Adan A, Alizadeh G, Kiraz Y, Nalbant A, Baran Y. Flow cytometry: Basic Principles and Applications. 2017, Critical Reviews in Biotechnology.

Işık S, Karaman M, Adan A, Kıray M, Bağrıyanık HA, Sözmen ŞÇ, Kozanoğlu İ, Karaman Ö, Baran Y, Uzuner N. Intraperitoneal mesenchymal stem cell administration ameliorates allergic rhinitis in the murine model. 2017, Eur Arch Otorhinolaryngol.

Amuk NG, Kurt G, Baran Y, Seyrantepe V, Kartal-Yandim M, Adan A, Sönmez MF. Effects of Cell-Mediated Osteoprotegerin Gene Transfer and Mesenchymal Stem Cell Applications on Orthodontically Induced Root Resorption of Rat Teeth. In Press, 2017, European Journal of Orthodontics.

Karaçavuş S, Yılmaz B, Taşdemir A, Kayaaltı Ö, Kaya E, İçer S, Ayyildiz O. Can Laws' be a potential PET image texture analysis approach for evaluation of tumor heterogeneity and histopathological characteristics in NSCLC? Basım Aşamasında, 2017, J Digital Imaging.

Karaçavuş S, Yılmaz B., Kayaaltı Ö, İçer S, Taşdemir A, Ayyildiz O, Eset K, Kaya E. Automatic Staging and Subtype Determination for Non Small Cell Lung Carcinoma Using PET Image Texture Analysis. 10(2), 123-126, 2016, International Journal of Biological, Biomolecular, Agricultural, Food and Biotechnological Engineering.


Kartal Yandım M, Adan A, Baran Y. Molecular mechanisms of drug resistance and its reversal in cancer. 2016, Critical Reviews in Biotechnology.

Kiraz Y, Adan A, Kartal Yandim M, Baran Y. Major apoptotic mechanisms and genes involved in apoptosis. 2016, Tumor Biology.

Adan A, Kiraz Y, Baran Y. Cell Proliferation And Cytotoxicity Assays. 2016, Curr Pharm Biotechnol.

Amuk NG, Kurt G, Baran Y, Seyrantepe V, Yandim MK, Adan A, Demir SA4, Kiraz Y, Sonmez MF. Effects of cell-mediated osteoprotegerin gene transfer and mesenchymal stem cell applications on orthodontically induced root resorption of rat teeth. 2016, Eur J Orthod.

Kiraz Y, Neergheen-Bhujun VS, Rummun N, Baran Y. Apoptotic Effects Of Non-Edible Parts Of Punica Granatum On Human Multiple Myeloma Cells. Basım Aşamasında, 2016, Tumor Biology.

Adan A, Baran Y. Fisetin and hesperetin induced apoptosis and cell cycle arrest in chronic myeloid leukemia cells accompanied by modulation of cellular signaling. 2016. Tumor Biology.

Nalbant A, Kiraz Y, Baran Y. T cells in Tumor Microenvironment. Basım Aşamasında, 2016, Tumor Biology.

Adan A, Alizada G, Kiraz Y, Nalbant A, Baran Y. Flow cytometry: Basic principles and applications. Basım Aşamasında, 2016, Critical Reviews in Biotechnology.

Kiraz Y, Adan A, Kartal Yandim M, Baran Y. Major apoptotic mechanisms and genes involved in apoptosis. Basım Aşamasında, 2016, Tumor Biology.

Mzava O, Tas Z, Icoz K, Magnetic micro/nanoparticle flocculation-based signal amplification for biosensing, International Journal Of Nanomedicine, vol:11, 2619-2631, 2016

Icoz K, Image Processing and Cell Phone Microscopy to Analyze the Immunomagnetic Beads on Micro-Contact Printed Gratings, Appl. Sci. 2016, 6(10), 279, 2016.

Icoz K, Mzava O, Detection of Proteins Using Nano Magnetic Particle Accumulation-Based Signal Amplification, Applied Sciences 6 (12), 394.

İ.A. İşoğlu, Y. Özsoy, S. Dinçer İşoğlu, Advances in micelle-based drug delivery: Cross-linked systems, Current Topics in Medicinal Chemistry, in press.

K. Salimi, M. Topuzoğulları, S. Dinçer, H.M. Aydın, E. Pişkin, “Microwave-asisted green approach for graft copolymerization of L-lactic acid onto starch”, Journal of Applied Polymer Science, 2016, 133, 42937.

M. Ertas, I. Yildirim, M. Kamasak, A. Akan, "Iterative Image Reconstruction Using Non-Local Means with Total Variation from Insufficient Projection Data", Journal of X-Ray Science and Technology, vol. 24, no. 1, pp. 1-8, 2016, DOI: 10.3233/XST-160529.


M. Kartal Yandım, A. Adan , Y. Baran. Molecular mechanisms of drug resistance and its reversal in cancer, Critical Reviews in Biotechnology. 2015, 24,1-11 (Epub ahead of print).

A. Adan, Y. Baran. A Novel Natural Product, KL-21, Inhibits Proliferation and Induces Apoptosis in Chronic Lymphocytic Leukemia Cells, Turkish Journal of Hematology, 2015, 32(2), 118-26.

M. Kartal Yandım, A. Adan, Y. Kiraz, Y. Baran. Rejenerative Medicine. Turkiye Klinikleri J Med Oncol-Special Topics, 2015, 8(2).

A. Adan, Y. Baran. The Pleiotropic Effects of Fisetin and Hesperetin on Human Acute Promyelocytic Leukemia Cells Are Mediated through Apoptosis, Cell Cycle Arrest and Alterations in Signaling Networks, Tumor Biology, 2015, 36(11),8973-84.

B. Tezcanlı Kaymaz, N. Selvi Günel, M. Ceyhan, V. Bozok Çetintaş, B. Özel, M. Kartal Yandım, S. Kıpçak, Ç. Aktan, A. Adan, Y. Baran, B. Kosova Can. Revealing Genome Wide mRNA and microRNA Expression Patterns in Leukemic Cells Highlighted "hsa-miR-2278" as a Tumor Suppressor for Regain of Chemotherapeutic İmatinib Response due to Targeting STAT5A. Tumor Biology, 2015, 36(10),7915-27.

A. Adan, Y. Baran. Fisetin and Hesperetin Induced Apoptosis and Arrested Cell Cycle in Chronic Myeloid Leukemia Cells Accompanied by Modulation of Cellular Signaling, Tumor Biology (Epub ahead of print).

A. Katgı, O.G. Sevindik, A.Adan, G.H. Ozsan, F. Yüksel, S.M. Solmaz, I. Alacacıoğlu, M.A. Ozcan, F. Demirkan, Y. Baran, O. Pişkin. Nilotinib Does Not Alter the Secretory Functions of Carotid Artery Endothelial Cells in a Prothrombotic or Antithrombotic Fashion. Clin Appl Thromb Hemost, 2015, 21(7), 678-83

Khaskheli, A.A., Talpur, F.N., Ashraf, M.A., Jawaid, S., Cebeci A., Afridi, H.I. (2015) Monitoring the Rhizopus oryzae lipase catalyzed hydrolysis of castor oil by ATR-FTIR spectroscopy. Journal of Molecular Catalysis B: Enzymatic. 113: 56-61.

Güngormüş C, Kolankaya D, Aydin E. Histopathological and Biomechanical Evaluation of Tenocyte Seeded Allografts on Rat Achilles Tendon Regeneration. Biomaterials Vol 51, May 2015:108–118.

Goldberg M, Manzi A, Aydin E, Singh G, Khoshkenar P, Birdi A, LaPorte B, Krauskopf A, Powell G, Chen J, Langer R. Development of a Nanoparticle- Embedded Chitosan Sponge for Topical and Local Administration of Chemotherapeutic Agents.
J Nanotechnol Eng Med. 2014 Nov;5(4):0409051-4090511.

Adan A, Baran Y. The Pleiotropic Effects of Fisetin and Hesperetin on Human Acute Promyelocytic Leukemia Cells Are Mediated through Apoptosis, Cell Cycle Arrest and Alterations in Signaling Networks. Tumor Biology, 2015; 36(11): 8973-8984.

Mutlu P, Kiraz Y, Gündüz U, BaranY. An Update On Molecular Biology And Drug Resıstance Mechanısms Of Multıple Myeloma. Critical Reviews in Oncology/Hematology2015; 96(3): 413-424.

Cincin ZB, Unlu M, Kiran B, Bireller ES, Kiraz Y, Baran Y, Cakmakoglu B*. Anti-proliferative, apoptotic and signal transduction effects of hesperidin in non-small cell lung cancer cells. Cellular Oncology, 2015; 38(3): 195-204.

E. Kahraman, A. Karagöz, S. Dinçer İşoğlu, Y. Özsoy, “Polyethylenimine modified and non-modified polymeric micelles used for nasal administration of carvedilol (or medication)", Journal of Biomedical Nanotechnology, 2015, 11, 890-899.

S. Emmrich, F. Engeland, M. El-Khatib, K. Henke, J. E. Katsman-Kuipers, C. M. Zwaan, A. Pich, D. Reinhardt , M. W. J. Fornerod, M. M. van den Heuvel-Eibrink, J. H. Klusmann, miR-139-5p controls translation in myeloid leukemia through EIF4G2, Oncogene, 2015. (DOI: 10.1038/onc.2015.247)

Y. Alapan, K. Icoz, U.A. Gurkan, "Micro -and nanodevices integrated with biomolecular probes" Biotechnology Advances 2015, 09, 01, doi :10 .1016 / j.biotechadv.2015.09.01

K. Icoz, V. A. Sanalan, M. A. Cakar, E. B. Ozdemir, S. Kaya, "Using Students’ Performance to Improve Ontologies for Intelligent E-Learning System" Educational Sciences: Theory and Practice, 2015, 15, 4 DOI: 10.12738/estp.2015.4.2645

J. J. Madsen, Y. Z. Ohkubo, G. H. Peters, J. H. Faber, E. tajkhorhsid, O. H. Olsen, Membrane interaction of the factor VIIIa discoidin domains in atomistic detail,Biochemistry, 2015, 54, 6123 (DOI: 10.1021/acs.biochem.5b00417)

K. Tasdemir, B. Yalcin, I. Yildirim, “Approximate Spectral Clustering with Utilized Similarity Information using Geodesic Based Hybrid Distance Measures” Pattern Recognition, Volume 48, Issue 4, April 2015, Pages 1465–1477,  DOI:10.1016/j.patcog.2014.10.023

K. Tasdemir, Y. Moazzen, I. Yildirim, "An Approximate Spectral Clustering Ensemble for High Spatial Resolution Remote-Sensing Images," IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, ,vol.8, no.5, pp.1996-2004, May 2015, DOI: 10.1109/JSTARS.2015.2424292.


LY. Aydemir, A. Adan, Y. Baran, A. Yemenicioglu. Bioactive, functional and edible film making properties of different protein isolates from Turkish hazelnut (Corylus avellana L.) meal obtained from oil extraction, Food Hydrocolloids, 2014; 36,130-142. 

S. Solmaz, A. Adan, B. Cincin, H. Ozdogu, C. Boga, B. Cakmakoglu,  I. Kozanoglu,  Y. Baran. Therapeutic Potential of Apigenin, a Plant Flavonoid, for Imatinib-Sensitive and Resistant Chronic Myeloid Leukemia Cells. Nutrition and Cancer, 2014, 66(4),599-612.

Kiraz Y, Unlu M, Kartal Yandim M, Baran Y. Molecular Biology of Stem Cells. Hematolog, 2014: 4(2); 255-265.

Unlu M, Kiraz Y, Kacı FN, Baran Y. Multidrug Resistance in Chronic Myeloid Leukemia. Turkish Journal of Biology, 2014;38(6):806-816.

M. Topuzoğulları, E.V. Bulmuş Zareie, E. Dalgakıran, S. Dinçer, “pH- and temperature-responsive amphiphilic diblock copolymers of 4-vinylpyridine and oligoethyleneglycol methacrylate synthesized by RAFT polymerization”, Polymer, 55(2): 525-534.

A. Wutka, V. Palagani, S. Barat, X. Chen, M. El Khatib, J. Götze, H. Belahmer, S. Zender, P. Bozko, N. P. Malek, R. R. Plentz, Capsaicin Treatment Attenuates Cholangiocarcinoma Carcinogenesis, PLoS ONE, 2014, 9, 1-9 (DOI:10.1371/journal.pone.0095605)

V. Palagani, P. Bozko, M. El Khatib, H. Belahmer, N. Giese, B. Sipos, N. P. Malek, R. R. Plentz, Combined inhibition of Notch and JAK/STAT is superior to monotherapies and impairs pancreatic cancer progression, Carcinogenesis, 2014, 35, 859-66 (DOI: 10.1093/carcin/bgt394)

B-D. Chan, K. Icoz, W. Huang, C-L. Chang and C. A. Savran, "On-demand weighing of single dry biological particles over a 5-order-of-magnitude dynamic range" Journal Article Lab Chip, 2014,14, 4188-4196, DOI: 10.1039/C4LC00765D, from themed collection Lab on a Chip 2014 HOT Articles

M. Ertas, I. Yildirim, M. Kamasak, A. Akan, "An Iterative Tomosynthesis Reconstruction Using Total Variation Combined with Non-local Means Filtering", Biomedical Engineering Online, 2014, DOI:10.1186/1475-925X-13-65, 13:65

E. Oznergiz, Y.E. Kiyak, M. Kamasak, and I. Yildirim, “Automated Nanofiber Diameter Measurement in SEM Images Using a Robust Image Analysis Method,” Journal of Nanomaterials, vol. 2014, Article ID 738490, 6 pages, 2014, DOI:10.1155/2014/738490

M. H. Asyalı, S. Kara, B. Yılmaz, Biyomedikal Mühendisliğinin Temelleri (Fundamentals of Biomedical Engineering), 782 pp., Ankara, Nobel Publications, 2014.

