Published or accepted to be published in journals covered by SCI, SSCI or AHCI

National

• Aaron Carass et al. and Et Al..
  (2017) Longitudinal Multiple Sclerosis Lesion Segmentation: Resource and Challenge.
  NeuroImage , Vol. 148, 77-102,

• Ertunc Erdil , Muhammad Usman Ghani , Lavdie Rada , Ali Ozgur Argunsah , Devrim Unay , Tolga Tasdizen and Mujdat Cetin.
  (2017) Nonparametric Joint Shape and Feature Priors for Image Segmentation.
  IEEE Transactions On Image Processing , Vol. 26, No. 11, 5312-5323,

• Henning Muller , Devrim Unay.
  (2017) Retrieval from and Understanding of Large-Scale Multi-Modal Medical Datasets: A Review.
  IEEE Transactions On Multimedia , Vol. 19, No. 9, 2093-2104,

• Devrim Unay , Bernard Gosselin , Olivier Kleynen , Vincent Leemans , Marie France Destain , Olivier Debeir.
  (2011) Automatic Grading of Bi-Colored Apples by Multispectral Machine Vision.
  Computers And Electronics In Agriculture , Vol. 75, No. 1, 204-212,

• Sureyya Ozogur-Akyuz , Devrim Unay , Alex Smola.
  (2011) Guest editorial: model selection and optimization in machine learning.
  Machine Learning , Vol. 85, No. 1, 1-2,

• Devrim Unay , Ahmet Ekin , Radu Jasinschi.
  (2010) Local Structure-based Region-of-Interest Retrieval in Brain MR Images.
  IEEE Trans. Information Technology In Biomedicine , Vol. 14, No. 4, 897-903,

• Devrim Unay , Bernard Gosselin.
  (2007) Stem and Calyx Recognition on ‘Jonagold’ Apples by Pattern Recognition.
  Journal Of Food Engineering , Vol. 78, No. 2, 597-605,

International

• Yigit Oktar , Mehmet Turkan.
  (2018) A review of sparsity-based clustering methods.
  Signal Processing , Vol. 148, No. 2018, 20-30,

• Ismail Agababaoglu , Ahmet Onen , Ayse Banu Demir , Safiye Aktas , Zekiye Altun , H Ersoz , A Sanli , N Ozdemir and Atila Akkoclu.
  (2017) Chaperonin (HSP60) and annexin-2 are candidate biomarkers for non-small cell lung carcinoma.
  Medicine (Baltimore) , Vol. 96, No. 6,

• M.U. Ghani , F. Mesadi , S.D. Kanik , A.O. Argunsah , A.F. Hobbiss , I. Israely , D. Unay , T. Tasdizen and M. Cetin.
  (2017) Dendritic Spine Classification using Shape and Appearance Features based on Two-Photon Microscopy.
  Journal Of Neuroscience Methods , No. 279, 13-21,

• Gülizar Çalışkan , Nuri Azbar.
  (2017) Energy Recovery from Conventional Biogas Digester Effluent with a Novel Bioreactor Configuration.
  Waste And Biomass Valorization , Vol. 8, No. 7, 2371-2381,

• Yuriy Mishchenko , Chueng-Ryong Ji.
  (2017) Dark matter phenomenology of high speed galaxy cluster collisions.
  European Physical Journal , Vol. 77,

• Oktay Kaplan , Burak Berber , Nezih Hekim , Osman Doluca.
  (2016) G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.
  Nucleic Acid Research , Vol. 44,

• Yuriy Mishchenko.
  (2016) Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse “shotgun” neuronal activity sampling.
  Journal Of Computational Neuroscience , No. 41,

• Tuğba Keskin Gündoğdu , İrem Deniz , Gülizar Çalışkan , Erdem Sefa Şahin , Nuri Azbar.
  (2016) Experimental design methods for bioengineering applications.
  Critical Reviews In Biotechnology , Vol. 36, No. 2, 368-388, ISBN: 0738-8551

• Yuksel Olgun , Safiye Aktas , Zekiye Altun , Gunay Kirkim , Deniz Kizmazoglu , Pinar Ercetin , Banu Demir , Dilek Ince , Kamer Mutafoglu , Bengu Demirag , Hulya Ellidokuz , Nur Olgun and Enis Alpin Güneri.
  (2016) Analysis of genetic and non genetic risk factors for cisplatin ototoxicity in pediatric patients.
  International Journal Of Pediatric Otorhinolaryngology , Vol. 90,

• David Cash , Chris Frost , Leonardo O. Iheme , Devrim Unay , Melek Kandemir , The Others.
  (2015) Assessing atrophy measurement techniques in dementia: Results from the MIRIAD atrophy challenge.
  NeuroImage , Vol. 123, 149-164,

• Yuriy Mishchenko.
  (2015) A function for fast computation of large discrete Euclidean distance transforms in three or more dimensions in Matlab.
  Signal, Image And Video Processing , Vol. 9,

• Osman Doluca , Jamie Withers , Trevor Loo , Patrick Edwards , Carlos Gonzalez , Vyacheslav Filichev.
  (2015) Interdependence of pyrene interactions and tetramolecular G4-DNA assembly.
  Organic & Biomolecular Chemistry , Vol. 13, No. 12, 3742-3748,

• Nezih Oktar , Yigit Oktar.
  (2015) Machine Learning and Neuroimaging.
  Journal Of Neurological Sciences Turkish , Vol. 32, No. 1, 1-4,

• Ayse Banu Demir , Ahmet Koc.
  (2015) High-Copy Overexpression Screening Reveals PDR5 as the Main Doxorubicin Resistance Gene in Yeast.
  PLoS One , Vol. 10, No. 12, 1-15,

• Rina Rudyanto , Sjoerd Kerkstra , Eva M. Van Rikxoort , Catalin Fetita , Pierre-Yves Brillet , Christophe Lefevre , Wenzhe Xue , Xiangjun Zhu , Jianming Liang , İlkay Öksüz , Devrim Ünay , The Others.
  (2014) Comparing algorithms for automated vessel segmentation in computed tomography scans of the lung: The VESSEL12 study.
  Medical Image Analysis , Vol. 18, No. 7, 1217-1232,

• Yuriy Mishchenko.
  (2014) Oscillations in rational economies.
  Plos ONE , Vol. 9,

• Osman Doluca , Tracy Hale , Patrick Edwards , Carlos Gonzalez , Vyacheslav Filichev.
  (2014) Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence‐Specific Detection of Double‐Stranded DNA.
  ChemPlusChem , Vol. 79, No. 1, 58-66,

• J.-C. Rah , E Bas , J Colonell , Y Mishchenko , B Karsh , R Fetter , E Myers , D Chklovskii , K Svoboda , T Harris , J Isaac.
  (2013) Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.
  Frontiers In Neural Circuits, , Vol. 7,

• Osman Doluca , Jamie Withers , Vyacheslav Filichev.
  (2013) Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes.
  Chemical Reviews , Vol. 113, No. 5, 3044-3083,

• H.A. Kirisli , M Schaap , C.T. Metz , A.S. Dharampal , W.B. Meijboom , D. Unay , The Others.
  (2013) Standardized evaluation framework for evaluating coronary artery stenosis detection, stenosis quantification and lumen segmentation algorithms in computed tomography angiography.
  Medical Image Analysis , Vol. 17, No. 8, 859-876,

• Mert Kaya , Devrim Unay.
  (2013) DressBoard: An Embedded Virtual Try-On System for Ties and Bowties.
  Journal Of Signal Processing Systems , Vol. 73, No. 2, 143-152,

• D Unay.
  (2012) Local and global volume changes of subcortical brain structures from longitudinally varying neuroimaging data for dementia identification.
  Computerized Medical Imaging And Graphics , Vol. 36, No. 6, 464-473,

• Devrim Unay , Cengizhan Ozturk , Maureen Stone.
  (2012) Single Syllable Tongue Motion Analysis Using Tagged Cine MRI.
  Computer Methods In Biomechanics And Biomedical Engineering , Vol. 17, No. 8, 853-864,

• Robert A. Brown , Josephine Wong , Burçak Alp.
  (2012) “ Strategies for direct engineering strong, native collagen-cell constructs: pre-polymerisation”.
  Journal Of Tissue Engineering And Regenerative Medicine , Vol. 6, No. 161,

• Yuriy Mishchenko , Liam Paninski.
  (2012) A Bayesian compressed-sensing approach for reconstruct- ing neural connectivity from subsampled anatomical data.
  Journal Of Computational Neuroscience , Vol. 33,

• Elise Hacioglu , Ayse Banu Demir , Ahmet Koc.
  (2012) Identification of respiratory chain gene mutations that shorten replicative life span in yeast.
  Experimental Gerontology , Vol. 47, No. 2, 149-153,

• M Rivera-Alba , S Vitaladevuni , Y Mishchenko , Z Lu , S Takemura , L Scheffer , I Meinertzhagen , D Chklovskii , G De Polavieja.
  (2011) Wiring economy and volume exclusion determine neuronal placement in the Drosophila brain.
  Current Biology , Vol. 21,

• Yuriy Mishchenko , Liam Paninski.
  (2011) Efficient methods for sampling spike trains in networks of coupled neurons..
  Annals Of Applied Statistics , Vol. 5,

• Yuriy Mishchenko , Joshua Vogelstein , Liam Paninski.
  (2011) A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data.
  Annals Of Applied Statistics , Vol. 5,

• Yuriy Mishchenko.
  (2011) Reconstruction of complete connectivity matrix for connectomics by sampling neural connectivity with fluorescent synaptic markers.
  Journal Of Neuroscience Methods , Vol. 196,

• Yuriy Mishchenko , Tao Hu , J Spacek , J Mendenhall , K Harris , D Chklovskii.
  (2010) Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.
  Neuron , Vol. 67,

• MG Uzunbas , O Soldea , D Unay , M Cetin , G Unal , A Ercil , A Ekin.
  (2010) Coupled Non-Parametric Shape and Moment-Based Inter-Shape Pose Priors for Multiple Basal Ganglia Structure Segmentation.
  IEEE Transactions On Medical Imaging , Vol. 29, No. 12, 1959-1978,

• Ayse Banu Demir , Ahmet Koc.
  (2010) Assessment of chronological lifespan dependent molecular damages in yeast lacking mitochondrial antioxidant genes.
  Biochemical And Biophysical Reearch Community , Vol. 400, No. 1, 106-110,

• Yuriy Mishchenko.
  (2010) On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers.
  Plos ONE , Vol. 5,

• Yuriy Mishchenko.
  (2009) Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs..
  Journal Of Neuroscience Methods , Vol. 176,

• Umber Cheema , Vivek Mudera , Burcak Alp.
  (2009) Identification of key factors in deep O2 cell perfusion for vascular tissue engineering.
  Nternational Journal Of Artificial Organs , Vol. 32,

• Alexandre Boutorine , Osman Doluca , Vyacheslav Filichev.
  (2009) Optimization of the sequence of twisted intercalating nucleic acids (TINA) forming triple helix with the polypurine tract of the proviral HIV DNA.
  Nucleic Acids Symp Series , Vol. 53, No. 1, 139-140,

• Osman Doluca , Emel Ordu , Halil Kısakesen , Richard Sessions , A Clarke , Candan Tamerler , Nevin Karagüler.
  (2008) Effects of cysteine/cystine engineering on thermal stability of formate dehydrogenase from Candida methylica.
  FEBS JOURNAL , Vol. 275, 398-398,

• Zimei Rong , E Leitao , J Popplewell , Burcak Alp , Pankaj Vadagam.
  (2008) Needle enzyme electrode for lactate measurement in vivo.
  IEEE Sensors Journal , Vol. 8(1), 113-,

• Umber Cheema , Robert Brown , Burcak Alp , AJ Mcrobert.
  (2007) Spatially defined oxygen gradients and vascular endothelial growth factor expression in an engineered 3D cell model.
  Cellular And Molecular Life Sciences , Vol. 65(1), 177,

• Umber Cheema , NS Nazhat , Burcak Alp.
  (2007) Fabricating tissues: Analysis of farming versus engineering strategies.
  Biotechnology And Bioprocess Engineering , Vol. 12 (1), 9-,

• Umber Cheema , Burcak Alp , Robert Brown.
  (2006) Perfusion of oxygen in 3D plastic compressed collagen constructs.
  European Cells And Materials , Vol. 11,

• C.-R. Ji , Y Mishchenko , A Radyushkin.
  (2006) Higher Fock state contributions to the gener- alized parton distribution of pion.
  Physical Review D , Vol. 73,

• Yuriy Mishchenko.
  (2006) Remedy for the fermion sign problem in the diffusion Monte Carlo method for few fermions with antisymmetric diffusion process.
  Physical Review E , Vol. 73,

• Y Mishchenko.
  (2005) Exploring properties of dark and visible mass distribution on different scales in the Universe.
  International Journal Of Modern Physics A , Vol. 20,

• C Ji , Y Mishchenko.
  (2005) Time to space conversion in quantum field theory of flavor mixing.
  Annals Of Physics , Vol. 315,

• B Bakker , M DeWitt , C-R Ji , Y Mishchenko.
  (2005) Restoring the equivalence between the light-front and manifestly covariant formalisms.
  Physical Review D , Vol. 72,

