Research Interest

Dr. Abasiyanik has been working on the development of bioanalytical techniques to analyze or monitor biomolecules which are important for early diagnosis of diseases, food/feed safety, and environmental purposes. Dr. Abasiyanik and his colleagues used nanomaterials and surface chemistry to design novel and super sensitive analytical techniques. He also analyzed host and pathogen markers to manage infectious diseases. By using epidemiologic methods, he studied the risk factors for gastric cancer and ulcer diseases in Turkey. Dr. Abasiyanik is one of the first scientists who worked on Helicobacter pylori in Turkey, which shed light on many studies. He founded a perfect ecosystem to train graduate students and alumni as potential entrepreneurs to write grants for the Governmental funds and to establish start-up companies based on their incubated ideas related to Biotech.

Medical Informatics: Detection of factors/biomarkers associated with diseases

My interest is to be able to figure out what factors and biomarkers (pathogen & host) are associated with diseases, which can be explained (detailed) from different perspectives.

  • Factors and biomarkers can be used to predict the severeness of the disease, which is useful information for the prognosis of a disease. Besides, for personalized medicine, different biological markers/ factors may affect the type of medicines (i.e, recipe) to manage the disease.
  • From the diagnostic perspective, we may eliminate false positive and negative results by analyzing more than different biomarkers and taking these factors into consideration. Even it is possible to forecast the prevalence of a microbial agent in an area by using internal and external data plus AI/ML technologies (mentioned below in detail).
  1. The recent interest under this title is “Sepsis and Septic Shock“: The major goal of this study is to predict the mortality risk of patients by using the ML algorithms based on the host and pathogen measurements of the longitudinally collected samples. For the study, I designed very sensitive DNA and protein analysis methods. We submitted our paper to Nature Communications. After the publication, I will add more info about it here.
  2. Recently seen that COVID-19 resulted in sepsis and why some people pass away because of COVID-19 why others do not is a crucial problem we need to answer. To address the question, we plan a similar study.
  3. My first interest under this topic is Helicobacter pylori and Gastric Diseases.  During my master’s and doctorate studies, my collaborators and I collected gastroenterological data. All the data were analyzed by using modern statistical methods.


  1. Fatih Abasıyanık,Hoang Van Phan, Krysta Wolfe, Jing Lin, Bhakti Patel, Bharathi Laxman, Steven R. White, Philip Verhoef, Gökhan M. Mutlu, and Savaş Tay, “Digital quantification of cytokines and bacteria predicts patient outcomes in sepsis”, Nature Communications, in review, (2020)
  2. Shamiluulu, S., Djakbarova, U., Omorov, R., Ersan, S., & Abasiyanik, M.  “Identification of critical risk factors on stomach disorders by means of a regression analysis.”, Biomedical Research, (2016) (impact factor: 0.3)
  3. Bayyurt, F.Abasiyanik, E.Sander, B.A.Salih, “Canonical correlation analysis of factors involved in the occurrence of peptic ulcers”, Digestive Diseases and Sciences (ISI), 52, 140-146 pp., (2007) (impact factor: 2.663) (cited by 20 papers)
  4. A.Salih, F.Abasiyanik, N.Bayyurt, E.Sander, “H pylori infection and other risk factors associated with peptic ulcers in Turkish patients: A retrospective study”, World Journal of Gastroenterology (ISI), 13, 3245-3248 pp., (2007) (impact factor: 3.387) (cited by 55 papers)


    1. Nizamettin Bayyurt, Fatih Abasiyanik, Ersan Sander, Barik A. Salih, “Canonical Correlation Analysis of Factors Involved in the Occurrence of Peptic Ulcers”, International Symposium on Health Informatics and Bioinformatics, Turkey ’07, Antalya, Turkey 39203


  1. K.U. “The forecasting of H. pylori prevalence by external environmental parameters with the help of ML, PhD thesis, Co-advisor, current.

Host-pathogen (e.g. Helicobacter pylori) interaction and determination of risk factors of Gastric Ulcer Diseases (GUD)

In the project, we intensively focused on Helicobacter pylori, a gram-negative bacterium, and its virulence factors. Helicobacter pylori colonize the stomachs of approximately 50% of the world’s population. The prevalence of infection ranges from 25% in developed countries to >90% in developing countries. For the first time in Turkey I figured out its prevalence in Turkish population is 84% and 64% for symptomatic and asymptomatic subjects respectively. In spite of high prevalence, only a small percentage of infected individual develop peptic ulcer disease (PUD) of which H. pylori plays an important role in the pathogenesis. The cytotoxin-associated gene (cagA) and vacuolating cytotoxin gene (vacA) are among virulence factors of H. pylori. We detected that antibodies to CagA antigen were prevalent in both symptomatic and asymptomatic subjects. Then, we focused on the diversity of cagA and vacA genes of different H pylori strains isolated from different patients. The H. pylori genome is very diverse because of the cag pathogenicity island (PAI) and allelic variations within the vacA gene. Such diversity affected the function and antigenicity of virulence factors associated with the disease outcome. Our observations showed that the cagA gene was detected in 57.1% of gastritis and 92.9% of PUD strains. The vacA-s1a-m1a, cagA, oipA, JHP912, JHP931 genotypes were more predominant in PUD, which makes cagA and vacA genes very critical suspects as virulence factors.

It was seen that some risk factors (alcohol, NSAIDs, aspirin, smoking) were highly associated with H. pylori infection (P values 0.009, 0.0372, 0.0001, 0.03 respectively). In our follow-up study, 1 g amoxicillin, 0.5 gr metronidazole, and 30 mg lansoprazole orally were given to each patient for 14 days and H. pylori eradication was achieved in 71% of the patients. Histological scores for H. pylori densities were significantly higher in the antrum and incisura angularis. Scores for mononuclear cell and neutrophil infiltration were significantly higher in regions with a high H. pylori density and improved progressively after eradication. We found that after H. pylori eradication, gastritis was healed whereas no significant improvement in atrophy or intestinal metaplasia was detected. We determined that garlic intake may indirectly inhibit the effect on the reproduction of H. pylori.


  1. Shamiluulu, S., Djakbarova, U., Omorov, R., Ersan, S., & Abasiyanik, F. “Identification of critical risk factors on stomach disorders by means of a regression analysis.”, Biomedical Research, (2016)
  2. Salih, F.Abasiyanik, N.Ahmed, “A preliminary study on the genetic profile of cag pathogenicity-island and other virulent gene loci of Helicobacter pylori strains from Turkey”, Infection, Genetics and Evolution (ISI), 7, 509-512 pp., (2007) (impact factor: 2.737) (cited by 33 papers)
  3. Bayyurt, M.F.Abasiyanik, E.Sander, B.A.Salih, “Canonical correlation analysis of factors involved in the occurrence of peptic ulcers”, Digestive Diseases and Sciences (ISI), 52, 140-146 pp., (2007) (impact factor: 2.663) (cited by 20 papers)
  4. A.Salih, F.Abasiyanik, N.Bayyurt, E.Sander, “H pylori infection and other risk factors associated with peptic ulcers in Turkish patients: A retrospective study”, World Journal of Gastroenterology (ISI), 13, 3245-3248 pp., (2007) (impact factor: 3.387) (cited by 55 papers)
  5. A.Salih, F.Abasiyanik, H.Saribasak, O.Sander, “A follow-up study on the effect of Helicobacter pylori eradication on the severity of gastric histology”, Digestive Diseases and Sciences (ISI), 50, 1517-1522 pp., (2005) (impact factor: 2.663) (cited by 62 papers)
  6. Şeker, F.Abasiyanik, B.A.Salih, “Rubella immune status of pregnant and non-pregnant women in Istanbul, Turkey”, Saudi Medical Journal (ISI) , 25, 575-579 pp., (2004) (impact factor: 0.9) (cited by 25 papers)
  7. F.Abasiyanik, M.Tunc, B.A.Salih, “Enzyme immunoassay and immunoblotting analysis of Helicobacter pylori infection in Turkish asymptomatic subjects”, Diagnostic Microbiology and Infectious Disease (ISI), 50, 173-177 pp., (2004) (impact factor: 2.342) (cited by 32 papers)
  8. A.Salih, F.Abasiyanik, “Does regular garlic intake affect the prevalence of Helicobacter pylori in asymptomatic subjects?”, Saudi Medical Journal (ISI), 24, 842-845 pp., (2003) (impact factor: 0.9) (cited by 17 papers)
  9. F.Abasiyanik, E.Sander, B.A.Salih, “Helicobacter pylori anti-CagA antibodies: Prevalence in symptomatic and asymptomatic subjects in Turkey”, Canadian Journal of Gastroenterology (ISI), 16, 527-532 pp., (2002) (impact factor: 2.121) (cited by 33 papers)


  1. Salih BA, Abasiyanik F, Ahmed N., “Genetic profile of the cag pathogenicity-island and other virulent gene loci of Helicobacter pylori “, XXth International Workshop on Helicobacter and related bacteria in chronic digestive inflammation, Istanbul/Turkey, 12, pp. 411 39326
  2. Nizamettin Bayyurt, Fatih Abasiyanik, Ersan Sander, Barik A. Salih, “Canonical Correlation Analysis of Factors Involved in the Occurrence of Peptic Ulcers”, International Symposium on Health Informatics and Bioinformatics, Turkey ’07, Antalya, Turkey 39203
  3. Fatih Abasıyanık, Aziz Tanrıseven, Bülent Keskinler, Barık Salih, “Immobilization of Helicobacter pylori Urease”, German-Turkish Conference and Project Marketplace on Applied Research and Innovation, Branschweig, Germany 39114
  4. Salih B.A. Abasiyanik, F. Sarıbaşak H, Sander E and Hüten O., “Serological and molecular typing of Helicobacter pylori following eradication”, 2nd Molecular and Diagnostic Microbiology Congress, Antalya-Turkey 37347
  5. Abasiyanik, F. Tunc M., and Salih, B.A., “Helicobacter pylori CagA status in asymptomatic subjects in Turkey”, 2nd Molecular and Diagnostic Microbiology Congress, Antalya-Turkey 37347
  6. Abasiyanik, F. and Salih, B.A., “Antibody to CagA antigen is not a predictive of peptic ulcer disease in Turkey.”, 101st general meeting of the American Society for Microbiology (ASM), Orlando, US 37043
  7. Abasiyanik, F., Acar, A., Sander, E. and Salih, B.A, “Immunoblot assay for the detection of Helicobacter pylori anti-CagA and anti-Vac-A antibodies in dyspeptic patients”, 1st National Molecular and Diagnostic Microbiology Congress, Nevşehir, Turkey 36617
  8. Seker, S., Abasiyanik, F. and Salih, B.A, “Intrauterine infections during pregnancy and congenital syndrome: A study on the immune status of aborted women and women of childbearing age.”, 1st National Molecular and Diagnostic Microbiology Congress, Nevşehir, Turkey 36617

Development of medical biosensors/assays

The monitoring of biomarkers is necessary for the early diagnosis of diseases, which help physicians to manage diseases. Biosensors such as glucose sensors become one of the most essential stat of the art technology in medicine especially in point of care testing. They are ideal for self-testing and for the construction of smart closets. In this project we designed biosensors targeting urea, glucose, galactose, cholesterol and prostate-specific antigen (PSA). In the first part of the project, we developed a skill to immobilize functional molecules (i.e, SE) (e.g., urease enzymes). Urease enzyme was immobilized by poly(1-vinyl imidazole) (PVI)/poly(acrylic acid) (PAA) and (PVI)/poly(2-acrylamido-2-methyl-1-propane sulfonic acid) (PAMS). Immobilized enzymes were more stable in different pH and temperature. To construct amperometric urease biosensors, we modified the copolymer to increase its conductivity as a network both to immobilize and transfer electrons as mediators (e.g., Poly(N-glycidylpyrrole-co-pyrrole) and poly (glycidylmethacrylate-co- vinylferrocene) (poly(GMA-co-VFc)). The performance of the sensor bearing poly(N-glycidylpyrrole-co-pyrrole) is as follows: LR: 0.1-0.7 mM, DL: 0.02 mM, analytical sensitivity: 4.5 mA/mM, response time (RT): 4 s. The amperometric response of the enzyme electrode remained constant for 15 days. In the second urea biosensor with poly(GMA-co-VFc), DL and LR were 0.06 mM and 0.1-1.5 mM respectively and it worked for 14 days. On the other hand, I fabricated a potentiometric urea biosensor. To prepare ammonium-selective electrodes, ammonium-selective membranes were prepared by using PVC containing palmitic acid. We interestingly used Helicobacter pylori urease as a SE. A broad range of LR (0.01 mM- 10 mM) was observed. All these biosensors were validated by using real human samples whose urea concentration was known.

Heart disease, coronary artery disease, hypertension, etc. are related to abnormal cholesterol level in blood, and give rise to public concern, necessitating prevention, detection and regular monitoring of abnormal cholesterol level in the modern world. Our amperometric cholesterol biosensor was fabricated by electro polymerization method of conducting polymers on pencil graphite electrode (PGE) after which apo-cholesterol oxidase (apo-ChOx) was immobilized onto FAD monolayer by reconstitution method. Thiophene-3-boronic acid and 3-aminophenyl boronic acid were electropolymerized onto PGE and modified with cholesterol oxidase. DL and LR were 0.22 µM and 0.8-4.8 µM respectively. Thiophene-3-boronic acid based electrode showed sensitivity 10 times higher response than that of one based on 3-aminophenyl boronic acid. A PSA immunosensor was designed based on different generations (G1, G2 and G3) of ferrocene(Fc) cored poly 3 amidiamine dendrimers (Fc-PAMAM) gold (Au) electrode. The self-assembled mono-layer principle (SAM) was used to fabricate the sensitive, selective and disposable immunosensor electrodes. Immobilized redox center (ferrocene) cored PAMAM dendrimers served as a layer for the further binding of anti-PSA antibodies. They were attached onto the modified Au surface (Au/Cys/Fc-PAMAMs/anti-PSA). Electrochemical differential pulse voltammetry (DPV) was used to detect DL (0.001 ng/ml). The Au/Cys/Fc PAMAM/anti-PSA immunosensor showed excellent performance with LR of 0.01 ng–100 ng/ml. The next biosensor system was an amperometric galactose biosensor having galactose oxidase (GAox) on poly (glycidyl methacrylate-co-vinylferrocene) (poly(GMA-co-VFc)) film. The biosensor exhibited a LR from 2 to 20 mM and DL of 0.1 mM, RT of 5 seconds. We changed mediator and polymer system with poly(N-glycidylpyrrole-co-pyrrole), whose DL, LR and RT as follows respectively: 0.025 mM, 2-16 mM, 5s. To construct glucose biosensor, we covalently immobilized glucose oxidase enzyme to electrode by using a novel copolymer system thiophene, thiophene-3-acetic acid, and dicyclopentadienyl iron-1,4-dienylmethyl-2-(thiophen-3-yl) acetate and the copolymer system we used for galactose biosensor called poly(GMA-co-VFc). The performance of these two systems were compared. The DL, LR and RT of the first system was 2.5 µM, 0.5-3 mM and ~4 seconds whereas those of the second system was 3.0 µM, 0.5-6 mM and 5 seconds.

On the other hand, at the University of Chicago, Dr Abasiyanik started to use ddPCR, which are a gold standard technique to detect circulating DNA/RNA fragments related to a disease or a pathogen in liquid biopsies, to design noval effective assays to detect HPV and SARS CoV-2. He participates in a study on the effective cheaper detection of the virus. The other study, of which he is the part, is trying to find out an answer to a scientific question on how the virus is transferred from one patient to another in ICUs at the hospitals.  During the study, we develop an effective DNA based method to detect viral antigens in samples. HPV is another ongoing study and we develop an effective method to screen the virus in risk groups. New days, Dr. Abasiyanik is working on Covid-19 as essential personnel and lead a team to analyze all patients samples.


  1. Emre Çevik, Mehmet Şenel, Fatih Abasıyanık, “Immobilization of urease on copper chelated EC-Tri beads and reversible adsorption”, African Journal of Biotechnology (ISI), 10, 34, pp., 6590-6597, (2011) (cited by 13 papers)
  2. Şenel, A. Coşkun, F. Abasiyanik, A. Bozkurt, “Immobilization of urease in poly (1-vinyl imidazole)/poly (acrylic acid) network”, Chemical Papers (ISI), 64, 1-7 pp., (2010) (impact factor: 1.198) (cited by 10 papers)
  3. Mehmet Şenel, Emre Çevik, Fatih Abasıyanık, Ayhan Bozkurt, “Entrapment of Urease in Poly (1-vinyl imidazole)/Poly (2-acrylamide-2-methyl-1-propane sulfonic acid) Network”, Journal of Applied Polymer Science (ISI), 119, 1931-1939 pp., (2011) (impact factor: 1.906) (cited by 6 papers)
  4. Emre Çevik, Mehmet Şenel, Fatih Abasıyanık, “An amperometric urea biosensor based on covalent immobilization of urease on copolymer of glycidyl methacrylate and vinylferrocene”, J Solid State Electrochem (ISI), DOI: 10.1007/s10008-011-1335-6 pp., (2012) (impact factor: 2.509) (cited by 12 papers)
  5. İbrahim Bozgeyik, Mehmet Şenel, Ergün Çevik, Fatih Abasıyanık, “A novel thin film amperometric urea biosensor based on urease-immobilized on poly(N-glycidylpyrrole-co-pyrrole)”, Current Applied Physics (ISI), 11,4, pp., 1083-1088, (2011) (impact factor: 2.058) (cited by 29 papers)
  6. Bahar Dindar, Emine Karakuş, Fatih Abasıyanık, “New urea biosensor based on urease enzyme obtained from Helicobacter pylori”, Applied Biochemistry and Biotechnology (ISI), 165, 5, 1308-1321 pp., (2011) (cited by 16 papers)
  7. Emre Çevik, Mehmet Şenel, Fatih Abasıyanık, “Construction of biosensor for determination of galactose with galactose oxidase immobilized on polymeric mediator contains ferrocene”, Current Applied Physics (ISI), 10, 1313-1316 pp., (2010) (impact factor: 2.058) (cited by 30 papers)
  8. Mehmet Şenel, İbrahim Bozgeyik, Emre Çevik, Fatih Abasıyanık, “A novel amperometric galactose biosensor based on galactose oxidase poly(N-glycidylpyrrole-co-pyrrole)”, Synthetic Metals (ISI), 160, 1, 440-444 pp., (2011) (impact factor: 2.526) (cited by 16 papers)
  9. Şenel, F. Abasıyanık, “Construction of a Novel Glucose Biosensor Based on Covalent Immobilization of Glucose Oxidase on Poly (glycidyl methacrylate-co-vinylferrocene)”, Electroanalysis (ISI), 22, 15, 1765-1771 pp., (2010) (impact factor: 2.851) (cited by 24 papers)
  10. F. Abasiyanik, M. Şenel, “Immobilization of glucose oxidase on reagentless ferrocene-containing polythiophene derivative and its glucose sensing application”, Journal of Electroanalytical Chemistry (ISI), 639, 21-26 pp., (2010) (impact factor: 3.235) (cited by 72 papers)
  11. Dervisevic, E. Çevik, M. Şenel, C. Nergiz, F Abasiyanik “Amperometric cholesterol biosensor based on reconstituted cholesterol oxidase on boronic acid functional conducting polymers”, Journal of Electroanalytical Chemistry 776, 18-24, (2016) (impact factor: 3.235) (cited by 17 papers)
  12. Çevik, O Bahar, M. Şenel, F Abasiyanik, “Construction of novel electrochemical immunosensor for detection of prostate specific antigen using ferrocene-PAMAM dendrimers”, Biosensors and Bioelectronics 86, 1074-1079, (2016) (impact factor: 8.173) (cited by 27 papers)


  1. Şenel M., Nergiz C., AbasiyanikF., “Reagentless Glucose Biosensor Based on Ferrocene Cored PAMAM Type Dendrimers”, 25th National Chemistry Congress with International Participation, BS-023, 123 pp., Turkey June 27 / July 2, 2011
  2. Şenel M., Nergiz C., AbasiyanikF., “Üreaz Enziminin Poli (Vinil Imidazol)/Poli (2-Akrilamido-2-Metil-1-Propansülfonik Asit) Sistemi İçerisine Immobilizasyonu”, 3. National Polymer Science and Technology Congress and Exhibition, Kocaeli, Turkey, PS115 12 – 14 May 2010
  3. AbasıyanıkF., Sakalar E., Şenel M., “Biyosensörlere genel bir bakış ve biyosavunmada kullanılan biyosensörler”; Chemical Biological Radiological and Nuclear (KBRN’08) Congress, Istanbul, Turkey, 2008


Graduate Thesis:

  1. Emre ÇEVIK, PhD, “Designing and comparison of novel smart biosensors for detection of prostate cancer”, Fatih University, Advisor, 2016
  2. Mehmet ŞENEL, PhD, “Development of enzyme based amperometric glucose biosensor”, Fatih University, Coadvisor, 2012

Devising electrochemical biosensors for environmental purposes

Environmental pollution is a worldwide problem affecting all people on the earth. Synthetic chemicals such as phenol, p-cresol, catechol, and 1,2,3-trihydroxybenzene (pyrogallol), with a wide range of usage in industrial area and have been reported as possible human carcinogens by the International Agency for Research on Cancer (IARC). Mutagenicity and toxicity of these compounds in the ecosystems makes their detection vital for the environment. Many standard procedures recommend to monitor these chemicals by using spectrophotometric, GC-MS, and other chromatographic methods. These methods suffer from complicated sample pretreatment and unsuitable on-site monitoring. In order to overcome these challenges, many efforts have been made for decades. Amperometric biosensors with enzymes as a sensing element (SE) have been proven to be a promising technique for this purpose. The amperometric biosensor as a type of electrochemical biosensors, measure the changes in the current on the working electrode due to direct oxidation of the products of a biochemical reaction. Several enzymes such as horseradish peroxidase, have been successfully immobilized on a transducer surface and employed in sensing applications.

I devised two hydrogen peroxide biosensors and three phenol nano-biosensors. In my first two biosensors, I fabricated novel amperometric hydrogen peroxide biosensors (AHPB) for the determination of H2O2. Catalase and horseradish peroxidase (HRP) enzymes as SE was immobilized on a glassy carbon electrode by poly (glycidylmethacrylate-co- vinylferrocene) (poly(GMA-co-VFc)) film. AHPB with HRP showed excellent results. Its amperometric response was measured at a fixed potential of +0.35V vs. Ag/AgCl in PBS. It showed a fast response of less than 4 s, a perfect linear range (LR) (2.0–30.0 mM) with a detection limit (DL) of 2.6 µM. The catalase bearing AHPB demonstrated slower response (<6 seconds), lower LR (0.5-14 mM) and DL (0.08 mM). I developed three electrochemical phenol nano-biosensors (EPNB). The first EPNB was constructed by poly(glycidylmethacrylate)-graphted iron oxide nanoparticles. The nanoparticles increased the electrodes’ surface area to immobilize more HRP as the SE onto electrodes. I precisely detected phenol, catechol, p-cresol, 2,2-  aminophenol and pyrogallol, catechol as analytes. The DL was 0.5 mM, the LR was 0.5 – 15.0 mM and the response time (RT) was too short (3 seconds). In my forth work, I used a poly (glycidylmethacrylate-co-vinyl ferrocene)-graphted iron oxide nanoparticles. This change dramatically improved the sensitivity of the EPNB. The sensor showed an excellent detection limit (25 µM), which meant that it was 20 times more sensitive than the first EPNB.  The next EPNM I developed was an amperometric bacterial (aromatic hydrocarbon) phenol biosensor. In this work, I utilized an engineered toluene-xylene monooxygenase (ToMO) enzyme instead of HRP as the SE. The biosensor was constructed by immobilization of E. coli TG1 cells expressing ToMO onto a gold electrode via chitosan and Fe3O4 nanocomposite. The detection limit was 0.5 µM.

Related Publication


  1. Mehmet Şenel, Emre Çevik, Fatih Abasiyanik, “A Novel Amperometric Hydrogen Peroxide Biosensor Based on Catalase Immobilization on Poly (glycidyl methacrylate-co-vinylferrocene)”, Analytical and Bioanalytical Electrochemistry, 3, 1, 14-25, (2011) (cited by 2 papers)
  2. Şenel, E.Çevik, M.F.Abasiyanik, “Amperometric hydrogen peroxide biosensor based on covalent immobilization of horseradish peroxidase on ferrocene containing polymeric mediator”, Sensors and Actuators B-Chemical (ISI), 145, 444-450 pp., (2010) (impact factor: 5.667) (cited by 98 papers)
  3. Emre Çevik, Mehmet Şenel, Abdulhadi Baykal, Fatih Abasiyanik, “A novel amperometric phenol biosensor based on immobilized HRP on poly (glycidylmethacrylate)-grafted iron oxide nanoparticles for the determination of phenol derivatives”, Sensors and Actuators B: Chemical, 173, 396-405, (2012) (impact factor: 5.667) (cited by 43 papers)
  4. E Çevik, M Şenel, A Baykal, F Abasıyanık. “Poly (Glycidyl Methacrylate-co-vinylferrocene)-grafted Iron Oxide Nanoparticles as an Electron Transfer Mediator for Amperometric Phenol Detection.” Current Applied Physics, 13, 8, 1611-1619, (2013) (impact factor: 2.116) (cited by 5 papers)
  5. Emre Çevik, Muammer Dervisevic, Ahmad Rabiu Gavba, K Cansu Yanik-Yildirim, Fatih Abasiyanik, Gönül Vardar-Schara, “Amperometric Monooxygenase Biosensor for the Detection of Aromatic Hydrocarbons”, Sensor Letters, Vol 14, 1-7, (2016) (cited by 1 paper)


  1. Emre Çevik, Mehmet Şenel, Abdulhadi Baykal, Fatih Abasiyanik, “An amperometric biosensor based on modified nanoparticles with an electron transfer mediator for the determination of phenol derivatives”, Current Opinion in Biotechnology, 22, S64, 2011

Graduate Thesis:

  1. Rabiu G AHMAD, M.Sc., “Microbial biosensor of phenolic compounds detection using chitosan-Fe3O4 bio- nanocomposite”, Supervisor: Abasiyanik Fatih, Fatih University 2014
  2. Emre ÇEVİK, M.Sc., “An amperometric biosensor based on modified nanoparticles with an electron transfer mediator for the determination of phenol derivatives”, Supervisor: Abasiyanik Fatih, Fatih University 2012


  1. Nanomaterials Based Biosensors: Amperometric Phenol Detection; E Çevik, M Şenel, F Abasiyanik; LAP LAMBERT Academic Publishing; 2012

Food and Feed Analysis

Nowadays, processed food composition and authenticity assessment are becoming a very important issue to protect the consumers from unlawful and/or unwanted substitution; for economic and health reasons. That is why we developed very sensitive, cheap, flexible, specific analytical methods to determine the exact composition of food or feedstuff. First of all, we developed two conventional gel electrophoresis-based PCR assays for qualitative analysis of ingredients in food. j We developed a multiplex PCR assay to detect ruminant, poultry, pork and fish ingredients in commercial food products and analyzed very well-known 93 commercial products in market. The assay’s sensitivity is lower than 0.01%. 35.1% of commercial products gave unexpected adulteration results. k Then, we changed the primers and used specific primers against soybean, poultry, horse and pork species to examine sausages in the market. We revealed that the samples which were claiming to have 100% beef content were found to be adulterated with poultry and soybean. To make our assay more sensitive and reliable we optimized qPCR for food analysis. As known qPCR can be classified into two categories: probe-based (i.e., TaqMan) DNA intercalating dyes (i.e., SYBR Green and EvaGreen). Although probe-based methods are sequence-specific, they are more expensive, labor intensive. SYBR Green qPCR and EvaGreen provides a flexible method without the need for individual probe design and complex optimization steps. We designed 4 EvaGreen or Sybr Green qPCR assays. The another advantages of these assays is that they could specifically discriminate amplicons belonging to different species based on high melting curve analysis. j In one of these studies, analysis of the reference sausages showed that the detection limit of the assay was 0.003% for beef and 0.001% for soybean species. We realized that 60% of beef samples labeled as 100% beef carried soybean residuals. On the other hand, 40% of poultry sausages did not match with claimed species in label by the assay analysis. kA very sensitive SYBR duplex qPCR detected food adulteries in commercial products. The lower limit of detection was found as <0.1%. We figured out that 20% of sausage-samples were adulterated. Then, l we devised another EvaGreen duplex qPCR specific against poultry and pork to analyze pet food whose LD is 3X10-3% for pork and 10-3% for poultry. Commercial products were analyzed and seen that 60% of the 100% beef samples were heavily contaminated with poultry residuals. These residuals are not in accordance with the ingredients labeled by the producer. m In another study, we focused on the development of qPCR assay for the detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The assay is used to verify reference ruminant feed samples. Our target organisms were ruminants and poultry.

In the next part of the project, we considered the effect of heat on food quality and its analysis by using biosensor technology. For this purpose, beef, pork, and chicken meat were baked at 200 oC for 10 to 50 min, and for 30 min at 30 to 210 oC and also cooked by boiling at 99 oC for 10 to 240 min. Further, a region of 374, 290, and 183-bp of mitochondrial DNA of beef, pork, and chicken, respectively, was amplified by real-time PCR. It was found that baking and boiling of the beef, pork, and chicken resulted in decreases in the detectable copy numbers of specific genes, which varied with the heating time and degree. We intended to devise an amperometric biosensor for the quality control of fish meat. First, we improved our enzyme immobilization skill by using food tech related invertase enzyme. We covalently immobilize the enzyme on PAMAM-dendrimer modified superparamagnetic iron oxide nanoparticles. PAMAM dendrimers increased immobilization capacity. The amount of immobilized enzymes on the surface-hyperbranched magnetite nanoparticle was up to 2.5 times (i.e., 250%) as much as that of magnetite nanoparticle modified with only amino silane. After the immobilization experiment, we devised a food nano-biosensor whose analyte was xanthine, a biomarker as a sign of spoilage in the food industry. When cellular respiration ceases nucleotides in muscle undergoes degradation in which xanthine is one of the metabolites. Normal range of xanthine for fresh raw meat is approximately from 0.17 to 0.64 nM or 23 to 86 μg/g. After the spoilage it can increase >1 µM. For xanthine detection we chose xanthine oxidase as a redox enzyme. The electrons released after the reaction was captured by REGO platinum-based nanocomposite electrodes which is able to detect xanthine with sensitivity of 21.98 μA/μM it has linear range of 1 to 40 μM, low detection limit of 0.003 μM, and excellent response time of 2 s. The parameters are enough to detect spoiled meat. In the 2-day-old meat xanthine concentration was nearly 4 μM after which it was gradually increasing till 5th day where beef and chicken meat started to show different results (as expected) which in final beef xanthine concentration reached 24 μM and chicken 17 μM in 20th day of storage.


  1. M Dervisevic, E Dervisevic, M Senel, E Cevik, F Abasiyanik, “Novel Amperometric Xanthine Biosensors Based on REGO-NP (Pt, Pd, and Au) Bionanocomposite Film”, Food Analytical Methods 10 (5), 1252-1263 (2017) (impact factor: 2.245)
  2. M Safdar, Y Junejo, K Arman, F Abasıyanık “A highly sensitive and specific Tetraplex PCR assay for soybean, poultry, horse and pork species identification in sausages: Development and Validation.” Meat science, (2014) (impact factor: 3.55) (cited by 27 papers)
  3. M Safdar, Y Junejo, K Arman, F Abasıyanık. “Rapid Bovine and Caprine Species Identification in Ruminant Feeds by Duplex Real-Time PCR Melting Curve Analysis Using EvaGreen Fluorescence Dye.” Molecular biotechnology, 1-7, (2014) (impact factor: 1.76) (cited by 14 papers)
  4. Safdar, F. Abasıyanık, “Development of fast multiplex real-time PCR assays based on EvaGreen fluorescence dye for identification of beef and soybean origins in processed sausages”, Food Research International, 54, 1652-1656, (2013) (impact factor: 4.196) (cited by 19 papers)
  5. Safdar, M., and F. Abasıyanık. “Simultaneous Identification of Pork and Poultry Origins in Pet Foods by a Quick Multiplex Real-Time PCR Assay Using EvaGreen Florescence Dye.” Applied Biochemistry and Biotechnology 171.7, 1855-1864, (2013) (impact factor: 1.919) (cited by 21 papers)
  6. Ergün Şakalar, Fatih Abasıyanık, “The development of dublex real-time PCR based on SYBR Green Florescence for rapid identification of ruminant and poultry origins in foodstuff”, Food Chemistry (ISI) , 130, 1050-1054 pp., (2012) (impact factor: 4.879) (cited by 20 papers)
  7. Şakalar, Ergün, Abasiyanik Fatih, “Effect of heat processing on DNA quantification of meat species.” Journal of Food Science 77.9, N40-N44, (2012) (impact factor: 2.307) (cited by 26 papers)
  8. Ergün Şakalar, Fatih Abasıyanık, “Qualitative analysis of meat and meat products by multiplex polymerase chain reaction (PCR) technique”, African Journal of Biotechnology (ISI), 10, 46, pp., 9376-9386, (2011) (impact factor: 0.96) (cited by 16 papers)
  9. Kerem Uzun, Emre Çevik, Mehmet Şenel, Hüseyin Sözeri, Fatih Abasıyanık, Abdülhadi Baykal, “Covalent Immobilization of Invertase on PAMAM-Dendrimer Modified Superparamagnetic Iron Oxide Nanoparticles”, Journal of Nanoparticle Research (ISI), 8, 3057-3067 pp., (2010) (impact factor: 2.33) (cited by 62 papers)


  1. Abasiyanik M, Kural S, Şakalar E, “Detection of milk origins in dairy products by using SYBR duplex real-time PCR (SDRT-PCR), ID1455, MIHREC 2014 Conference Proceeding, KL, Malaysia, 12/2 41730
  2. Şakalar Ergün – Fatih Abasıyanık, “The usage of bioinformatics tools for SYBR Green based multiplex identification of food DNA”, 4th International Congress On Food and Nutrition Together wth The 3rd Safe Consortium International Congress On Food Safety, Istanbul, Turkey 40817
  3. Sakalar E, Abasiyanik F, “The development of simultaneously DNA analysis method for rapid identification of soybean and poultry origins in foodstuff”, Proceedings of International Food Congress/Novel Approaches in Food Industry (NAFI 2011) Izmir/Turkey, 1, 123 pp
  4. Sakalar E, Bektik E, Abasiyanik F, “Impacts of thermal processing on the determination of DNA in beef, chicken, and pork”, Proceedings of International Food Congress/Novel Approaches in Food Industry (NAFI 2011) Izmir/Turkey, 2, 516 pp 26-29 May 2011
  5. Sakalar E, Abasiyanik F, “Quantitative specification method of soybean in meat products by DNA based molecular technique”, Proceedings of International Food Congress/Novel Approaches in Food Industry (NAFI 2011) Izmir/Turkey, 2, 517 pp 26-29 May 2011
  6. Sakalar E, Abasiyanik F, Yener B, Turmus H, “Gelatin Production”, Proceedings of International Food Congress/Novel Approaches in Food Industry (NAFI 2011) Izmir/Turkey, 2, 1068 pp 26-29 May 2011
  7. Şakalar Ergün, Fatih Abasıyanık, “Molecular food analysis: rapid identification of the species origin of meats in foodstuff by multiplex PCR”, The 1 St International Symposium On Traditional Foods From Adriatic To Caucasus, Tekirday, Turkey 40269
  8. Şakalar Ergün, Abasiyanik F, “A molecular genetic approach to the quantitative analysis of processed meat by real-time PCR Techniques”, 3rd International Congress On Food and Nutrition – EU Quality Low-Input Food Project Final Conference, Antalya, Turkey 39904

Graduate Thesis:

  1. Muammer DERVISEVIC, M.Sc., “Amperometric Biosensor for detection of xanthine level for meat freshness control”, Advisor, Fatih University 2015
  2. Zehra EKİNCİ, M.Sc., “Development of Evagreen real-time PCR assay for the molecular identification of potato brown rot disease causing Agent R. solanacearum”, Advisor,Fatih University 2014
  3. Sibel KURAL, M.Sc., “Detection of milk origins in dairy products by SYBR duplex real-time PCR”, Advisor, Fatih University 2013
  4. Serap KEÇECİ, M.Sc., “Qualitative and quantitative detection of milk powder in UHT and pasteurized milk”, Advisor, Fatih University 2013
  5. Muhammad SAFDAR, M.Sc., “Multiplex analysis of animal and plant species origin in feedstuffs and foodstuffs by modern pcr techniques: Qualitative-PCR & Real time PCR”, Advisor, Fatih University 2013
  6. Ergün ŞAKALAR , M.Sc., “A molecular genetic approach to the quantitative analysis of processed meat by real-time PCR techniques and rapid identification of the species origin of meats in foodstuff by multiplex PCR”, Advisor, Fatih University 2008

The determination of the mutagenic, toxic/genotoxic potential of chemicals and pollutants

The interaction of ionic porphyrins and phthalocyanines with DNA and proteins (e.g., BSA) was studies. While the ionic groups provide binding of porphyrazines to some biomacromolecules such as DNA and proteins, the symmetrical octakis functionalization of those planar molecules may also promote several interesting supramolecular interactions. Moreover, we examined the effects of some chemicals (e.g., tetracationic phthalocyanines, protoporphyrin IX (PpIX), Pp dopamine conjugate (DppIX), commercial antibiotics) on cancer cell and bacterial cell viability, binding efficiency on DNA and BSA (Bovine serum albumin). PpIX and DPpIX with and without irradiation were active against two Gram-negative strains (E. coli and Pseudomonas. aeruginosa) with the same MIC value (128 µg/ml). Besides, the MIC values for both PpIX and DPpIX against Bacillus subtilis were 100 µg/ml in dark, whereas they were 80 µg/ml after irradiation. Cell viability decreased significantly in cells (e.g., HeLa and SHSY5Y) treated with irradiated compounds regarding to the unirradiated ones. Activities of trimethoprim-sulfamethoxazole (SXT) as a common antibiotic against bacteria isolates (e.g., E. coli) may vary according to geographical locations. E. coli is more resistance to SXT in Rize province of Turkey. This is higher than the recommended value for resistance to this drug.

In the second part of the project, we developed and improved methods to monitor mutagenicity, toxicity, and genotoxicity in environmental samples. Seawater samples were collected from different locations in Bosporus of Istanbul, Turkey. Three different organic solvents were examined to detect the mutagenic effects of the pollutants by the AMES (Salmonella/Microsome Mutagenicity Test System) in sea water. The results of our research showed that samples from Eminönü, Kasımpaşa, Balat and Eyüp exhibit strong mutagenicity which may cause life threatening diseases such as cancer. We optimized random amplified polymorphic DNA (iRAPD) approach to monitor the level of genotoxicity of chemicals by using a model organism (i.e., Planaria). Then, we tested the method by using ethidium bromide as a known mutagenic chemical and proved that this method could monitor “detectable DNA effects” by observing appearance or disappearance of bands, increase or decrease in band intensities after gel electrophoresis. Moreover, we applied the same technology (i.e., iRAPD) to the different organs of the same fish body from the Bosporus of Istanbul by assessing genotyping difference among them, which may tell us the rate of mutagenic changes during development because of the pollutants in the sea. Inter and intra tissue DNA alterations were detected.