E. Akdoğan, E. Kaplanoğlu, B. Yılmaz, Biyomedikal Mühendisliğinin Temelleri (Fundamentals of Biomedical Engineering), Rehabilitasyon Mühendisliği ve Yardımcı Teknolojiler (Rehabilitation Engineering and Assistive Technologies), Ankara, Nobel Publications, 2014.

M. H. Asyalı, B. Yılmaz, K. Polat, K. İçöz, Biyomedikal Mühendisliğinin Temelleri (Fundamentals of Biomedical Engineering), Biyosinyal İşleme (Biosignal Processing), Ankara, Nobel Publications, 2014.

T. Özdür, B. Yılmaz, Sait N. Mutlu “Bir Göz İçi Basıncı Ölçüm Cihazı (An Intraocular Pressure Measurement Device)”, TPE (Turkish Patent Institute), 2014/13817, (submitted)

Yılmaz, B., S. Korkmaz, D.B. Arslan, E. Güngör, M.H. Asyalı, Like/Dislike Analysis Using EEG: Determination of Most Discriminative Channels and Frequencies, Computer Methods and Programs in Biomedicine, 113(2), 705-713, (2014)

Kayaaltı, Ö., B. H. Aksebzeci, İ. Ö. Karahan, K. Deniz, M. Öztürk, B. Yılmaz, S. Kara, M. H. Asyalı, On The Staging of the Liver Fibrosis Using Image Processing, Applied Soft Computing, 25, 399–413 (2014)


A. Adan, E. Apohan, Y. Baran. Resveratrol and quercetin induced apoptosis of human 232B4 chronic lymphocytic leukemia cells by activation of caspase-3 and cell cycle arrest. Hematology, 2013, 18(3),144-50.

A. Adan, M. Kartal-Yandim, G.Iskender, Y. Baran. Novel Agents Targeting Bioactive Sphingolipids for the Treatment of Cancer, Current Medicinal Chemistry, 2013, 20, 108-122.

BT. Kaymaz, N. Selvi, A. Adan, Ç. Aktan, C. Gündüz, G. Saydam, F. Şahin , VB. Çetintaş, Y. Baran, B. Kosova. Suppression of STAT5A and STAT5B Chronic Myeloid Leukemia Cells via siRNA and Antisense-Oligonucleotide Applications with the Induction of Apoptosis, American Journal of Blood Research, 2013; 3(1), 58-70.

A. Adan, A. Arslanoglu. Purification and biochemical characterization of an extracellular lipase from a psychrotolerant Pseudomonas fluorescens KE38, Turkish Journal of Biology, 2013, 37,538-546.

HD. Kiper, B. Tezcanli, A. Adan, N. Selvi, CB. Avci, BK. Kosova, G. Iskender, MK. Yandım, C. Gunduz, F. Sahin, Y. Baran, G. Saydam . STAT pathway in the regulation of zoledronic acid-induced apoptosis in chronic myeloid leukemia cells, Biomedicine and Pharmacotherapy, 2013; 67(6), 527-532.

Khaskheli A. A., Talpur F. N., Demir A. S., Cebeci A. and Jawaid S. (2013) A highly selective whole cell biocatalysis method for the production of two major bioactive conjugated linoleic acid isomers. Biocatalysis and Agricultural Biotechnology 4: 328–332.

Kiper HD, Tezcanli B, Gokbulut AA, Selvi N, Avci CB, Kosova BK, Iskender G, Yandım MK, Gunduz C, Sahin F, Baran Y, Saydam G. STAT pathway in the regulation of zoledronic acid-induced apoptosis in chronic myeloid leukemia cells. Biomedicine and Pharmacotherapy2013; 67(6):527-532.

G. Uzunalan, M. Tuzlakoglu Ozturk, S. Dinçer, and K. Tuzlakoglu, “A Newly Designed Collagen-Based Bilayered Scaffold for Skin Tissue Regeneration”, J of Composites and Biodegradable Polymers (inaugrual issue), invited research article, Dec 2013, 1, 8-15.

Z. Ozdemir, M. Topuzogullari, I.A. Isoglu, S. Dincer, “RAFT-mediated synthesis of poly(N-(2-hydroxypropyl)methacrylamide-b-4-vinylpyridine) by conventional and microwave heating”, Polymer Bulletin, 2013, 2857-2872.

M. Topuzogullari, R.C. Koc, S. Dincer Isoglu, M. Bagirova, Z. Akdeste, S. Elcicek, O.N. Oztel, S. Yesilkir Baydar, S. Canim Ates, A.M. Allahverdiyev, “Conjugation, characterization and toxicity of lipophosphoglycan-polyacrylic acid conjugate for vaccination against leishmaniasis”, J of Biomedical Science, 2013, DOI:10.1186/1423-0127-20-35.