• Y Mishchenko , C Ji.
  (2005) A novel variational approach for quantum field theory: example of study of the ground state and phase transition in nonlinear sigma model..
  International Journal Of Modern Physics A , Vol. 20,

• A Capolupo , C Ji , Y Mishchenko , C Vitiello.
  (2004) Phenomenology of flavor oscilla- tions with nonperturbative effects from quantum field theory.
  Physics Letters B , Vol. 594,

• Burcak Alp , Joe Andrews , Gerard Markx.
  (2003) Building of structured biomaterials using AC electrokinetics.
  IEE Engineering In Medicine And Biology , Vol. 22 (6), 91,

• CE Verduzco-Lique , Burcak Alp , Gill Stephens , Gerard Markx.
  (2003) Construction of biofilms with defined internal architecture using dielectrophoresis and flocculation.
  Biotechnology And Bioengineering , Vol. 83(1) 34-4,

• Y Mishchenko , C Ji.
  (2003) Molar mass estimate of dark matter from the dark mass distribution measurements.
  Physical Review D , Vol. 68,

• Burcak Alp , Gill Stephens , Gerard Markx.
  (2002) Formation o artificial, structured microbial consortia (ASMC) by dielectrophoresis.
  Enzyme And Microbial Technology , Vol. 31, (35-43,

• Gerard Markx , Burcak Alp , A McGilchrist.
  (2002) Electro-orientation of Schizosaccharomyces pombe in high conductivity media.
  Journal Of Microbiological Methods , Vol. 50, (52-62,

• C Ji , Y Mishchenko.
  (2002) The general theory of quantum field mixing.
  Physical Review D , Vol. 65,

• C Ji , Y Mishchenko.
  (2001) Nonperturbative vacuum effect in the quantum field theory of meson mixing.
  Physical Review D , Vol. 64,

• Burcak Alp , Selma Mutlu , Mehmet Mutlu.
  (2000) Glow-discharge-treated Cellulose Acetate (CA) membrane for a high linearity single-layer glucose electrode in food industry.
  Food Research International , Vol. 33(2), 107,

• Selma Mutlu , Burcak Alp , Serpil Ozmelles , Mehmet Mutlu.
  (1997) Amperometric determination of enzymatic activity by multienzyme biosensors.
  Journal Of Food Engineering , Vol. 33(1-2), 8,

Published or accepted to be published in journals covered by other indexes

National

• Yurıy Mishchenko , Mustafa Cömert , Murat Kaya.
  (2017) Beyin bilgisayar arayüzü için DVM makine öğrenme yöntemi kullanılarak EEG verilerinden sağ ve sol el hareket düşüncelerinin tespiti.
  TÜBAV Bilim Dergisi , Vol. 10, No. 3, 1-20,

International

• Ayse Banu Demir , Namik Demir.
  (2017) Epigenetic Basis of Twin Discordance in Diseases: Future Benefits.
  GYNECOLOGY OBSTETRICS & REPRODUCTIVE MEDICINE , Vol. 24,

• Osman Akirmak , Cagdas Tatar , Ziya Gokalp , Yuriy Mishchenko.
  (2017) Design of an Accessible, Powered Myoelectrically Controlled Hand Prosthesis.
  TEM Journal , Vol. 6, No. 3, 479-483,

• Yuriy Mishchenko.
  (2016) Application of the radial distribution function for quantitative analysis of neuropil microstructure in stratum radiatum of CA1 region in hippocampus.
  Medical Research Archives , Vol. 4,

• Mikael Molin , Ayse Banu Demir.
  (2014) Linking Peroxiredoxin and Vacuolar-ATPase Functions in Calorie Restriction-Mediated Life Span Extension.
  İnternational Journal Of Cell Biology , Vol. 2014, 1-12,

• Gulizar Caliskan , Gokhan Giray , Tugba Keskin Gundogdu , Nuri Azbar.
  (2014) Anaerobic Biodegradation of Beer Production Wastewater at a Field Scale and Explotation of Bioenergy Potential of Other Solid Wastes from Beer Production.
  International Journal Of Renewable Energy & Biofuels , Vol. 2014 (2014, 1-15,

Published or accepted to be published in refereed journals

• Duygu Karaalp , Gülizar Çalışkan , Nuri Azbar.
  (2013) Performance Evaluation of a Biogas Reactor Processing Chicken Manure with High Solids Content.
  Journal Of Selcuk University Natural And Applied Science ,