
Tags
Brain Imaging
A Physical Model for MR-DTI Based Connectivity Map Computation
Yoruk E., Acar B., Bammer R.
Lecture Notes in Computer Science, Vol. 3749 / Part 1, pp. 213-220, Springer, 2005 (MICCAI 2005, Palm Springs, CA)
Conference
Tags
CT Colonography
Computer Aided Detection Of Polyps In Virtual Colonoscopy Using 3D Heat Diffusion Fields
Konukoglu E., Acar B., Paik D., Beaulieu C.F., Napel S.
In Proceedings of.The 5th Int. Symposium on Virtual Colonoscopy, Boston, MA, USA, 2004
Journal
Tags
CT Colonography
Registration of Central Paths and Colonic Polyps between Supine and Prone Scans in CT Colonography
Li P., Napel S., Acar B., Paik D.S., Jeffrey, Jr. R.B., Beaulieu C.F.
Medical Physics, October 2004, Vol. 31, Issue: 10, pp. 2912-2923
Journal
Tags
CT Colonography
Surface Normal Overlap: A Computer-Aided Detection Algorithm With Application to Colonic Polyps and Lung Nodules in Helical CT
Paik D.S., Beaulieu C.F., Rubin G.D., Acar B., Jeffrey Jr R.B., Yee J., Dey J., Napel S.
IEEE Transactions on Medical Imaging, June 2004, Vol. 23-6, pp. 661-675
Journal
Tags
Brain Imaging
Characterizing Non-Gaussian Diffusion by Using Generalized Diffusion Tensors
Liu C., Bammer R., Acar B., Moseley M.E.
Magnetic Resonance in Medicine, May 2004, Vol. 51, pp. 924-937.
Patent
Tags
Brain Imaging
Characterization and Correction of Spatial Gradient Field Nonuniformities.
Bammer R., Markl M., Acar B., Pelc N., Moseley M.E.
US Patent Office: US6969991 17/06/2004 (Licensed by GE)
Conference
Tags
Brain Connectomes, Brain Imaging
Comparative Assessment Of DT-MRI Fiber Tractography Algorithms
Acar B., Bammer R., Moseley M.E.
Proceedings of ISMRM 2003, pp. 2164, July 2003, Toronto, Canada
Conference
Tags
Brain Imaging
Generalized Diffusion Tensor Imaging (GDTI) Using Higher Order Tensor (HOT) Statistics
Liu C., Bammer R., Acar B., Moseley M.E.
Proceedings of ISMRM 2003, pp. 242,July 2003, Toronto, Canada
Journal
Tags
Brain Imaging
Analysis and generalized correction of the effect of spatial gradient field distortions in diffusion-weighted imaging
Bammer R., Markl M., Barnett A., Acar B., Alley M.T., Pelc N.J., Glover G.H., Moseley M.E.
Magnetic Resonance in Medicine, September 2003, Vol. 50-3, pp. 560-569.
Journal
Tags
Brain Imaging
In vivo MR Tractography Using Diffusion Imaging
Bammer R., Acar B., Moseley M.E.
European J. of Radiology, 2003, Vol. 45-3, pp.223-234
Patent
Tags
ECG
Methods of characterizing ventricular operations and applications thereof
Malik, M., Acar B., Batchvarov V.N.
US Patent Office: US6438409 20/08/2002
Conference
Tags
CT Colonography
3D Differential Descriptors for Computer Aided Diagnosis of Colonic Polyps in CTC
Acar B., Beaulieu C.F., Paik D.S., Yee J., Jeffrey, Jr. R.B., Napel S.