Cevik S, Sanders AA, Van Wijk E, Boldt K, Clarke L, van Reeuwijk J, Hori Y, Horn N, Hetterschijt L, Wdowicz A, Mullins A, Kida K, Kaplan OI, van Beersum SE, Man Wu K, Letteboer SJ, Mans DA, Katada T, Kontani K, Ueffing M, Roepman R, Kremer H, Blacque OE. Active transport and diffusion barriers restrict Joubert Syndrome-associated ARL13B/ARL-13 to an Inv-like ciliary membrane subdomain. PLoS Genet. 9(12):e1003977. doi: 10.1371/journal.pgen.1003977.

S. Emmrich, J. E. Katsman-Kuipers, K. Henk, M. E. Khatib, R. Jammal, F. Engeland, F. Dasci, C. M. Zwaan, M. L. den Boer, L. Verboon, J. Stary, A. Baruchel, V. de Haas, A. A. Danen-van Oorschot, M. Fornerod, R. Pieters, D. Reinhardt, J. H. Klusmann, M. M. van den Heuvel-Eibrink, miR-9 is a tumor suppressor in pediatric AML with t(8;21), Leukemia, 2013,  28, 1022-32 (DOI:10.1038/leu.2013.357)

M. El Khatib, P. Bozko, V. Palagani, N. P. Malek, L. Wilkens, R. R. Plentz, Activation of Notch signaling is required for cholangiocarcinoma progression and is enhanced by inactivation of p53 in vivo, PLoS One, 2013, 8, 1-9 (DOI: 10.1371/journal.pone.0077433

M. E. Stankov, M. El Khatib, B. Kumar Thakur, K. Heitmann, D. Panayotova-Dimitrova, J. Schoening, J. P. Bourquin, N. Schweitzer, M. Leverkus, K. Welte, D: Reinhardt, Z. Li, S. H. Orkin, G. M. Behrens, J. H. Klusmann, Histone deacetylase inhibitors induce apoptosis in myeloid leukemia by suppressing autophagy, Leukemia, 2013, 28, 577-88 (DOI:10.1038/leu.2013.264)

S. Zender, I. Nickeleit, T. Wuestefeld, I. Sörensen, D. Dauch, P. Bozko, M. El-Khatib, R. Geffers, H. Bektas, M. P. Manns, A. Gossler, L. Wilkens, R. Plentz, L. Zender, N. P. Malek. A critical role for notch signaling in the formation of cholangiocellular carcinomas, Cancer Cell, 2013, 23, 784-95 (DOI: 10.1016/j.ccr.2013.04.019)

M. El Khatib, A. Kalnytska, V. Palagani, U. Kossatz, M. P. Manns, N. P. Malek, L Wilkens, R. R. Plentz, Inhibition of hedgehog signaling attenuates carcinogenesis in vitro and increases necrosis of cholangiocellular carcinoma, Hepatology, 2013, 57, 1035-45 (DOI: 10.1002/hep.26147)

B-D. Chan, K. Icoz, R.L. Gieseck, and C.A. Savran, “Selective weighing of individual microparticles using a hybrid micromanipulator-nanomechanical resonator system,” IEEE Sensors, vol. 13, no. 8, pp. 2857-2862, 2013.

I. Yildirim, R. Ansari, I.S. Yetik, M. Shahidi, "Direct Regularized Estimation of Retinal Vascular Oxygen Tension Based on an Experimental Model", Annals of Biomedical Engineering, 2285- 2295 pp., 2013, DOI: 10.1007/s10439-013-0831-5

G. Gunay, I. Yildirim, "A Fast Regularized Least-Squares Method for Retinal Vascular Oxygen Tension Estimation using a Phosphorescence Lifetime Imaging Model", Biomedical Engineering Online, 2013, DOI: 10.1186/1475-925X-12-106

M. Ertas, I. Yildirim, M. Kamasak, A. Akan, "Digital breast tomosynthesis image reconstruction using 2D and 3D total variation minimization", Biomedical Engineering Online, 2013, DOI: 10.1186/1475-925X-12-112

S. Seyyedi, K. Cengiz, M. Kamasak, and I. Yildirim, "An Object-Oriented Simulator for 3-D Digital Breast Tomosynthesis Imaging System", Computational and Mathematical Methods in Medicine, 2013, DOI: http://dx.doi.org/10.1155/2013/250689

Yılmaz, B., E. Çiftçi, An FDTD-Based Computer Simulation Platform for Shock Wave Propagation in Electrohydraulic Lithotripsy, Computer Methods and Programs in Biomedicine, 110, 389-398, (2013)

Kaya, K.A., B. Yılmaz, A new tool for QT interval analysis during sleep in healthy and obstructive sleep apnea subjects: a study on women, Turkish Journal of Electrical Engineering and Computer Sciences, 21, 1504–1513 (2013)


O. Purclutepe , G. Iskender, HF. Kiper, B. Tezcanli, N. Selvi, CB. Avci, B. Kosova, A. Adan,  F. Sahin, Y. Baran, G. Saydam. Enalapril-Induced Apoptosis of Acute Promyeloctic Leukemia Cells  Involves STAT5A. Anticancer Research, 2012, 32, 2885-2894.

Aydin E. and Cebeci Aydin A. (2012) Milk Hygiene Education in Turkey, in EU Leonardo Da Vinci Programme, HMILK: Key Components of Milk Hygiene from Farm to Consumer Project Reports, SERKA Development Agency. Eds Cebeci Aydin A, Tutar H., Sakiroglu M. pp 36-43.

Can G, Cakir Z, Kartal M, Gunduz U, Baran Y. Apoptotic Effects of Resveratrol, a Grape Polyphenol, on Imatinib Sensitive and Resistant K562 Cronic Myeloid Leukemia Cells. Anticancer Research, 2012; 32(7): 2673-8.

Kaplan OI, Doroquez DB, Cevik S, Bowie RV, Clarke L, Sanders AA, Kida K, Rappoport JZ, Sengupta P, Blacque OE.Endocytosis genes facilitate protein and membrane transport  in C.elegans sensory cilia. Curr Biol.22(6):451-60. doi: 10.1016/j.cub.2012.01.060.

S. Cetinel, S.Dinçer, A. Cebeci, E. Oren, JD. Whitteker, D. Schwartz, NG. Karaguler, C. Tamerler, M. Sarikaya, “Peptides to bridge biological-platinum materials interface”, Bioinspired, Biomimetic and Nanobiomaterials, 2012, 1, 143-53, DOI:10.1680.

V. Palagani, M. El Khatib, U. Kossatz, P. Bozko, M. R. Müller, M. P. Manns, T. Krech, N. P. Malek, R. R. Plentz, Epithelial mesenchymal transition and pancreatic tumor initiating CD44+/EpCAM+ cells are inhibited by γ-secretase inhibitor IX, PLoS One, 2012, 7, 1-11 (doi: 10.1371/journal.pone.0046514)

V. Palagani, M. El Khatib, T. Krech, M. P. Manns, N. P. Malek, R. R. Plentz, Decrease of CD44-positive cells correlates with tumor response to chemotherapy in patients with gastrointestinal cancer, Anticancer Res, 2012, 32, 1747-55

B-D. Chan, F. Mateen, C-L. Chang, K. Icoz, and C.A. Savran, “A Compact Manually Actuated Micromanipulator,” Journal of Microelectromechanical Systems, vol. 21, no. 1, pp. 7-9, 2012.

Y.Z. Ohkubo, T.V. Pogorelov, M.J. Arcario, G.A. Christensen, E. Tajkhorshid, Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model, Biophysical Journal 2012, 9, 2130 (DOI: 10.1016/j.bpj.2012.03.015


A. Adan, M. Kartal, Y. Baran. Molecular Biology of Breast Cancer. Book Chapter, Molecular Approaches to Breast Cancer, 2011, ISBN: 978-975-483-928-9.

Cebeci A. and Gurakan G.C. (2011) Comparative typing of L. delbrueckii subsp. bulgaricus strains using multilocus sequence typing and RAPD-PCR. European Food Research and Technology 233:377–385.

Aydin E, Planell Josep A, Hasirci V. Hydroxyapatite Nanorod – Reinforced Biodegradable Poly(L-lactic acid) Composites for Bone Plate Applications.
Journal of Materials Science: Materials in Medicine 2011;22(11):2413-27.

Baran Y, Zencir S, Çakır Z, Öztürk E, Topçu Z*.  Imatinib-induced apoptosis; A possible link to topoisomerase enzyme inhibition. Journal of Clinical Pharmacy and Therapeutics, 2011; 36(6): 673-679.

Adan A, Kartal M, Baran Y. Meme Kanserinin Moleküler Biyolojisi (Molecular Biology of Breast Cancer). 2011, Kitap Bölümü, Meme Kanserine Moleküler Yaklaşım Molecular Approaches to Breast Cancer, ISBN: 978-975-483-928-9.

Şener, E., N. Yüksel, D. K. Yıldız, B. Yılmaz, Ö. Özdemir, Y. Çağlar, E. Değirmenci, The Impact of Subconjuctivally Injected EGF and VEGF Inhibitor on Experimental Corneal Neovascularization in Rat Model, Current Eye Research, 36(11), 1005–1013 (2011)


Gurakan G. C., Cebeci A., Ozer B. (2010) Probiotic dairy beverages: Microbiology and Technology, in Development and manufacture of yoghurt and other functional dairy probiotics. CRC Press. Ed. Fatih Yildiz

Shokouhi B, Coban C, Hasirci V, Aydin E, Dhanasingh A, Shi N, Koyama S, Akira S, Zenke M and Sechi AS. The Role of Multiple Toll-Like Receptor Signalling Cascades on Interactions Between Biomedical Polymers and Dendritic Cells. Biomaterials 2010;31(22):5759-5771.

