Kocer Lab. on Emerging Viral Diseases


Our research includes the detection of genetic variations in influenza viruses, understanding the functions of these variations, and risk assessment. With the inclusion of next-generation sequencing technology in scientific studies, it has become easier to detect minor variants as well as major variants in the virus genome. In fact, in some studies, it has been shown that minor variants in the virus population have an important role in antigenic changes that allow the virus to escape from the immune system and mutations that increase virus permeability (Poon et al., 2016; Dinis et al., 2016). Therefore, close follow-up of these genetic changes is very important in selecting the most accurate influenza strains in vaccine production and in developing more effective antivirals. Our main objectives are to detect genetic variations in the genomes of human influenza viruses by next-generation sequencing, to perform in silico structural analysis based on the locations of the variations in the genome, and to look at the phylogenetic origins of the gene segments. Although rare, gene reassortment can be seen between seasonal influenza viruses. For this reason, with the help of phylogenetic analysis, investigating the frequency of such reassortment events that may occur during co-infection with different subtypes and determining the origins of viral genes are among our research topics, as well. In summary, our main goal is to examine influenza A viruses with the help of various molecular and bioinformatic analysis, focusing on the detection of new variants and the determination of the functions of these variations. Such studies form the basis for the development of diagnostic kits against current strains and the production of effective antivirals and vaccines.



Group Members

Kocer Lab. on Emerging Viral Diseases

Research Group Leader

Zeynep KOÇER
+90 232 299 41 00 (5151)
+9 0 232 299 41 65

Muhammet Ekin AZBAZDAR PhD Student  ekin.azbazdar@ibg.edu.tr

Feray YILMAZ Researcher  feray.yilmaz@ibg.edu.tr

Mert DİKMENOĞULLARI PhD Student  mert.dikmenogullari@ibg.edu.tr

Nidanur IŞIN MSc Student  nidanur.isin@ibg.edu.tr

Zeynep KAVALCI PhD Student  zeynep.kavalci@ibg.edu.tr

Mukesh NİTİN Post-Doc Researcher  mukesh.nitin@ibg.edu.tr

İlhan Mert ÖZALP Undergraduate Student  ilhan.ozalp@std.ibg.edu.tr

Oğulcan KARATOPRAK Undergraduate Student  None

Ayşegül KARADENİZ MSc Student  aysegul.karadeniz@std.ibg.edu.tr

Former Members

Yavuz MERCAN Research Assistant  yavuz.mercan@ibg.edu.tr

Öykü DURAK MSc Student  oyku.durak@ibg.edu.tr

Mert DİKMENOĞULLARI MSc Student  mert.dikmenogullari@ibg.edu.tr

Gaye ÇOKYÜCEL Undergraduate Student  gaye.cokyucel@msfr.ibg.edu.tr

Furkan ÇÖVEN PhD Student  furkan.coven@ibg.edu.tr

Emre Mert ASAR MSc Student  emremert.asar@ibg.edu.tr

Atakan DALKILIÇ MSc Student  atakan.dalkilic@msfr.ibg.edu.tr

Fatih DİNÇ Visiting Researcher  fatih.dinc@msfr.ibg.edu.tr

TANSU BIÇAKCIOĞLU PhD Student  tansu.bicakcioglu@msfr.ibg.edu.tr

Fatma YAVUZ Undergraduate Student  fatma.yavuz@msfr.ibg.edu.tr

Bulut OKUMUŞOĞLU MSc Student  bulut.okumusoglu@ibg.edu.tr

Fatma YAVUZ Undergraduate Student  fatma.yavuz@msfr.ibg.edu.tr

İlhan Mert ÖZALP Undergraduate Student  ilhan.ozalp@std.ibg.edu.tr

Duygu Elif BAYRAM Undergraduate Student  duygu.bayram@ibg.edu.tr

Pınar KURTULMUŞ MSc Student  pinar.kurtulmus@ibg.edu.tr

Beyza KARAKUŞ MSc Student  beyza.karakus@ibg.edu.tr

Ayşegül KARADENİZ MSc Student  aysegul.karadeniz@std.ibg.edu.tr

Selected Publications

Arif E. Cetin, Zeynep A. Kocer, Seda Nur Topkaya, Ziya Ata Yazici. Handheld Plasmonic Biosensor for Virus Detection in Field-Settings. Sensors and Actuators B: Chemical. 2021 October ; 344 : 130301. doi:10.1016/j.snb.2021.130301. Download

Zanin M, Koçer ZA, Poulson RL, Gabbard JD, Howerth EW, Jones CA, Friedman K, Seiler J, Danner A, Kercher L, McBride R, Paulson JC, Wentworth DE, Krauss S, Tompkins SM, Stallknecht DE, Webster RG. Potential for Low-Pathogenic Avian H7 Influenza A Viruses To Replicate and Cause Disease in a Mammalian Model. Journal of virology. 2017 January ; 91 (3) . doi:10.1128/JVI.01934-16. Download

