Kocer Lab. on Emerging Viral Diseases
RESEARCH INTERESTS
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
zeynep.kocer@ibg.edu.tr
+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
Zeynep KAVALCI
PhD Student
zeynep.kavalci@ibg.edu.tr
Mukesh NİTİN
Post-Doc Researcher
mukesh.nitin@ibg.edu.tr
İlhan Mert ÖZALP
MSc Student
ilhan.ozalp@std.ibg.edu.tr
Zeynep UZUNTUNA
MSc Student
zeynep.uzuntuna@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
Mert DİKMENOĞULLARI
PhD Student
mert.dikmenogullari@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
Nidanur IŞIN
MSc Student
nidanur.isin@ibg.edu.tr
Beyza KARAKUŞ
MSc Student
beyza.karakus@ibg.edu.tr
Pınar KURTULMUŞ
MSc Student
pinar.kurtulmus@ibg.edu.tr
Gökhan Erdem ŞAHAY
Undergraduate Student
gokhan.sahay@std.ibg.edu.tr
İlhan Mert ÖZALP
Undergraduate Student
ilhan.ozalp@std.ibg.edu.tr
Ayşegül KARADENİZ
MSc Student
aysegul.karadeniz@std.ibg.edu.tr
Ayşegül KARADENİZ
MSc Student
aysegul.karadeniz@std.ibg.edu.tr
Hatice Aygün KARAÇAY
Visiting Researcher
None
Gökhan Erdem ŞAHAY
Undergraduate Student
gokhan.sahay@std.ibg.edu.tr
Selected Publications
Muhammet Ekin AZBAZDAR, Zeynep Ahsen KOÇER. İnfluenza B Virüslerinin Epidemiyolojisinde Demografi, Antijenik Özellikler ve Filogenetik İlişkilerin Bağlantısı. Türk Mikrobiyoloji Cemiyeti Dergisi. 2025 March ; 55(1) : 73-92. doi:10.54453/TMCD.2025.42744. Download
Bai Y, Lei H, Song W, Shin SC, Wang J, Xiao B, Koçer ZA, Song MS, Webster R, Webby RJ, Wong SS, Zanin M. Amino acids in the polymerase complex of shorebird-isolated H1N1 influenza virus impact replication and host-virus interactions in mammalian models.. Emerging microbes & infections. 2024 December ; 13 (1) : 2332652. doi:10.1080/22221751.2024.2332652. Download
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 : 16
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
Projects
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Inactive Trivalent Flu Vaccine Formulation, Finished
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 : Identification of factors driving the emergence and spread of avian influenza viruses withzoonotic potential, 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
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Genetic and Phenotypic Contribution of Swine Influenza Viruses to the Ecological and Evolutionary Dynamics of Human Influenza A Viruses, Ongoing
Awards
- 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
Contact
Kocer Lab. on Emerging Viral Diseases
Research Group Leader
Zeynep KOÇER
zeynep.kocer@ibg.edu.tr
+90 232 299 41 00
(5151)
+9
0 232 299 41 65