  1. Tugba Sagir, Salih Gencer, Nurufe Kemikli, Fatih Abasiyanik, Sevim Isik and Ramazan Ozturk, “Photodynamic activities of protoporphyrin IX and its dopamine conjugate against cancer and bacterial cell viability” (ISI), Medical Chemistry Research, DOI: 101007/S00044-011-9951-3 pp., (2012) (impact factor: 1.607) (cited by 3 papers)
  2. Özturk, Ş.Kalay, A.Kalkan, A.Turkan, F.Abasiyanik, Z.A.Bayir, A.Gul, “DNA and BSA binding studies of novel tetracationic phthalocyanines”, Journal of Porphyrins and Phthalocyanines (ISI), 12, 932-941 pp., (2008) (impact factor: 1.217) (cited by 15 papers)
  3. Kose, F. Abasiyanik, B.A Salih, “Antibiotic resistance rates of Escherichia coli urinary tract isolates in Rize province, Turkey”, J Infect Developing Countries, 1, 2, 147-150, pp., (2007) (cited by 13 papers)
  4. Petek, F.Abasiyanik, I.Uzonur, E.Okus, “Acetone soluble mutagenicity assessment tested by a salmonella/microsome system (AMES) in the strait of marmara (Black Sea and the Sea of Marmara)”, Fresenius Environmental Bulletin (ISI), 13, 1449-1452 pp., (2004) (impact factor: 0.67) (cited by 2 papers)
  5. Uzonur, F.Abasiyanik, B.Bostanci, M.Eyidemir, N.Ocba, C.Yanik, M.Petek, “Re-exploring Planaria as a Model Organism for Genotoxicity Monitoring by an ‘Improved Random Amplified Polymorphic DNA’ approach”, Fresenius Environmental Bulletin (ISI), 13, 1420-1426 pp., (2004) (impact factor: 0.67) (cited by 1 paper)
  6. Uzonur, F.Abasiyanik, S.Cam, K.Cobanli, A.E.Elmas, H.Erdogan, S.Hizal, D.S.Karabulut, M.Ozdemir, F.A.Yesil, M.Petek, “A preliminary report on target organ genotoxicity biomonitoring by an “improved random amplified polymorphic DNA” assay”, Fresenius Environmental Bulletin (ISI), 13, 1453-1456 pp., (2004) (impact factor: 0.67) (cited by 4 papers)


  1. Ramazan Öztürk, Şaban Kalay, Ali Türkan,  Fatih Abasıyanık, Ahmet Gül, Ayfer Kalkan, Zehra A. Bayı, “Turkish Topic: Yeni Tetrakatyonik Ftalosiyaninlerin DNA ve BSA ile Etkileşimlerinin Spektroskopik Yöntemlerle İncelenmesi”, 3. National Affinity Tech. Congress, Bursa, Turkey 39083
  2. Uzonur, F. Abasiyanik, H. Ocba, H. Alindirmaz, M. Emin Kanpak, B. A. Aydin, A. Sirkeci, N. Durgun, “A new approach in detecting in-vivo & in-vitro DNA damage: DNA restoration via restorase enzyme”, 13th International Symposium on Environmental Pollution and its Impact on Life in the Mediterranean Region, Thessaloniki, Greece 38596
  3. İrem Uzonur, Delal Kilinc, Hansa Erimez, Serap Memik, Fatma Ozsoy, Fatih Abasiyanik, Mustafa Petek, “Hot Diet Caused DNA Damage in Buccal Mucousa as Detected by an Improved RAPD Assay”, HGM2004 Human Genome Meeting, Berlin/Germany 38078
  4. Abasıyanık F, Ulaşlı M, Petek M, “Turkish Topic: Kullanılmakta Olan Bazı Pestisitlerin ve Herbisitlerin Sitotoksik ve Mutajenik Etkilerinin Araştırılması”, XIII. National Cancer Congress, Antalya, Turkey 36281

The Biotechnology Technology Transfer and Education Center

In 2013, I founded the biotechnology transfer and education center, whose aim to transfer biotechnology from the universities, institutes and research centers to the market, industry and end users (e.g., start-up companies, research development and innovation (RDI) departments of companies, schools, etc.) and develop hard skills of biotechnology workers and students. The infrastructure of my center involves a well-designed web site to establish communications between clients and announce every news about technology transfer, a smart classroom for online and offline educational purpose, offices for organizations. At first, all stakeholders were visited as an inventory work. I visited 50 start-up / mature companies and 50 scientists and 3 technology transfer offices. I signed cooperation agreements with all stakeholders. I made contracts with research centers and departments (e.g., Bionanotechnology R&D center, Bio-fuel Center, Genetics and Bioengineering Department) at Fatih University to use their facilities as an incubation center on behalf of my entrepreneurs and start-up companies.

I organized >35 workshops, >30 seminars, one congress and several grant writing camps. During these camps, senior or graduate students, and alumni wrote grants for techno-initiative capital support program fund under the supervision of our experts. The professional group I hired incubated their ideas and polished them before the last submission. >15 projects were prepared under the control of the supervision of the center and > 6 among them were supported. I personally was the partner of two start-up companies and the advisor of 3 start-up companies. One of the techno-initiative projects I helped was also submitted to a project competition organized by International Siemens Company and the project earned the first prize.

Resulting Publication(s) (if applicable):

  1. Sevda Yaşar ÇİMEN, Supervisor: Fatih Abasiyanik, Master of Science Thesis, “The effects of applied biotechnology education for teachers and pre-service teachers on their biotechnological skills”, Fatih University, 2014
  2. Project Coordinator and the head of organization committee, “Biyo&Nano Teknoloji Kongresi, 1-3 Ekim 2013, Istanbul Kitabi”, (the booklet of Bio&nano Technology Congress, October 1-3, 2013, Istanbul), Fatih University, 2013

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