Aydin E, Hasirci V. Biodegradable Hard Tissue Implants. (Invited review) Journal of Siberian Federal University, Biology 2010;3(1):3-17.

Cevik S, Hori Y, Kaplan OI, Kida K, Toivenon T, Foley-Fisher C, Cottell D, Katada T, Kontani K, Blacque OE. Joubert syndrome Arl13b funtions at ciliary membranes and stabilizes protein transport in Caenorhabditis elegans. J Cell Biol. 188(6):953-69. doi: 10.1083/jcb.200908133.

Kaplan OI, Molla-Herman A, Cevik S, Ghossoub R, Kida K, Kimura Y, Jenkins P, Martens JR, Setou M, Benmerah A, Blacque OE.The AP-1 clathrin adaptor facilitates cilium formation and functions with RAB-8 in C.elegans ciliary membrane transport. J Cell Sci.  123(Pt 22):3966-77. doi: 10.1242/jcs.073908.

S.Dinçer, M.Türk, A.Karagöz, G.Uzunalan, "Potential c-myc Antisense Oligonucleotide Carriers: PCl/PEG/PEI and PLL/PEG/PEI", Artificial Cells, Blood Substitutes, and Biotechnology, 1-12 pp., 2010, DOI: 10.3109/10731199.2010.506852.

A.Karagöz, S.Dinçer, "Microwave-Assisted Synthesis of Poly(e- caprolactone)-block-poly(ethylene glycol) and Poly(lactide)-block-poly(ethylene glycol)", Macromolecular Symposia, 131-137 pp., 2010, DOI: 10.1002/masy.200900170.

M. El-Khatib, F. Geara, M. J. Haddadin, H. Gali-Muhtasib, Cell death by the quinoxaline dioxide DCQ in human colon cancer cells is enhanced under hypoxia and is independent of p53 and p21, Radiat Oncol, 2010, 5, 1747-55 (DOI: 10.1186/1748-717X-5-107)

K. Icoz, and C.A. Savran, “Nanomechanical Biosensing with Immunomagnetic Separation”, Applied Physics Letters, vol. 97, 123701, 2010.

J. Lee, K. Icoz, A. Roberts, A.D. Ellington and C.A. Savran, “Diffractometric Detection of Proteins Using Microbead-Based Rolling Circle Amplification”, Analytical Chemistry, vol. 82, no 1, pp. 197-202, 2010.

Yılmaz, B., U. Cunedioğlu, E. Baysoy, Usage of Spline Interpolation in Catheter-based Cardiac Mapping, Turkish Journal of Electrical Engineering and Computer Sciences, 18(6), 989-1002 (2010)

Yılmaz, B., M. H. Asyalı, E. Arıkan, S. Yetkin, F. Özgen, Sleep stage and obstructive apneaic epoch classification using single-lead ECG, BioMedical Engineering Online, 9:39 (2010)

Baysoy, E., U. Cunedioğlu, B. Yılmaz, Simultaneous Mapping of Endocardium and Epicardium from Multielectrode Intrachamber and Intravenous Catheters: A Computer Simulation-based Validation, Journal of Electrocardiology, 43(1), 56-62 (2010)


Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M.  Emprically controlled mapping of he Caenorhabditis elegans protein- protein interactome network.Nat Methods. 6(1):47-54.

Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M. An emprical framework for binary interactome mapping. Nat Methods. 6(1):83-90. doi: 10.1038/nmeth.1280.

S. Dinçer , E. K. Oskay , A. K. Piskin , N. D. Zeybek , E. Pişkin, Growth inhibition of SK-MEL-30 human melanoma cells by antisense c-myc oligonucleotides delivered by poly(N-isopropylacrylamide)/poly(ethyleneimine) copolymer, Journal of Tissue Engineering and Regenerative Medicine, DOI: 10.1002/term.239.

Cunedioğlu, U. and B. Yılmaz, Combination of Computer Simulations and Experimental Measurements as the Training Dataset for Statistical Estimation of Epicardial Activation Maps from Venous Catheter Recordings, IEEE Transactions on Biomedical Engineering, 56(3), 837–845 (2009)

Sunay, A. S., U. Cunedioğlu and B. Yılmaz Feasibility of Probabilistic Neural Networks, Kohonen SOM and Fuzzy Clustering for Source Localization of Ventricular Focal Arrhythmias from Intravenous Catheter Measurements, Expert Systems, 26(1), 70–81 (2009)


Cebeci A. and Gurakan G.C. (2008) Molecular methods for identification of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus using methionine biosynthesis and 16S rRNA genes. Journal of Dairy Research 75: 392-398.