Radiology, December 2002, Vol. 225(P), pp. 405 (88th Annual Meeting of Radiological Society of North America (RSNA 2002), Chicago, USA, 1-6 December 2002)
Journal
Tags
CT Colonography
Edge Displacement Field Based-Classification for Improved Detection of Polyps in CT Colonography
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey, Jr. R,B,, Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2002, Vol. 21-12, pp. 1461-1467
Conference
Tags
CT Colonography
Using Optical Flow Fields For Polyp Detection In Virtual Colonoscopy
Acar B., Napel S., Paik D., Gokturk S.B., Tomasi C., Beaulieu C.F.
In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 637-644.
Conference
Tags
CT Colonography
A Learning Method For Automated Polyp Detection
Gokturk S.B., Tomasi C., Acar B., Paik D., Beaulieu C.F., Napel S.
In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 85-9
Conference
Tags
CT Colonography
Assessment of an optical flow field-based polyp detector for CT colonography
Acar B., Beaulieu C.F., Paik D.S., Gokturk S.B., Tomasi C., Yee J., Napel S.
In Proceedings of 23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2001), Istanbul, Turkey, 25-28 October 2001
Journal
Tags
CT Colonography
A statistical 3D pattern processing method for computer aided detection of polyps in CT colonography
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Paik D.S., Jeffrey R.B., Jr., Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2001, Vol. 20-12, pp. 1251-1260
Conference
Tags
CT Colonography
Registration of Supine and Prone CT Colonography Data: Method and Evaluation
Acar B., Napel S., Paik D.S., Li P., Yee J., Beaulieu C.F., Jeffrey Jr. R.B.
Radiology, November 2001, Vol. 221(P), pp. 332 (87th Annual Meeting of Radiological Society of North America (RSNA 2001), Chicago, USA, 25-30 November 2001).
Conference
Tags
CT Colonography
Medial axis registration of supine and prone CT colonography data
Acar B., Napel S., Paik D.S., Li P., Yee J., Jeffrey Jr. R.B., Beaulieu C.F.
In Proceedings of EMBC 2001, Istanbul, Turkey, 25-28 October 2001
Patent
Tags
ECG
Methods of characterizing ventricular operations and applications thereof
Acar B., Batchvarov V.N., Malik, M.
European Patent Office: EP1038498 27/09/2000
Journal
Tags
ECG
QT dispersion does not represent electrocardiographic interlead heterogeneity of ventricular repolarization
Malik, M., Acar, B., Gang, Y., Yap, Y.G., Hnatkova, K., Camm, A.J.
Journal Of Cardiovascular Electrophysiology, 11(8), 835-843 (2000)
Journal
Tags
ECG
Analysis of 12-lead T-wave morphology for risk stratification after myocardial infarction
Zabel, M., Acar, B., Klingenheben, T., Franz, M.R., Hohnloser, S.H., Malik, M.
Circulation, 102(11), 1252-1257 (2000)
Journal
Tags
ECG
Automatic Ectopic Beat Elimination In Short-term Heart Rate Variability Measurement
Acar, B., Savelieva, I., Hemingway H., Malik, M.
Computer Methods And Programs In Biomedicine, 63(2), 123-131 (2000)
Journal
Tags
ECG
SVD Based Online Exercise ECG Signal Orthogonalization
Acar, B., Köymen, H.
IEEE Transactions On Biomedical Engineering, 46(3), 311-321 (1999)
Journal
Tags
ECG
Spatial, Temporal And Wavefront Direction Characteristics Of 12-Lead T Wave Morphology
Acar, B., Yi, G., Hnatkova K., Malik, M.
Medical & Biological Engineering & Computing, 37(5), 574-584 (1999)
Journal
Tags
ECG
New approaches to T-wave analysis from surface ECG
Acar, B.
Cardiac ElectroPhysiology Review (CEPR), 3(4), 319-323 (1999), CEPR has been merged into Journal of Interventional Cardiac Electrophysiology
Conference
Tags
Biomechanics
MRI and DTI Analyses Combined Provide A Powerful Tool for Quantifying Deformation Along Human Muscle Fibers In Vivo
Pamuk U., Karakuzu A., Acar B., Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK