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

International

  • Sezgi Adalıoğlu and Gülizar Çalışkan.
    (2019) Effect of Nutrient, Light Intensity and Temperature on the Growth Rates and Metabolism of a Stress-Resistant Bacillariophyta – Entomoneis sp. - in Izmir Bay (Aegean Sea).
    Mediterranean Marine Science ,
  • Gülizar Çalışkan and 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 and Chueng-Ryong Ji.
    (2017) Dark matter phenomenology of high speed galaxy cluster collisions.
    European Physical Journal , Vol. 77,
  • Tuğba Keskin Gündoğdu , İrem Deniz , Gülizar Çalışkan , Erdem Sefa Şahin and Nuri Azbar.
    (2016) Experimental design methods for bioengineering applications.
    Critical Reviews In Biotechnology , Vol. 36, No. 2, 368-388, ISBN: 0738-8551
  • 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,
  • 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 and Vyacheslav Filichev.
    (2015) Interdependence of pyrene interactions and tetramolecular G4-DNA assembly.
    Organic & Biomolecular Chemistry , Vol. 13, No. 12, 3742-3748,
  • 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 and 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,
  • 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,
  • 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,
  • 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.
    (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 , Tao Hu , J Spacek , J Mendenhall , K Harris , D Chklovskii.
    (2010) Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.
    Neuron , Vol. 67,
  • 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,
  • 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,
  • 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,
  • 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 , NS Nazhat , Burcak Alp.
    (2007) Fabricating tissues: Analysis of farming versus engineering strategies.
    Biotechnology And Bioprocess Engineering , Vol. 12 (1), 9-,
  • 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 , 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,
  • 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,
  • 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,
  • 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,
  • C Ji , Y Mishchenko.
    (2002) The general theory of quantum field mixing.
    Physical Review D , Vol. 65,
  • 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.
    (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

  • 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,
  • 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 ,
  • Gülizar Çalışkan , Tuğçe Mutaf , Suphi Öncel , Murat Elibol.
    (2019) GREEN SYNTHESIS OF METAL NANOPARTICLES USING MICROALGA Galdieria sp..
    CMBEBIH 2019 Proceedings Of The International Conference On Medical And Biological Engineering, 16–18 May 2019 Banja Luka, Bosnia And Herzegovina
    ISBN: 978-3-030-17970-0
  • Tuğçe Mutaf , Gülizar Çalışkan , Suphi Öncel , Cafer Meydan , Murat Elibol.
    (2019) Biogenic Nanoparticle Synthesis Using Marine Alga Schizochytrium sp..
    CMBEBIH 2019 Proceedings Of The International Conference On Medical And Biological Engineering, 16–18 May 2019 Banja Luka, Bosnia And Herzegovina
  • Murat Kaya , Çiğdem Çiğdem Aci , Yuriy Mishchenko.
    (2018) A passive brain-computer interface for monitoring mental attention state.
    26th Signal Processing And Communications Applications Conference SIU2018
  • Gülizar Çalışkan , Tuğçe Mutaf , Merve Türemen , Aslı Demir , Murat Elibol.
    (2018) Preparation of Biocomposite Material Using Chitosan-Aloe vera- Silver Nanoparticles Synthesized in Centaury Plant Extract and Their Synergistic Activities on Textile Industry.
    4. International Symposium On Composite Materials-KOMPEGE 2018
  • Sezgi Adalıoğlu , Gülizar Çalışkan.
    (2018) Farklı Işık Şiddetlerinin, Fotosentetik Mikroalg Kültürlerindeki Kimyasal Değişimleri.
    4. International Symposium On Composite Materials-KOMPEGE 2018
  • Yuriy Mishchenko.
    (2017) Developing a 3- to 6-state slow cortical potentials Brain-Computer Interface for high performance control of a 3D robotic manipulator.
    BIT / BITs 8th Annual World Congress Of NeuroTalk 2017
  • Y Mishchenko , M Kaya , H Yanar , E Ozbay.
    (2016) Characterization of the key properties of electroencephalographic signal for noninvasive brain machine/computer interface applications.
    Society For Neuroscience Annual Meeting 2016
  • Gülizar Çalışkan , Sezgi Adalıoğlu.
    (2016) İzmir Körfezinde Mevsimsel Değişimlerin Ditylum brightwellii Üzerindeki Etkisi ve Büyüme Kinetiğinin Matematiksel Modellenmesi.
    Türkiye Deniz Bilimleri Konferansı
  • M Kaya , H Yanar , Y Mishchenko.
    (2016) Developing computational infrastructure for an EEG- based brain computer interface.
    24th IEEE Signal Processing And Communications Applications Conference SIU2016
  • Erkan Ozbay , Yuriy Mishchenko , Murat Kaya , Hilmi Yanar.
    (2016) Control of a virtual robotic hand manipulator using a non-invasive EEG-based brain-machine interface.
    Proceedings Of 1st International Mediterranean Science And Engineering Congress (IMSEC 2016)
    1006-1007,
  • H Yanar , Y Mishchenko.
    (2016) A hidden Markov Model of electroencephalographic brain activity for advanced EEG-based brain computer interfaces.
    24th IEEE Signal Processing And Communications Applications Conference SIU2016
  • Y Mishchenko , M Kaya.
    (2015) Detecting the attention state of an operator in continuous attention task using EEG-based Brain-Computer Interface.
    23rd IEEE Signal Processing And Commu- Nications Applications Congress SIU2015
  • O Akirmak , M Miman , Y Mishchenko.
    (2014) A system for lane-tracking suitable for day and night conditions.
    4th Regional Project Fair Of East Mediterranean Universities
  • M Kaya , Y Mishchenko , H Seckin.
    (2014) Methods for direct brain-computer communications using a Brain-Computer Interface.
    4th Regional Project Fair Of East Mediterranean Universities
  • Y Mishchenko.
    (2014) ”Reconstructing functional connectivity in complete neural populations by randomized sparse sampling.
    COSYNE 2014 Conference
  • E Onel , Y Mishchenko , M Miman.
    (2014) The relationships between use features of Information Management Systems.
    Congress On Information Management Systems YBS2014
  • Sezgi Adalıoğlu , Gülizar Çalışkan.
    (2014) Growth Rate in Response to pH Levels and Different Size Fraction Of Plankton in Izmir Bay.
    Congress On Information Management Systems YBS2014
  • Gülizar Çalışkan , Tuğba Keskin Gündoğdu , Gökhan Giray , Nuri Azbar.
    (2013) A REFERENCE PROCESS FOR BIOENERGY RECOVERY FOR THE EVALUATION OF BEER INDUSTRY WASTES .
    Istanbul International Solid Waste, Water And Wastewater Congress (3W)
  • Duygu Karaalp , Gülizar Çalışkan , Nuri Azbar.
    (2013) Performance Evaluation of a Biogas Reactor Processing Chicken Manure with High Solids Content .
    The International Conference On Environmental Science And Technology (ICOEST)
  • Gülizar Çalışkan , Barış Ayhan , Nuri Azbar.
    (2012) BİRA SANAYİ ATIKLARININ BİYOENERJİYE DÖNÜŞÜMÜNÜN İNCELENMESİNDE ÖRNEK BİR ÇALIŞMA .
    Ulusal Katı Atık Yönetimi (UKAY)
  • Y Mishchenko.
    (2012) Fluorescent co-localization synaptic markers for connectome reconstructions.
    8th FENS Forum Of Neuroscience
  • Gülizar Çalışkan , Barış Ayhan , Nuri Azbar.
    (2011) SOLID WASTE MANAGEMENT AT BEER FACTORIES AND ENERGY RECOVERY.
    Türk Alman Katı Atık Günleri (TAKAG)
  • Y Mishchenko , L Paninski.
    (2011) Efficient methods for sampling spike trains in networks of coupled neurons.
    COSYNE 2011 Conference
  • J Vogelstein , T Machado , Y Mishchenko , A Packer , R Yuste , L Paninski.
    (2010) Methods for in vitro neural circuit inference from population calcium imaging data.
    COSYNE 2010 Conference
  • Y Mishchenko , J Vogelstein , L Pan.
    (2009) Statistical reconstruction of neural connectiv- ity from the data produced.
    Society For Neuroscience Annual Meeting 2009
  • J Vogelstein , Y Mishchenko , A Packer , T Machado , R Yuste , L Paninski.
    (2009) Towards confirming neural circuit inference from population calcium imaging..
    Society For Neuroscience Annual Meeting 2009
  • J Vogelstein , Y Mishchenko , A Packer , T Machado , R Yuste , L Paninski.
    (2009) Towards confirming neural circuit inference from population calcium imaging.
    NIPS 2009 Workshop On Connectivity Inference In Neuroimaging
  • Burcak Alp , Umber Cheema , Vivek Mudera , Robert Brown.
    (2008) Rapid tissue fabrication by plastic compression.
    Biomed 2008
  • Burcak Alp , Gordon Blunn , Robert Brown.
    (2007) Automated Rapid Tissue Fabrication Device:Prototype and Proof of Principle, Plastic.
    Reconstructive And Aesthetic Surgery Stem Cell And Tissue Engineering Symposium
  • Burcak Alp , Zimei Rong , Umber Cheema , Robert Brown.
    (2007) Measurement of glucose and oxygen concentration in biomimetic constructs.
    TERMIS, European Chapter Meeting
  • Umber Cheema , Burcak Alp , AJ Macrobert , Robert Brown.
    (2007) Monitoring Oxygen Depletion at the Core of Engineered Implants.
    The Stem Cell And Tissue Engineering In Plastic, Reconstructive And Aesthetic Surgery
  • Burcak Alp , Gerard Markx.
    (2006) Patterning of mammalian cells by dielectrophoresis for the study of their interaction through NOTCH signalling.
    Biodielectrics: Theories, Mechanisms, Applications
  • Burcak Alp , Zimei Rong , Vivek Mudera , Pankaj Vadgama , Robert Brown.
    (2006) Glucose monitoring in plastic compressed and double compressed collagen constructs: Implication for tissue engineering.
    TERMIS, European Chapter Meeting
  • Burcak Alp , Paul Kemp , Richard Wolowacz , Gerard Markx.
    (2004) On-line monitoring of cell biomass in skin tissue constructs using dielectric spectroscopy.
    The Eight World Congress On Biosensors
  • Burcak Alp , Gerard Markx.
    (2002) Patterning of cells in AC electric fields.
    Electromagnetic Methods In Pharmacy And Medicine
  • Yuriy Mishchenko - -.
    (2009) Nontrivial vacuum solutions in flavor mixing and critical phenomena.
    VDM Verlag: Saarbrucken ,
    Author
  • Y Mishchenko , C Ji.
    General formulation of flavor mixing in Quantum Field Theory.
    115-149
    O Kovras.
    Focus on Quantum Field Theory.
    (2005), Nova Science Publisher,
  • C Ji , Y Mishchenko , A Shalaby.
    Duality and canonical transformations in the scalar field theory.
    1487-1510
    S Pandalai.
    Recent Developments in Physics.
    (2004), Transworld Research Network, Vol. 5,
  • Y Mishchenko , C Ji.
    Distribution of mass in galaxy cluster CL0024 and the particle mass of dark matter.
    217-239
    J Val Blain.
    Progress in Dark Matter Research.
    (2004), Nova Science Publisher,