Faculty Members

Prof. Dr. Seda Nur TOPKAYA ÇETİN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Prof. Dr. Mehmet INAN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Prof. Dr. Gökhan KARAKÜLAH

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Prof. Dr. Şerif ŞENTÜRK

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Prof. Dr. Serhat TOZBURUN

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Assoc. Prof. Hani ALOTAİBİ

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Assoc. Prof. Muhammed Kasım DİRİL

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Assoc. Prof. Ezgi KARACA EREK

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Assoc. Prof. Evin ÖZEN İŞCAN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Assoc. Prof. Serap ERKEK ÖZHAN

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Assoc. Prof. Muhammed ÜÇÜNCÜ

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Asst. Prof. Gülçin ÇAKAN AKDOĞAN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Asst. Prof. Gülcan AKGUL

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Asst. Prof. Merve TÜRKER BURHAN

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Asst. Prof. Bilgi GÜNGÖR

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Asst. Prof. Zeynep Ahsen KOÇER

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Asst. Prof. Sibel KALYONCU UZUNLAR

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Faculty Members with 13/b-4 Appointment

Prof. Dr. Hülya AYAR KAYALI

IZMIR INTERNATIONAL BIOMEDICINE AND GENOME INSTITUTE

Assoc. Prof. Yavuz OKTAY

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Assoc. Prof. Duygu SAĞ

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Faculty Members with 40/a Appointment

Prof. Dr. Şerife Esra ERDAL BAĞRIYANIK

IZMIR INTERNATIONAL BIOMEDICINE AND GENOME INSTITUTE

Prof. Dr. Şermin GENÇ

IZMIR INTERNATIONAL BIOMEDICINE AND GENOME INSTITUTE

Prof. Dr. Sinan GÜVEN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Assoc. Prof. Dr. Arif Engin ÇETİN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Foreign Faculty Members

Asst. Prof. Athanasia PAVLOPOULOU

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Researchers

Dr. Ece SÖNMEZLER ADALI

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Elçin ÇAĞATAY

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Ece ÇAKIROĞLU

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Abdullah DEĞİRMENÇAY

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Duygu ERDOĞAN

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Meryem Beyza AVCI

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Sude ERİŞ

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Uğur Faruk KALKAN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Güldane Bilge KILIÇ

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Çağla NİĞDE

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Merve UÇA APAYDIN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Habibe GÖREN

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Dr. Aslı KORKMAZ

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Aytül Gül METE

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Belgüzar KARADAĞ

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Dr. Burcu ÖZDEN YÜCEL

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

Dr. Gülten KURU

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Gökçen BİLİCİ GÜLER

DEPARTMENT OF GENOMICS AND MOLECULAR BIOTECHNOLOGY

Dr. Şeyma Nur YILDIZ

DEPARTMENT OF BIOMEDICINE AND HEALTH TECHNOLOGIES

2026/2027 Eğitim Öğretim Yılı Güz Yarıyılı İlan Metni

YÖKAK ÇALIŞMALARI KAPSAMINDA OLUŞTURULAN KALİTE KOMİSYONU ÇALIŞMA GRUPLARI

Özdeğerlendirme Raporu
B.1.5 Öğretim Planı IBG Senato Karar Ekleri
B.1.5 Öğretim Planı IBG Senato Karar Örneği
B.1.5 Öğretim Planı Üst yazı
B.1.5 Öğretim Planı Enstitü kurul kararı
B.1.5 Öğretim Planı Biyotıp ve Sağ.Tekn. YL. Prog
B.1.5 Öğretim Planı Biyotıp ve Sağ.Tekn.DR Prog
B.1.5 Öğretim Planı Moleküler Biyoloji ve Genetik DR Prog
B.1.5 Öğretim Planı Moleküler Biyoloji ve Genetik YL Prog
B.1.2 Programın ders dağılım dengesi (2025-2026 güz Biyotıp ve Sağlık Tekn. YL-DR ders prog.)
B.1.2 Programın ders dağılım dengesi (2025-2026 güz Mol.Biy.ve Genetik YL-DR ders prog.)
B.1.2 Programın ders dağılım dengesi 2024-2025 Bahar Ders Programı
B.3.1 Öğrenme kaynakları (biorender bilgisayar programı kullanılması)
B.3.4 Dezavantajlı gruplar (Engelsiz Kariyer)
B.4.1 Atama, yükseltme ve görevlendirme kriterleri (2547 SK Ek 34.md göreve başlayış)
IBG rapor

Anabilim Dalı Sekreteri

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Enstitü Sekreteri

Download (DOCX, 17KB)

Evrak İşleri Kayıt Görevlisi

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Kurul İşleri Görevlisi

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Mali İşler Görevlisi

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Öğrenci İşleri Görevlisi

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Özel Kalem

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Personel İşleri Görevlisi

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Sivil Savunma Görevlisi

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Taşınır Kayıt Kontrol Yetkilisi

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Anabilim Dalı Sekreteri

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Enstitü Sekreteri

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Evrak İşleri Kayıt Görevlisi

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Kurul İşleri Görevlisi

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Mali İşler Görevlisi

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Öğrenci İşleri Görevlisi

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Özel Kalem

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Personel İşleri Görevlisi

Download (DOCX, 18KB)

Sivil Savunma Görevlisi

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Taşınır Kayıt Kontrol Yetkilisi

Download (DOCX, 16KB)

Anabilim Dalı Sekreteri

Download (DOCX, 13KB)

Enstitü Sekreteri

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Evrak İşleri Kayıt Görevlisi

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Kurul İşleri Görevlisi

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Mali İşler Görevlisi

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Öğrenci İşleri Görevlisi

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Özel Kalem

Download (DOCX, 13KB)

Personel İşleri Görevlisi

Download (DOCX, 18KB)

Sivil Savunma Görevlisi

Download (DOCX, 14KB)

Taşınır Kayıt Kontrol Yetkilisi

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Download (PDF, 242KB)

Download (PDF, 127KB)

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Enstitü Sekreterliği

İdari Birimler

Mukaddes AKKEÇELİ

ENSTİTÜ SEKRETERLİĞİ

Tel: +90 232 412 86 54

Gamze GÜVEN

ÖĞRENCİ İŞLERİ

Tel: +90 232 412 86 66

Naciye YILDIZ

PERSONEL İŞLERİ/ANA BİLİM DALI SEKRETERLİĞİ

Tel: +90 232 412 86 63

Haktan GÜNER

İDARİ VE MALİ İŞLER/TAŞINIR KAYIT YETKİLİSİ

Tel: +90 232 412 67 63

Özlem ALKU

ÖZEL KALEM/YÖNETİM KURULU İŞLERİ/BELGE OFİSİ

Tel: +90 232 412 86 51

Mukaddes AKKEÇELİ

ENSTİTÜ SEKRETERLİĞİ

Tel: +90 232 412 86 54

Gamze GÜVEN

ÖĞRENCİ İŞLERİ

Tel: +90 232 412 86 66

Naciye YILDIZ

PERSONEL İŞLERİ/ANA BİLİM DALI SEKRETERLİĞİ

Tel: +90 232 412 86 63

Haktan GÜNER

İDARİ VE MALİ İŞLER/TAŞINIR KAYIT YETKİLİSİ

Tel: +90 232 412 67 63

Özlem ALKU

ÖZEL KALEM/YÖNETİM KURULU İŞLERİ/BELGE OFİSİ

Tel: +90 232 412 86 51

Number of Academic And Administrative Staff

• 1 Foreign National Faculty Members
• 7 Researchers
• 5 Administrative Office

Izmir International Biomedicine And Genome Institute Graduated Student Number ( Last 8 Years )

CURRENT STUDENTS

Anabilim Dalı Başkanıhttp://debis.deu.edu.tr/akademiktr/index.php?cat=3&akod=20140107

Anabilim Dalı Akademik Personel Listesi

Moleküler Biyoloji ve Genetik Yüksek Lisans Programı 

Moleküler Biyoloji ve Genetik Doktora Programı 

Enstitü Tanıtım videosu bu sekmeden ulaşabilirsiniz.

PhD ADVISOR ASSIGNMENT FORM

PhD ADVISOR CHANGE FORM

PhD Co-Advisor Assigment Form

PhD PhD Qualifying Exam Application Form

PhD PHD THESIS DEFENSE EXAM REPORT

PhD QUALIFYING EXAM RESULT EVALUATION REPORT FORM

PhD THESIS DEFENSE APPLICATION FORM

PhD Thesis Evaluation Form

PhD THESIS MONITORING COMMITTEE CHANGE FORM

PhD THESIS MONITORING COMMITTEE FORMATION FORM

PhD THESIS MONITORING COMMITTEE REPORT

PhD THESIS MONITORING FORM

PhD THESIS MONITORING REPORT FORM

PhD THESIS PROPOSAL / TITLE / CONTENT CHANGE FORM

PhD THESIS PROPOSAL FORM

MSc ADVISOR ASSIGNMENT FORM

MSc ADVISOR CHANGE FORM

MSc MASTER’S THESIS DEFENSE APPLICATION FORM

MSc MASTER’S THESIS DEFENSE EXAM REPORT

MSc ONLINE MASTER’S THESIS DEFENSE EXAM REPORT

MSc SECOND THESIS ADVISOR ASSIGNMENT FORM

MSc THESIS EVALUATION FORM

MSc THESIS PROPOSAL / TITLE / CONTENT CHANGE FORM

MSc THESIS PROPOSAL FORM

İzmir Uluslararası Biyotıp Ve Genom Enstitüsü Yatay Geçiş Öğrenci Kabul Koşulları

STUDENT

Termination form

Graduation request form

Freezing rights form

Special students form

Exmatriculation form

PERSONNEL

Annual leave form

Application form for domestic and overseas assignment

Facult member assignement tracking form

Termination of employment form

Application and Admission Process to the Master’s Program

kjkjlk

Danışman Atama Formu

Guest Student Application Form

1-Thesis guide

2-Thesis submission process

3-Plagiarism Report

4- TURNITIN Plagiarism Program User Guide

5-Thesis Plagiarism Analysis Program

Download (DOCX, 605KB)

PhD program

Prof. Dr. Şermin GENÇ

INSTITUTE DIRECTOR

Prof. Dr. Şerif ŞENTÜRK

INSTITUTE VICE DIRECTOR

Assoc. Prof. Serap ERKEK ÖZHAN

INSTITUTE VICE DIRECTOR

Prof. Dr. Gökhan KARAKÜLAH

MEMBER

Assoc. Prof. Hani ALOTAİBİ

MEMBER

Dr. Öğr. Üyesi Ezgi KARACA EREK

MEMBER

Mukaddes AKKEÇELİ

INSTITUTE SECRETARY

Prof. Dr. Şerif ŞENTÜRK

INSTITUTE VICE DIRECTOR

Assoc. Prof. Serap ERKEK ÖZHAN

INSTITUTE VICE DIRECTOR

Prof. Dr. Şermin GENÇ

INSTITUTE DIRECTOR

• Head of Department

• Biomedicine And Health Technologies
• Biomedicine And Health Technologies

• • • Molecular Biology And Genetics
    • Molecular Biology And Genetics

QUALITY COMMISSION WORKING GROUPS ESTABLISHED WITHIN THE SCOPE OF YÖKAK

Mission and Vision

Our mission is to train distinguished, talented scientists and academics to become essential parts of the international health community. We will organize educational activities to share knowledge and experience, to develop technology and tools to resolve global health problems, and to improve human welfare. Additionally, we will form partnerships with other national and international research centers to become an innovative training center.

Our vision is to become an internationally respected, nationally prestigious institute, able to introduce countless scientific discoveries, and to become a pioneering education and research center that translates novel findings in the life sciences to benefit society’s health and welfare.

Enstitümüz web sayfasından  “Özel Öğrenci Başvuru Formu”nu alınız.

Özel Öğrenci Başvuru Formunun Enstitü web sayfasında Akademik Takvimde ilan edilen tarihlerde Enstitümüze teslim edilmesi gerekmektedir.

“Özel Öğrenci” olarak almaya karar verdiğiniz ders/derslerin, koordinatörü ve Anabilim Dalı Başkanı ile görüşerek derse katılma isteğinizi bildiriniz.

Özel Öğrenci Başvuru formunu doldurarak imzaları tamamlayınız.

Onaylattığınız “Özel Öğrenci Başvuru Formu”, “Kimlik Fotokopisi”, “Öğrenci Belgesi”, “İngilizce Yeterlik Belgesinin Resmi Onaylı Örneği”ni  teslim ediniz.

Özel Öğrenci Başvuru Formunun eksiksiz olarak doldurulması ve istenilen belgelerin eksiksiz Enstitü web sayfasında Akademik Takvimde ilan edilen tarihler arasında Enstitüye teslim edilmesi gerekmektedir.

Belirtilen tarihler arasında başvurular yapılmadığı takdirde başvurular kabul edilmeyecektir

Hak Dondurma Dilekçesi

Hizmet Damgalı Pasaport Talep Formu

Özel Öğrenci Başvuru Formu

Öğrenci İlişik Kesme Formu

Mezuniyet Belgesi Talep Dilekçesi

Başka kurumdan/Diğer Anabilim Dalından Almak İstenen Ders İle İlgili Dilekçe

PERSONEL İŞLERİ

Rektörlüğe Gönderilecek 39. Görevlendirme Formu

GÖREVLENDİRME TAKİP FORMU

Görevlendirme Talep Formu (TR)

Görevlendirme Talep Formu (İNG)

Yıllık İzin Formu

Personel İlişik Kesme Belgesi

Mal Bildirim Formu

IBG_PhD_Danısman Atama Formu

IBG_PhD_Danışman Degisikligi Formu 

IBG_PhD_II. Tez Danısmanı Atama Formu

IBG_PhD_Doktora Yeterlik Sınavı Basvuru Formu

IBG_PhD_Doktora Yeterlik Sonuc Degerlendirme Tutanak Formu

IBG_MSc/PhD_Tez Önerisi Formu

IBG_Etik_Kurul_Onay_Kılavuzu

IBG_MSc/PhD_Tez Önerisi Baslıgı-Icerigi Degisiklik Formu

IBG_PhD_Tez Izleme Komitesi Olusturma

IBG_PhD_Tez Izleme Komite Uyeleri Degistirme Formu

IBG_PhD_Tez Izleme Raporu Formu

IBG_PhD_Tez Izleme Formu

IBG_PhD_Tez Izleme Komitesi Tutanagı

IBG_PhD_Tez Savunma Basvuru Formu

IBG_PhD_Tez Savunma Sinavi Tutanagı

IBG_MSc/PhD_Tez Degerlendirme Formu

IBG_MSc_Danısman Atama Formu

IBG_MSc_Danışman Degisikligi Formu

IBG_MSc_II. Tez Danısmanı Atama Formu

IBG_MSc/PhD_Tez Önerisi Formu

IBG_Etik_Kurul_Onay_Kılavuzu

IBG_MSc/PhD_Tez Önerisi Baslıgı-Icerigi Degisiklik Formu

IBG_MSc_Tez Savunma Basvuru Formu

IBG_MSc_Tez Savunma Sınavı Tutanagı

IBG_MSc_Cevrim İci Tez Savunma Sınavı Tutanagı

IBG_MSc/PhD_Tez Degerlendirme Formu

Doktora Başvuru, Kayıt, Eğitim Süreci

**Doktora Mezuniyet Makalesi Niteliklerine İlişkin Enstitü Kurulu Kararı için tıklayınız.

Yüksek Lisans Başvuru, Kayıt, Eğitim Süreci

YÜKSEK LISANS

DOKTORA

Bölüm Başkanı

• • Biyotıp ve Sağlık Teknolojileri Yüksek Lisans
  • Biyotıp ve Sağlık Teknolojileri Doktora

Anabilim Dalı Başkanı

Moleküler Biyoloji ve Genetik Yüksek Lisans Programı

Moleküler Biyoloji ve Genetik Doktora Programı 

Moleküler Biyoloji ve Genetik Bütünleşik Doktora Programı

İzmir International Biomedicine and Genome Institute Surveys

Course Term Student Survey

Thesis Term Student Survey

Faculty Member Survey

Graduate Follow-up and Satisfaction Survey

Council of Higher Education, Graduate Training Regulation

IZMIR INTERNATIONAL BIOMEDICINE  AND GENOME INSTITUTE ACADEMIC AND ADMINISTRATIVE STAFF NUMBERS

• 7 Faculty Members
• 3 Foreign Faculty Members
• 1 Foreign Visiting Professor
• 3 Foreign Specialist
• 1 Instructor
• 13 Administrative Staff

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ ÖĞRENCİ SAYILARI ( SON 2 YIL)

Tez Yazım Kılavuzu

Tez Teslim İşlemleri

İntihal Raporu Beyan Belgesi

DEÜ TURNITIN İntihal Programı Kullanma Kılavuzu

Tez İntihal Analiz Programı 

DEÜ Bilimsel Araştırma Projeleri

YÖK Bilimsel Araştırma ve Yayın Etiği Yönergesi

Yurtdışı Yükseköğretim Diploma ve Denkliği Yönetmeliği

YÖK Lisansüstü ve Öğretim Yönetmeliği

DEÜ Muafiyet ve İntibak Yönergesi

DEÜ Akademik Danışmanlık Yönergesi

DEÜ Lisansüstü Eğitim ve Öğretim Yönetmeliği

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Misyonumuz, sağlık alanında uluslararası camiada etkin olabilecek seçkin, yetenekli bilim insanları ve akademisyenler yetiştirmek, insanlığın refah düzeyini arttırmak ve küresel sağlık sorunlarını azaltmaya yönelik bilgi, deneyim, teknoloji ve araç geliştirmeye yönelik eğitim faaliyetleri düzenlemek, ulusal ve küresel düzeyde eğitim ve araştırma paydaşları ile ortaklıklar oluşturarak inovatif bir eğitim merkezi olmaktır.

Vizyon

Ülkemizde en çok tercih edilen, dünya çapında saygın, uluslararası standartta, yaşam bilimlerindeki yeni bilimsel bilgiyi toplumun sağlık ve refahı için kullanılabilir hale dönüştüren, yaptığı bilimsel keşifler ile dünya çapında sağlık ve bilim politikalarına yön veren bir eğitim ve araştırma kurumu olmaktır.

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Enstitü Sekreterliği

İdari Birimler

Mukaddes AKKEÇELİ

INSTITUTE SECRETARY

Phone : +90 232 412 86 54

Gamze GÜVEN

STUDENT AFFAIRS

Phone : +90 232 412 86 66

Naciye YILDIZ

HUMAN RESOURCES/DEPARTMENT SECRETARY

Phone : +90 232 412 86 63

Haktan GÜNER

ADMINISTRATIVE AND FINANCIAL AFFAIRS/CHATTELS REGISTRATION

Phone : +90 232 412 67 63

Özlem ALKU

EXECUTIVE ASSISTANT/BOARD AFFAIRS/DOCUMENT OFFICE

Phone : +90 232 412 86 70

Download (PDF, 242KB)

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ ANKETLERİ

DERS DÖNEMİ ÖĞRENCİ ANKETİ

TEZ DÖNEMİ ÖĞRENCİ ANKETİ

ÖĞRETİM ÜYESİ ANKETİ 

Mezun İzleme ve Memnuniyet Anketi 

LİSANSÜSTÜ PROGRAMLARA BAŞVURU

YUKSEK LISANS

DOKTORA

BÜTÜNLEŞİK DOKTORA

YABANCI ÖĞRENCİ BİLGİLENDİRME FORMU  (ÖĞRENİM VİZESİ VE İKAMETGÂH TEZKERESİ ALABİLMEK ICİN YAPILACAK ISLEMLER)

Mukaddes AKKEÇELİ

ENSTİTÜ SEKRETERİ

Telefon : +90 232 412 86 54

YÖKAK ÇALIŞMALARI KAPSAMINDA OLUŞTURULAN KALİTE KOMİSYONU ÇALIŞMA GRUPLARI

Prof. Dr. Şermin GENÇ

ENSTİTÜ MÜDÜRÜ

Prof. Dr. Şerif ŞENTÜRK

ENSTİTÜ MÜDÜR YARDIMCISI

Doç. Dr. Serap ERKEK ÖZHAN

ENSTİTÜ MÜDÜR YARDIMCISI

Prof. Dr. Gökhan KARAKÜLAH

ÜYE

Doç. Dr. Hani ALOTAİBİ

ÜYE

Dr. Öğr. Üyesi Ezgi KARACA EREK

ÜYE

Prof. Dr. Şerif ŞENTÜRK

ENSTİTÜ MÜDÜR YARDIMCISI

Doç. Dr. Serap ERKEK ÖZHAN

ENSTİTÜ MÜDÜR YARDIMCISI

Prof. Dr. Şermin GENÇ

ENSTİTÜ MÜDÜRÜ

Mukaddes AKKEÇELİ

ENSTİTÜ SEKRETERLİĞİ

Tel: +90 232 412 86 54

Gamze GÜVEN

ÖĞRENCİ İŞLERİ

Tel: +90 232 412 86 66

Naciye YILDIZ

PERSONEL İŞLERİ/ANA BİLİM DALI SEKRETERLİĞİ

Tel: +90 232 412 86 63

Haktan GÜNER

İDARİ VE MALİ İŞLER/TAŞINIR KAYIT YETKİLİSİ

Tel: +90 232 412 67 63

Özlem ALKU

ÖZEL KALEM/YÖNETİM KURULU İŞLERİ/BELGE OFİSİ

Tel: +90 232 412 86 51

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ

Prof. Dr. Şermin GENÇ

ENSTİTÜ MÜDÜRÜ

Prof. Dr. Şerif ŞENTÜRK

ENSTİTÜ MÜDÜR YARDIMCISI

Doç. Dr. Serap ERKEK ÖZHAN

ENSTİTÜ MÜDÜR YARDIMCISI

Enstitümüz kadrosunda bulunan Öğretim Üyeleri

Prof. Dr. Seda Nur TOPKAYA ÇETİN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Prof. Dr. Mehmet İNAN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Prof. Dr. Gökhan KARAKÜLAH

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Prof. Dr. Şerif ŞENTÜRK

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Prof. Dr. Serhat TOZBURUN

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Doç. Dr. Hani ALOTAİBİ

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Doç. Dr. Muhammed Kasım DİRİL

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Doç. Dr. Ezgi KARACA EREK

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Doç. Dr. Evin ÖZEN İŞCAN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Doç. Dr. Serap ERKEK ÖZHAN

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Doç. Dr. Muhammed ÜÇÜNCÜ

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Öğr. Üyesi Gülçin ÇAKAN AKDOĞAN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Öğr. Üyesi Gülcan AKGÜL

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Öğr. Üyesi Merve TÜRKER BURHAN

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Öğr. Üyesi Bilgi GÜNGÖR

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Öğr. Üyesi Zeynep Ahsen KOÇER

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Öğr. Üyesi Sibel KALYONCU UZUNLAR

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Enstitümüzde 13/b-4 ile görevli Öğretim Üyeleri

Prof. Dr. Hülya AYAR KAYALI

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ

Doç. Dr. Yavuz OKTAY

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Doç. Dr. Duygu SAĞ

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Enstitümüzde 40/a ile görevli Öğretim Üyeleri

Prof. Dr. Şerife Esra ERDAL BAĞRIYANIK

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ

Prof. Dr. Şermin GENÇ

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ

Prof. Dr. Sinan GÜVEN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Doç. Dr. Arif Engin ÇETİN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Yabancı Uyruklu Öğretim Üyeleri

Dr. Öğr. Üyesi Athanasia PAVLOPOULOU

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Araştırmacılar

Dr. Ece SÖNMEZLER ADALI

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Elçin ÇAĞATAY

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Ece ÇAKIROĞLU

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Abdullah DEĞİRMENÇAY

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Duygu ERDOĞAN

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Meryem Beyza AVCI

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Sude ERİŞ

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Uğur Faruk KALKAN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Güldane Bilge KILIÇ

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Çağla NİĞDE

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Merve UÇA APAYDIN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Habibe GÖREN

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Aslı KORKMAZ

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Aytül Gül METE

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Belgüzar KARADAĞ

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Burcu ÖZDEN YÜCEL

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

Dr. Gülten KURU

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Gökçen BİLİCİ GÜLER

GENOM BİLİMLERİ VE MOLEKÜLER BİYOTEKNOLOJİ ANA BİLİM DALI

Dr. Şeyma Nur YILDIZ

BİYOTIP VE SAĞLIK TEKNOLOJİLERİ ANA BİLİM DALI

İZMİR ULUSLARARASI BİYOTIP VE GENOM ENSTİTÜSÜ MEZUNLARIMIZ ( SON 8 YIL)

EĞİTİME DEVAM EDEN ÖĞRENCİ SAYILARI

OVERVIEW

In the post-genomics era, there is undoubtedly a plethora of accumulated genomic, genetic and proteomic data. However, there is a growing gap between the biological molecules (DNA, RNA and proteins) with experimentally determined function/structure and the ones that have not been assigned to any functional/structural annotation. To handle this overwhelming amount of information, we apply bioinformatics and systems biology methods for processing, analyzing, and interpreting biological data in a meaningful way.

RESEARCH INTERESTS

My main research interests include:

• Application of bioinformatics methods for the analysis and meta-analysis of cancer genetics and genomics data.
• Phylogenetics & Comparative genomics.
• Analysis of biological sequences
• Biological networks.
• Development of bioinformatics pipelines for the analysis of biological data.

Lab Members

Pavlopoulou lab is currently seeking highly motivated graduate students interested in biostatistics. If interested, please contact athanasia.pavlopoulou@deu.edu.tr

Collaborations
www.compgen.org/home
dielectricsgroup.physics.ntua.gr/georgakilas

brianicarr@hotmail.com

OVERVIEW

Hepatocellular carcinoma (HCC) appears to consist of several poorly-defined phenotypes, with several distinct poor prognostic factors, such as high alpha-fetoprotein (AFP) and presence of portal vein thrombosis (PVT). Recently, systemic inflammation has been identified as a major independent poor prognosis factor, based on the Glasgow score that utilizes serum C-reactive protein (CRP) and albumin levels. This implicated the tumor microenvironment (inflammation) in prognosis and thus as an influence on the biology of the tumor itself.

RESEARCH INTERESTS

Our over-all aims are to: A, identify distinct clinical HCC profiles/phenotypes; to B, study the effects of inflammatory mediator influence on HCC growth and invasion in vitro; and C, to continue our previous studies on multikinase drug resistance in HCC cells and to learn how to enhance the effects of these agents on HCC growth inhibition.

RESEARCH HIGHLIGHTS

We have collaborated with a group of 15 Turkish institutions that treat HCC, to assemble a 1700 HCC patient database for phenotype analysis. We have published one paper (in Oncology) with 3 more in press, to show that Turkish HCC, which is predominantly HBV based- and thus similar to Chinese but not Western HCC in this respect- is broadly similar to western HCC, with regard to presence of PVT, importance of AFP and our identification of the characteristics of that 50% of patients that do not have elevated AFP levels. Interestingly, HCC in different regions of Turkey may have marked variations, such as the high incidence of HDV infection in HCC patients in the Diyabakir region.

We have worked on the significance of albumin and C-reactive protein (CRP) on HCC biology. We reasoned that to have such important clinical prognostic significance (high CRP and low albumin predict poor outcomes). These 2 proteins must have effects. Directly or indirectly on HCC biology. In 2017 we published 2 papers to show that low albumin levels were associated with more aggressive tumor parameters of larger tumors and more portal vein invasion, that could explain the poor prognosis 8by contrast, higher serum albumin levels were associated with smaller tumors). We followed this up, by showing that pure albumin in tissue culture could slow HCC cell line growth a limit invasiveness. This sets the scene for future experiments to test these ideas in animals. We have recently shown that high CRP levels are associated with larger and more aggressive tumors in Turkish HCC patients (in press) and we are beginning to study the actions of pure CRP on and in (CRP is synthesized by cells of liver origin) HCC cells in culture.

In collaboration with the labs of Profs Nese Atabey and Esra Erdal, we are working in the development of Regorafenib-resistant and double Regorafenib/Sorafenib resistant HCC cell lines, to examine both the peculiarities of their cell signaling compared to the parental cells and also to identify possible mechanisms of limiting their resistance to drug growth-inhibitory actions. Furthermore, since both Sorafenib and Regorafenib are FDA-approved for treating HCC patients, they are quite toxic (multiple side-effects) and thus we are examining ways to enhance the effects on HCC cells of both drugs when used at low concentrations.

Growth Factor Signaling in Cancer

nese.atabey@deu.edu.tr Members [tippy title=”Ayşim Güneş, Postdoctoral Fellow”] Ayşim GÜNEŞ, PhD a.gkizil@hotmail.com [/tippy] [tippy title=”Erkan Kahraman, Postdoctoral Fellow”] Erkan KAHRAMAN, PhD erkankahraman@gmail.com [/tippy] [tippy title=”Hande Topel, PhD Student”] Hande Topel [/tippy] [tippy title=”Yeliz Yılmaz, PhD Student”] Yeliz YILMAZ yelizyg@gmail.com [/tippy] Ezgi Bağırsakçı, MSc Student Mesude Angın, MSc Student Dehan Çömez, MSc Student Gülsün Bağcı, MSc Student

OVERVIEW

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer and the third leading cause of cancer-related deaths worldwide. Hepatocyte growth factor (HGF)/c-Met signaling is particularly important in the development of HCC as it controls growth, survival, migration and differentiation of tumor cells. Others and we have shown that abnormalities in HGF/c-Met signaling are implicated in tumor development and progression in a variety of cancers. The increase in c-Met expressing stem/progenitor cells in the liver is required for hepatocarcinogenesis, and high c-Met expression is correlated with metastasis, poor prognosis, and drug resistance. An elevated HGF level is uncommon in tumorigenesis except for breast tumors. Therefore, ligand-independent c-Met activation in HCC is a critical phenomenon that should be investigated further.

RESEARCH INTERESTS

Our group is focused on signaling pathways that modulate the growth, motility, and invasion of hepatocellular carcinoma and using this molecular knowledge to improve the diagnosis and treatment of HCC. Our aim is to understand the molecular mechanisms behind the aggressive behavior and drug resistance in HCC and to translate this molecular knowledge to improve diagnosis and treatment.

Currently, our projects encompass:

1) The molecular mechanisms of HGF/c-Met mediated invasion and metastasis in HCC,
2) The effects of tumor microenvironment on the regulation of signaling networks and cellular behaviors of HCC,
3) The roles of non-coding RNAs in the regulation of c-Met signaling in HCC,
4) Fabrication and validation of a new lab-on-a-chip device for early diagnosis of metastasis.

In the next 5 years, we aim to:

• Identify the role of HGF/c-Met signaling in the regulation of glucose metabolism in HCC and further use this knowledge for developing strategies to prevent HCC.
• Understand the functional role of the HGF/c-Met axis in acquired sorafenib resistance in HCC cells and to improve targeted therapies of HCC patients.
• Fabricate and validate a Lab-on-a-chip (LOC) system that can predict the metastatic and invasive ability to circulate tumor cells (CTCs) in HCC and that can also determine the effects of drugs on tumor metastasis.

Lab members:

Atabey lab is currently seeking highly motivated PhD students. If interested, please contact nese.atabey@deu.edu.tr

Etkinlik başvurularınız için aşağıdaki formu doldurduktan sonra lütfen etkinlik sorumlumuza e-posta ile iletiniz.

Cell Culture Room

• Class II Biosafety Air Cabinet Thermo Scientific Holten Safe 2010 (3 Pcs)
• Refrigerator +4 Ugur – USS 748 Lt. Vertical Vertical (1 Unit)
• CO2 Incubator Thermo Scientific Hepa Class 100 (1 pc)
• Water Bath General Purpose Core- NB9 (1 Unit)
• Phase Contrast Inverted Microscope Olympus – CKX41 (1 Piece)
• Table Top Centrifuge Hettich Universal 320 (1 pc)
• Vortex Device Genie2 (1 Piece)
• Fume Hood (1 pcs)
• Vacuum Pump KNF lab (3 Pcs)
• Autoclave table systec DE-45 (1 pcs)

B008 Sterilization chamber

• Ice Maker Brema – IF90 (1 Piece)
• Semi Analytic Balance Sartorius (1 Piece)
• Analytical Balance Sartorius (1 unit)
• Sterilization Oven (1 unit)
• Autoclave – Small size (2 pcs)

Use of all devices in laboratory B005

• Precision Balance Sartorius GE512-OCE 1 piece
• Cell Concentration Determination Device Beckman Coulter 1 Unit
• Ultra Pure Water Device Thermo TKA Smart2pure 12UV / UF 1 piece
• Gel Imaging Device 1 Unit
• Deep freezer -20 Siemens 1 unit
• Deep freezer +4 Siemens 1 unit
• Deep Freezers -20 Bosch – GSN51AW30 3 pieces
• Refrigerator +4 Ugur USS 748 LT. Vertical Vertical 2 Pieces
• High Voltage Power Supply Thermo OWL -EC300XL2 1 Unit
• Low Voltage Power Supply Thermo OWL -EC3000XL2 1 Unit
• Electronic Bunzen Integra 1440 1 Unit
• Laboratory Type Microwave Oven Bosch HMT 72G420 1 Unit
• Vacuum Pump KNF N840 FT 18 34 LT / DK 10 1 Unit
• Mechanical Mixer Boeco-Multishaker PSU20 1 Unit
• Mechanical Mixer Wisestir-MSH-20A 1 piece
• PCR Rotary Table Top Microfluid Beckman Coulter – 22R Centrifuge 1 Piece
• General Purpose Desktop Microfuge Beckman Coulter Allegra X-15 R Centrifuge 1 Unit
• Quick Precision Mini Centrifuge IKA Mini G 1 Pcs
• Deep Freezers -86 Thermo Forma 1 Unit
• Western blot, mini vertical electrophoresis, 1 set
• Nanodrop / spectrophotometer 1 unit
• Heater block 1 piece
• Pullers 1 Unit
• Gradient PCR device 1 unit
• Vortex (Genie 2) device 4 pieces
• WMSC10 with magnetic stirrer / heater 1 unit
• PCR- SimpliAmp / Thermal cycler Applied Biosystems 1 Unit
• Stuart orbital Incubator SI500 1 Unit

IBG-AELEC Secretariat

Tuba AKUNAL
tuba.akunal@deu.edu.tr
+90(232) 412 67 70
www.ibg.deu.edu.tr/en/ibg-aelec

Address

Izmir International Biomedicine and Genome Institute (iBG-izmir)
Dokuz Eylul Universitesi Saglik Yerleskesi
Balcova 35340 Izmir/TURKEY

Dokuz Eylul University Izmir International Biomedicine and Genome Institute is established on 09/03/2015 by the Council of Ministers after the approval of the University Senate.

The Institute has two departments: Genome Sciences and Molecular Biotechnology and Biomedicine and Health Technologies. Genome Sciences and Molecular Biotechnology has M.Sc., Ph.D. and Integrated Ph.D. programs in “Molecular Biology and Genetics”.

Our programs are interdisciplinary and international. The institute provides students with the opportunity to conduct basic and translational research.

All of the programs are taught in English.

Dokuz Eylül Üniversitesi İzmir Uluslararası Biyotıp ve Genom Enstitüsü üniversite Senatosu tarafından onaylanarak, 09/03/2015 tarihinde Bakanlar Kurulu Kararı ile kurulmuştur.

Enstitünün Genom Bilimleri ve Moleküler Biyoteknoloji ve Biyotıp ve Sağlık Teknolojileri isimli iki anabilim dalı mevcuttur. Genom Bilimleri ve Moleküler Biyoteknoloji A.D.’da “Moleküler Biyoloji ve Genetik” Yüksek Lisans, Doktora ve Bütünleşik Doktora programları bulunmaktadır.

Programlarımız disiplinler arası ve uluslararası özellik taşımaktadır. Enstitümüzde öğrencilere temel ve uygulamalı araştırmaların ön planda olduğu araştırmalar yapma olanağı sunulmaktadır.

Programların tamamında öğretim dili İngilizcedir.

• List of critical equipments for USP
  • 3L, 5L, 10L glass bioreactors and 50L wave bioreactor
  • Biosafety cabinet class II
  • Cell culture CO2 incubators
  • Shaker CO2 incubator
  • Osmometer
  • Metabolic analyser
  • Cell counter
• List of critical equipments for DSP
  • TFF system
  • AKTA system
  • Viral filtration system

• Upstream Process Development (USP)
  • Mammalian cell culture process development for production of monoclonal antibodies and recombinant protein
  • Clone Selection based on the productivity and quality
  • Single cell selection
  • Cell line adaptation (Serum free or suspension)
  • Master cell bank (MCB) & working cell bank (WCB) generation
  • Media development (chemically defined)
  • Development of nutrients & feed strategy to increase culture growth and productivity (animal component free)
  • Scale up studies
  • Development of key aspects of monitoring & control technology
  • Scale down model for process characterization
  • Design of experiments (DOE) for optimization
  • Process Analytical Technology (PAT) Development
  • Production at pilot scale for preclinical and early clinical stage studies
  • Transfer technology and support
• Downstream Process Development (DSP)
  • Development of recombinant therapeutic proteins and monoclonal antibody purification process
  • Prefiltration process development (right pre filtration selection to reduce the bioburden)
  • Chromatographic separation
  • Ultrafiltration and diafiltration development
  • Virus clearance studies
  • Scale down model for process characterization
• cGMP Manufacturing service
  • iBG-Izmir will provide service to biotech industries for the production of recombinant proteins in bulk for their clinical trials and commercial use. Initially we will be able to provide up to 200L production capacity and in later phase up to 1000L. GMP facility is under construction will be ready to provide service in 2017

iBG-Izmir biopharmaceuticals unit has the caliber to provide service to the biotech industries for complete upstream and downstream process development including cell line development. We have perfect team of scientist with industrial and academic back ground with the capability to deliver and execute to meet the defined product quality.

We provide the following services below for biotech industries. If you are looking for the recombinant protein or biosimilar product development and/or for small scale manufacturing for preclinical studies please contact us we will be happy to help you.

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464.

Serhat Tozburun, Cedric Blatter, Meena Siddiqui, Eelco F. J. Meijer, and Benjamin J. Vakoc. Phase-stable Doppler OCT at 19 MHz using a stretched-pulse mode-locked laser. Biomedical Optics Express 2018; 9(3): 952-961. doi: 10.1364/BOE.9.000952.

Meena Siddiqui, Ahhyun S. Nam, Serhat Tozburun*, Norman Lippok, Cedric Blatter & Benjamin J. Vakoc. High-speed optical coherence tomography by circular interferometric ranging. Nature Photonics 2018 Jan 26; 12: 111–116. doi: 10.1038/s41566-017-0088-x.

Brian I. Carr, Hikmet Akkiz, Oguz Üsküdar et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464. doi: 10.4172/clinical-practice.1000393.

Sag D, Özkan M, Kronenberg M, Wingender G. Improved Detection of Cytokines Produced by Invariant NKT Cells. Sci Rep 2017 Nov 30; 7(1):16607. doi: 10.1038/s41598-017-16832-1.

U. Blache, J. Guerrero, S. Güven, A.S. Klar, A. Scherberich. Microvascular Networks and Models, In vitro Formation, in: W. Holnthoner, A. Banfi, J. Kirkpatrick, H. Redl (Eds.),. Vascularization for Tissue Engineering and Regenerative Medicine. Springer International Publishing Cham, 2017, pp. 1-40.

Cigdem Ozen, Meltem Ceylan Unlusoy, Nazanin Aliary, Mehmet Ozturk, Oya Bozdag Dundar. Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives. J Pharm Pharm Sci 2017 Nov; 20 (1): 415-427. doi:10.18433/J38P9R.

Gökhan Karakülah. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics 2017 Nov; 17. doi:10.1016/j.ygeno.2017.11.002.

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Oct 31;32(4):e391-e396. doi:10.5301/ijbm.5000300.

Refolo MG, D’Alessandro R, Lippolis C, Carella N, Cavallini A, Messa C, Carr BI. IGF-1R tyrosine kinase inhibitors and Vitamin K1 enhance the antitumor effects of Regorafenib in HCC cell lines. Oncotarget 2017 Sep 30; 8(61):103465-103476. doi:10.18632/oncotarget.21403.

Onur Tokel, Ahmet Turnalı, Ghaith Makey, et al. In-chip microstructures and photonic devices fabricated by nonlinear laser lithography deep inside silicon. Nature Photonics 2017 Sep; 11: 639–645. doi:10.1038/s41566-017-0004-4.

Ozen C, Ceylan-Unlusoy M, Ozturk M, Bozdag-Dundar O. A novel chromonyl thiohydantoin with anti-proliferative action on primary hepatocellular carcinoma cells. Med Chem Res 2017 Sep; 1-8. doi:10.1007/s00044-017-2037-0.

Yuqing Zhu, Vahid Serpooshan, Sean Wu, Utkan Demirci, Pu Chen, Sinan Güven. Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly. In: Methods in Molecular Biology. Humana Press 2017 Sep; 1-12. doi: 10.1007/7651_2017_68.

Lina Zelinger, Gökhan Karakülah*, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J. Brooks, Anand Swaroop. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative Ophthalmology & Visual Science 2017 Sep; 58: 4422-4435. doi: 10.1167/iovs.17-21805.

Ozturk M, Batur T, Ekin U, Erdogan A, İscan E, Keles U, Oz O, Ozen C. Molecular Pathogenesis of Liver Cancer. J Gastrointest Cancer. 2017 Jul 17 (Review). doi: 10.1007/s12029-017-9957-2. [Epub ahead of print].

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Aug 28. doi: 10.5301/ijbm.5000300.

Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017 Aug; 95(4):491-499. doi: 10.1139/bcb-2016-0190.

Yılmaz Y, Güneş A, Topel H, Atabey N. Signaling Pathways as Potential Therapeutic Targets in Hepatocarcinogenesis. J Gastrointest Cancer 2017 Aug 18. doi: 10.1007/s12029-017-9958-1.

Carr BI, Guerra V. Validation of a Liver Index and Its Significance for HCC Aggressiveness. J Gastrointest Cancer 2017 Jun 20. doi: 10.1007/s12029-017-9971-4.

Ezgi Karaca*, João P.G.L.M. Rodrigues, Andrea Graziadei, Alexandre M.J.J. Bonvin, Teresa Carlomagno. M3: an integrative framework for structure determination of molecular machines. Nature Methods 2017. doi: 10.1038 / nmeth.4392.

Alural B, Ayyildiz ZO, Tufekci KU, Genc S, Genc K. Erythropoietin Promotes Glioblastoma via miR-451 Suppression. Vitam Horm. 2017;105:249-271. doi: 10.1016/bs.vh.2017.03.002. Epub 2017 Apr 19. PubMed PMID: 28629521.

Gökhan Karakülah. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 (in press), doi: 10.1515/jib-2017-0009.

Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J. 2017 Aug; 284(15): 2513-2526. doi: 10.1111/febs.14139.

Akyerli C., Yuksel S., Can O., Erson-Omay Z., Oktay Y.*, Cosgun E., Ulgen E., Erdemgil Y., San A., von Deimling A., Gunel M., Yakicier C., Pamir M.N., Ozduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. Journal of Neurosurgery. 2017 Jun; 16:1-13. doi: 10.3171/2016.11.

Schneider F, Waithe D, Clausen MP, Galiani S, Koller T, Ozhan G, Eggeling C, Sezgin E. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS. Mol Biol Cell. 2017 Jun 1;28(11): 1507-1518. doi: 10.1091/mbc.E16-07-0536.

Oktay Y., Boylu C.A., Özduman K. Gliom Gelişiminde Genetik Yatkınlığın Rolü. Türk Nöroşirürji Dergisi. 2017 May; 27(2): 122-130.

Gökhan Karakülah, Aslı Suner. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 (in press), doi:10.1016/j.ygeno.2017.05.008.

Bağırsakçı E., Şahin E., Atabey N., Erdal E. & Carr B.I. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology. 2017 May 10. doi:10.1159/000471807.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar 30; 7:45661. doi:10.1038/srep45661.

Marino IR, Carr B.I. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15(Suppl 2):1-6.

Alural B, Genc S, Haggarty S. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biology Psychiatry. 2017 Feb; 6;73:87-103 doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Pinato D., Sharma R., Allara E., Yen C., Arizumi T., Kubota K., Bettinger D., Jang J.W., Smirne C., Kim Y.W., Kudo M., Howell J., Ramaswami R., Burlone M.E., Guerra V., Thimme R., Ishizuka M., Stebbing J., Pirisi M. & Carr B.I. The ALBI grade provides objective hepatic reserve estimation across each BCLC stage of hepatocellular carcinoma. J. Hepatology, 2017 Feb; 66(2): 338-346. doi:http://dx.doi.org/10.1016/j.jhep.2016.09.008.

van Waalwijk van Doorn LJ, Gispert JD, Kuiperij HB, et al. Improved Cerebrospinal Fluid-Based Discrimination between Alzheimer’s Disease Patients and Controls after Correction for Ventricular Volumes. J Alzheimers Dis. 2017 Jan 24; 56(2):543-555. doi: 10.3233/JAD-160668

Park CG, Park Y & Suh BC. The HOOK region of voltage-gated Ca2+ channel β subunits senses and transmits PIP2 signals to the gate. J Gen Physiol. 2017 Jan 13. doi:10.1085/jgp.201611677.

Arslan N, Guzel O, Kose E, Yılmaz U, Kuyum P, Aksoy B, Çalık T. Is ketogenic diet treatment hepatotoxic for children with intractable epilepsy? Seizure. 2016 Dec; 43: 32-38. doi:10.1016/j.seizure.2016.10.024.

Ebru Diler, Turgay Unver & Gökhan Karakülah. Differential Expression of Hyperhydricity Responsive Peach miRNAs. Journal of Integrative Bioinformatics. 2016 Dec; 13(5): 308. doi:10.2390/biecoll-jib-2016-308.

İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14; 1-12. doi:10.1007/s12079-016-0368-0.

Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLoS ONE. 2016 Dec 9; 11(12): e0167698. doi:10.1371/journal.pone.0167698.

Calibasi Kocal G, Güven S, Foygel K, Goldman A, Chen P, Sengupta S, Paulmurugan R, Baskin Y, Demirci U. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow. Sci Rep. 2016 Dec 2; 6:38221. doi: 10.1038/srep38221.

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah*, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Reports. 2016 Nov 22; 17(9): 2460-2473. doi:http://dx.doi.org/10.1016/j.celrep.2016.10.074.

Arslan N, Kose E, Guzel O. The Effect of Ketogenic Diet on Serum Selenium Levels in Patients with Intractable Epilepsy. Biol Trace Elem Res. 2016 Nov 21. doi:10.1007/s12011-016-0897-7.

Erbayraktar Z, Alural B, Erbayraktar RS, Erkan EP. Cell division cycle 7-kinase inhibitor PHA-767491 hydrochloride suppresses glioblastoma growth and invasiveness. Cancer Cell Int. 2016 Nov 18;16:88. eCollection 2016. doi:10.1186/s12935-016-0364-8.

Muhammad Ayaz Mustufa, Cigdem Ozen, Imran Ali Hashmi, Afshan Aslam, Jameel Ahmed Baig, Gokhan Yildiz, Shoaib Muhammad, Imam Bakhsh Solangi, Naim ul Hasan Naqvi, Mehmet Ozturk and Firdous Imran Ali. Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma. BMC Cancer. 2016, Nov 14; 16: 883. doi:10.1186/s12885-016-2942-5.

Büyüköz M, Erdal E, Alsoy Altinkaya S. Nanofibrous gelatin scaffolds integrated with NGF-loaded alginate microspheres for brain tissue engineering. J Tissue Eng Regen Med. 2016 Nov 12. doi: 10.1002/term.2353.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A. Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma. OncoTargets and Terapy. 2016, Nov 9; 9: 6843—6855. doi:10.2147/OTT.S117743.

Carr B.I., Guerra V., Giannini E.G. et al. A Liver Index and its Relationship to Indices of HCC Aggressiveness. J Integr Oncol. 2016 Oct;5(4). pii: 178. doi: 10.4172/2329-6771.1000178.

Erkan D, Kayali HA. Replacement of Soybean Meal with Animal Origin Protein Meals Improved Ramoplanin A2 Production by Actinoplanes sp. ATCC 33076. Appl Biochem Biotechnol. 2016 Sep;180(2):306-21. doi:10.1007/s12010-016-2100-1.

Hani Alotaibi, Nese Atabey, Kasım Diril, Esra Erdal, Mehmet Ozturk. Molecular Mechanisms of Hepatocellular Carcinoma, Chapter Hepatocellular Carcinoma Part of the series Current Clinical Oncology. Springer. 2016, Aug 27; 43-63. doi:10.1007/978-3-319-34214-6_3.

Alagoz Y., Gurkok T.,  Zhang B. & Unver T. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology. Sci Rep. 2016 Aug 3; 6:30910. doi: 10.1038/srep30910.

Bakır Y., Eldem V., Zararsız G. & Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. Plant Genome. 2016 Jul; 9(2). doi:10.3835/plantgenome2015.09.0080.

Marsano A, Medeiros da Cunha CM, Ghanaati S, Gueven S, Centola M, Tsaryk R, Barbeck M, Stuedle C, Barbero A, Helmrich U, Schaeren S, Kirkpatrick JC, Banfi A, Martin I. Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling. Stem Cells Transl Med. 2016 Jul 26. doi: 10.5966/sctm.2015-0321.

Pavlopoulou A., Oktay Y., Vougas K., Louka M., Vorgias C.E., Georgakilas A.G. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 2016, Jul 19; 380(2):485-493. doi: 10.1016/j.canlet.2016.07.018.

Carr B.I., Guerra V., Giannini E.O. et al. An HCC Aggressiveness Index and Blood GTP, Blirubin and Platelet Levels. J. Integrative Oncology. 2016 Jun 20; 5:172. doi: 10.4172/2329-6771.1000172.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N. & Özduman K. IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Sci Rep. 2016 Jun 10; 6: 27569. doi: 10.1038/srep27569.

Yilmaz Y, Atabey N, Erdal E & Brian I. Carr. Platelets, Microenvironment and Hepatocellular Carcinoma. Biochemistry & Analytical Biochemistry, 2016 June 29; 5:281 (Review). doi:10.4172/2161-1009.1000281.

Antonio Mazzoccaa, Giovanni Ferrarob, Giovanni Misciagnac, Brian I. Carr. A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm. Medical Hypotheses, 2016, Aug; 93: 132-137. doi:10.1016/j.mehy.2016.05.027.

Karakülah G, Karakuş M, Suner A, Demir S, Arserim SK, Töz S, Özbel Y. sandflyDST: a dynamic web-based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe, and user study. Medical and Veterinary Entomology, 2016 June 24. doi:10.1111/mve.12182.

Can Küçük, Xiaozhou Hu, Qiang Gong, Bei Jiang, Adam Cornish, Philippe Gaulard, Timothy McKeithan, Wing C. Chan. Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. The American Journal of Pathology, 2016 June; 186(6): 1435-1441. doi:10.1016/j.ajpath.2016.02.011.