Blacque OE, Cevik S, Kaplan OI.Intraflagellar transport: from molecular characterisation to mechanism.Front Biosci. 2008 Jan 1;13:2633-52. Review.

S. Dincer, C. Tamerler, M. Sarıkaya, E. Piskin, "'Photoresponsive peptide–azobenzene conjugates that specifically interact with platinum surfaces", Surface Science, 1757–1762 pp., 2008, DOI: 10.1016/j.susc.2008.03.011.

K. Icoz, B. D. Iverson, and C.A. Savran, “Noise analysis and sensitivity enhancement in immunomagnetic nanomechanical biosensors”, Applied Physics Letters, vol. 93, pp. 013902, 2008.


U.O.S. Seker, B. Wilson, S. Dincer, I.W. Kim, E.E. Oren, J.S. Evans, C. Tamerler, M. Sarikaya, "Adsorption Behavior of Linear and Cyclic Genetically Engineered Platinum Binding Peptides", Langmuir, 7895-7900 pp., 2007, DOI: 10.1021/la700446g.

M. Turk, S. Dincer and E. Piskin, "Smart and cationic poly(NIPA)/PEI block copolymers as non-viral vectors: in vitro and in vivo transfection studies", Journal of Tissue Engineering and Regenerative Medicine, 377-378 pp., 2007, DOI: 10.1002/term.47.

Z.M.O. Rzaev, S. Dincer, E. Piskin, "Functional copolymers of N-isopropylacrylamide for bioengineering applications", Progress in Polymer Science, 534-595 pp., 2007, DOI: 10.1016/j.progpolymsci.2007.01.006.

Yılmaz, B. and U. Cunedioğlu, Source Localization of Focal Ventricular Arrhythmias using Linear Estimation, Correlation, and Back Propagation Networks, Computers in Biology and Medicine, 37, 1437–1445 (2007)

Yılmaz, B. Epicardial Potential Distribution Reconstruction from Recordings of Intravenous and Transthoracic Mapping Catheters: A Feasibility Study, Medical Engineering & Physics, 29, 937–945 (2007)

Erdurmuş, M., R. Yağcı, B. Yılmaz, I. F. Hepşen, C. Türkmen, B. Aydın ve R. Karadağ, Inhibitory Effects of Topical Thymoquinone on Corneal Neovascularization, Cornea, 26, 715–719 (2007)

Yılmaz, B. ve R. S. MacLeod, Generalized Training Subset Selection for Statistical Estimation of Epicardial Activation Maps From Intravenous Catheter Measurements, Computers in Biology and Medicine, 37, 328–336 (2007)


Hasirci V, Vrana E, Zorlutuna P, Ndreu A, Yilgor P, Basmanav B, Aydin E. Nanobiomaterials: A review of the existing science and technology, and new approaches.
Journal of Biomaterials Science - Polymer Edition 2006;17(11):1241-1268.

Baran Y, Gunduz U, Ural AU. Cross-resistance to cytosine arabinoside in human acute myeloid leukemia cells selected for resistance to vincristine. Experimental Oncology, 2006; 28(2): 163-165.

S. Dinçer, Z.M.O. Rzaev, E Pişkin, “Synthesis and Characterization of Stimuli-Responsive Poly(N-isopropylacrylamide-co-N-vinyl-2-pyrrolidone)”, Journal of Polymer Research, 121-131 pp., 13, 2006, DOI: 10.1007/s10965-005-9014-x.

Bülent Yılmaz, Epicardial Activation Mapping from Transcoronary and Transpericardial Catheter Measurements: A Canine Heart Model, Türk Aritmi, Pacemaker ve Elektrofizyoloji Dergisi, Oct 2006.


Baran Y, Gündüz U, Ural AU. Expression of multidrug resistance (MDR1) gene in human promyelocytic leukemia cell line selected with vincristine. Turkish Journal of Cancer, 2005; 35(2): 88-92.

Önalan G*, Selam B, Baran Y, Cincik M, Onalan R, Gündüz U, Ural AU, Pabuççu R. Serum and follicular fluid levels of soluble Fas, soluble Fas ligand and apoptosis of luteinized granulosa cells in PCOS patients undergoing IVF. Human Reproduction2005; 20(9): 2391-2395.

Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M.Towards a proteome-scalemap of the human protein-protein interaction network. Nature. 20;437(7062):1173-8.

S. Dinçer, M. Türk, E. Pişkin, "Intelligent Polymers as nonviral vectors", Gene Therapy, S139-S145 pp., 2005 , DOI: 10.1038/sj.gt.3302628.

Yılmaz, B., R. S. MacLeod, B.B. Punske, B. Taccardi ve D. H. Brooks. Venous Catheter Mapping of Epicardial Ectopic Activation: Training Set Selection for Statistical Estimation, IEEE Transactions on Biomedical Engineering, vol. 52, No. 11,1823-1831 (2005).