Koçer ZA, Krauss S, Zanin M, Danner A, Gulati S, Jones JC, Friedman K, Graham A, Forrest H, Seiler J, Air GM, Webster RG. Possible basis for the emergence of H1N1 viruses with pandemic potential from avian hosts.. Emerging microbes & infections. 2015 July ; 4 (7) : e40. doi:10.1038/emi.2015.40. Download

Koçer ZA, Carter R, Wu G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains.. PloS one. 2015 July ; 10 (7) : e0133795. doi:10.1371/journal.pone.0133795. Download

Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG, Wu G. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses.. Scientific Reports. 2014 December ; 4 : 7455. doi:10.1038/srep07455. Download

Jones JC, Sonnberg S, Koçer ZA, Shanmuganatham K, Seiler P, Shu Y, Zhu H, Guan Y, Peiris M, Webby RJ, Webster RG. Possible role of songbirds and parakeets in transmission of influenza A(H7N9) virus to humans.. Emerging infectious diseases. 2014 March ; 20 (3) : 380-5. doi:10.3201/eid2003.131271. Download

Koçer ZA, Jones JC, Webster RG. Emergence of Influenza Viruses and Crossing the Species Barrier.. Microbiology spectrum. 2013 December ; 1 (2) . doi:10.1128/microbiolspec.OH-0010-2012. Download

SJCEIRS H9 Working Group.. Assessing the fitness of distinct clades of influenza A (H9N2) viruses.. Emerging microbes & infections. 2013 November ; 2 (11) : e75. doi:10.1038/emi.2013.75. Download

Koçer ZA, Obenauer J, Zaraket H, Zhang J, Rehg JE, Russell CJ, Webster RG. Fecal influenza in mammals: selection of novel variants.. Journal of virology. 2013 November ; 87 (21) : 11476-86. doi:10.1128/JVI.01544-13. Download

Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni RS, D'Elia T, Morris PF, Rogers SO. Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya.. PloS one. 2013 July ; 8 (7) : e67221. doi:10.1371/journal.pone.0067221. Download

D'souza NA, Kawarasaki Y, Gantz JD, Lee RE Jr, Beall BF, Shtarkman YM, Koçer ZA, Rogers SO, Wildschutte H, Bullerjahn GS, McKay RM. Diatom assemblages promote ice formation in large lakes.. The ISME journal. 2013 August ; 7 (8) : 1632-40. doi:10.1038/ismej.2013.49. Download

Rogers SO, Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni R, D'Elia T. Ecology of subglacial lake vostok (antarctica), based on metagenomic/metatranscriptomic analyses of accretion ice.. Biology. 2013 March ; 2 (2) : 629-50. doi:10.3390/biology2020629. Download

Koçer ZA, Krauss S, Stallknecht DE, Rehg JE, Webster RG. The potential of avian H1N1 influenza A viruses to replicate and cause disease in mammalian models.. PloS one. 2012 January ; 7 (7) : e41609. doi:10.1371/journal.pone.0041609. Download

ZA Kocer, AG Gozen, S Onde, Z Kaya. Indirect organogenesis from bud explants of Juniperus communis L.: Effects of genotype, gender, sampling time and growth regulator combinations. Dendrobiology. 2011 January ; 66 : 33-40. Download

Total : 14

Selected Book Chapters

One Health: People, Animals and the Environment (2014). Emergence of influenza viruses and crossing the species barrier. ASM Press (American Society for Microbiology).

Total : 1


The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Inactive Trivalent Flu Vaccine Formulation, Finished

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Assessment of Pandemic Risk for Influenza Viruses in Shorebirds via Molecular Approach, Ongoing

DEÜ BAP - Dokuz Eylul University Scientific Research Projects Coordination Unit - RD : Assessing the contribution of genetic variations and reassortment events that occurred in influenza viruses during 2018-2019 and 2019-2020 seasons in Aegean Region, Turkey, Finished

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Ülkemizde ve Dünyada Halk Sağlığını En Fazla Tehdit Eden HPV ve Influenza Kaynaklı Enfeksiyonlara Karşı Tanı Kitleri, İlaç Formülasyonları ve Aşı Geliştirilmesi (Turkish), Ongoing

Other National Funding Body - RD : Balb/c Farelerde Perflorooktan Sülfonik Asit ve Perflorooktanoik Asit Maruziyetinin İnterlökin17 Sinyal Yolağı ve İndüklenmiş Akciğer Hasarı Üzerine Etkilerinin İncelenmesi, Ongoing

DEÜ BAP - Dokuz Eylul University Scientific Research Projects Coordination Unit - RD : İklim Değişikliğine Uyum Kapsamında Toprak Sağlığı Araştırmaları Canlı Laboratuvarı (LivingLab), Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : KORUNMA VE TEDAVİ ULUSAL PLATFORMU, Ongoing


  • 2232 Yurda Dönüş Araştırmacı Dolaşım Programı by TUBITAK, 2018

Academic Memberships

  • Turkish Society of Microbiology, 2018
  • International Society for Influenza and Other Respiratory Diseases, 2013
  • Ecology and Evolutionary Biology Society of Turkey, 2017


Kocer Lab. on Emerging Viral Diseases

Research Group Leader

Zeynep KOÇER
+90 232 299 41 00 (5151)
+9 0 232 299 41 65