Zeynep Firtina Karagonlar, Doğukan Koç, Eren Şahin, Sanem Tercan Avci, Mustafa Yilmaz, Neşe Atabey, Esra Erdal. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and Biophysical Research Communications, 2016 June 3; 474(3): 482-490. doi:10.1016/j.bbrc.2016.04.137.

Yakup Bakır, Vahap Eldem, Gökmen Zararsız, Turgay Unver. Global Transcriptome Analysis Reveals Significant Differences in Gene Expression Patterns Between The Non-Hyperhydric and Hyperhydric Leaves of Prunus persica. The Plant Genome, 2016, May; 9(2): 1-9.

Salimi R, Yener N, Safari R. Use and Evaluation of Newly Synthesized Fluorescence Probes to Detect Generated OH• Radicals in Fibroblast Cells. J Fluoresc. 2016 May; 26(3):919-24. doi: 10.1007/s10895-016-1780-9.

Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated hepatocyte growth factor expression as an autocrine c‐Met activation mechanism in acquired resistance to sorafenib in hepatocellular carcinoma cells. Cancer Sci. 2016 Apr; 107(4):407-416 doi: 10.1111/cas.12891.

Carr BI & Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and Its Relationship to Liver Enzyme Levels. Oncology 2016 Mar 15; 90(4). doi: 10.1159/000444394.

Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites. Am J Surg Pathol, 2016 Mar 11. doi: 10.1097/PAS.0000000000000634.

Carr BI & Guerra V. Low Alpha-Fetoprotein Levels Are Associated with Improved Survival in Hepatocellular Carcinoma Patients with Portal Vein Thrombosis. Digestive Diseases and Sciences, 2016 Feb 26; 61(3):937-947. doi: 10.1007/s10620-015-3922-3.

Ferroudj S, Yildiz G, Bouras M, Iscan E, Ekin U, Ozturk M. Role of fanconi anemia/BRCA pathway genes in hepatocellular carcinoma chemoresistance. Hepatol Res. 2016 Feb 16. doi: 10.1111/hepr.12675.

Carr BI & Guerra V. Hepatocellular Carcinoma Extrahepatic Metastasis in Relation to Tumor size and Alkaline Phosphatase Levels. Oncology 2016 Feb 12; 90(3):1-7. doi: 10.1159/000443480.

Durmaz I, Guven EB, Ersahin T, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine. 2016 Jan 15; 23(1):42-51. doi: 10.1016/j.phymed.2015.11.012.

Wingender G. From the deep sea to everywhere? Environmental antigens for iNKT cells. Arch Immunol Ther Exp, 2015 Dec 24 (Review). doi: 10.1007/s00005-015-0381-7.

Güzel O, Yılmaz U, Uysal U, Arslan N. The effect of olive oil-based ketogenic diet on serum lipid levels in epileptic children. Neurol Sci. 2015 Dec 23; 1-6. doi: 10.1007/s10072-015-2436-2.

Namkoong B, Guven S, Ramesan S, Liaudanskaya V, Abzhanov A, Demirci U. Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomaterialia, 2015 Dec 07. doi: 10.1016/j.actbio.2015.12.004.

Hanna RN, Cekic C, Sag D, Tacke R, Thomas GD, Nowyhed H, Herrley E, Rasquinha N, McArdle S, Wu R, Peluso E, Metzger D, Ichinose H, Shaked I, Chodaczek G, Biswas SK, Hedrick CC. Patrolling Monocytes Control Tumor Metastasis to the Lung. Science. 2015, Nov 20; 350(6263): 985-90.

Wingender G & Kronenberg M. Characterization of human T cell subsets via surface markers. Cytometry A, 2015, Oct 27; 87A; 1067-1069.

D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015 Oct 19; 16(18):1-8. doi: 10.1517/14656566.2015.1101065.

Wingender G, Sag D, Kronenberg M. NKT10 cells: a novel iNKT cell subset. Oncotarget. 2015 Sept 29; 6(29): 26552-26553 (Review). doi: 10.18632/oncotarget.5270.

Wingender G, Birkholz A, Sag D, Farber E, Chitale S, Howell AR, Kronenberg M. Selective conditions are required for the induction of iNKT cell hypo-responsiveness by antigenic stimulation. The Journal of Immunology. 2015 Sept 9; 195: 3838-3848. doi: 10.4049/jimmunol.1500203.

Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. Journal of Experimental & Clinical Cancer Research. 2015 Sept 2; 34(1):90. doi: 10.1186/s13046-015-0210-1.

Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Seminars in Oncology. 2015 Aug; 42(4):672-678. doi: 10.1053/j.seminoncol.2015.05.004.

Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. The International Journal of Biochemistry & Cell Biology. 2015 Aug; 65:169-181. doi: 10.1016/j.biocel.2015.05.025.

Hu X, Chan WC, Kücük C. Generation of a genetically engineered aggressive nk-cell leukemia cell line with stable IL2 expression. Acta Medica International. 2015 Jul; 2(2):78-84. doi: 10.5530/ami.2015.3.6.

Ozhan G and Weidinger G. Wnt/β-catenin signaling in heart regeneration. Cell Regen (Lond). 2015 Jul 8; 4(1):3. doi: 10.1186/s13619-015-0017-8

Alotaibi H, Basilicata MF, Shehwana H, Kosowan T, Schreck I, Braeutigam C, Konu O, Brabletz T, Stemmler MP. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2015 June; 1849(6):731-742. doi: 10.1016/j.bbagrm.2015.01.005.

Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28; 9:209. doi: 10.3389/fncel.2015.00209.

Dilek Cevik, Gokhan Yıldız & Mehmet Ozturk. Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations. World J Gastroenterol. 2015 Jan 7; 21(1): 311–317. doi: 10.3748/wjg.v21.i1.311.

Alural B, Duran GA, Tufekci KU, Allmer J, Onkal Z, Tunali D, Genc K, Genc S. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells. Frontiers in Immunology. 2014 Sep 30; 5:475. doi: 10.3389/fimmu.2014.00475.

* Current address IBG.

İzmir Uluslararası Biyotıp ve Genom Enstitüsü, Türkiye Büyük Millet Meclisi’nde 16/02/2015 tarihinde kabul edilen ve 9 Mart 2015 tarihli, 29290 sayılı T.C. Resmî Gazete’de yayımlanan 2015/7321 sayılı karar doğrultusunda; Dokuz Eylül Üniversitesi Rektörlüğü bünyesinde faaliyet gösteren Hemodiyaliz-Transplantasyon Enstitüsünün adının İzmir Uluslararası Biyotıp ve Genom Enstitüsü olarak değiştirilmesiyle çalışmalarına başlamıştır.

07/04/2015 tarihli ve 439 sayılı Senato kararı ile 28/04/2015 tarihli Yükseköğretim Kurulu (YÖK) Yürütme Kurulu kararı doğrultusunda, Genom Bilimleri ve Moleküler Biyoteknoloji Anabilim Dalı ile Biyotıp ve Sağlık Teknolojileri Anabilim Dalı kurulmuştur.

10/08/2016 tarihli YÖK Yürütme Kurulu toplantısında, Genom Bilimleri ve Moleküler Biyoteknoloji Anabilim Dalı bünyesinde Moleküler Biyoloji ve Genetik Tezli Yüksek Lisans Programı (İngilizce) ile Doktora Programı (İngilizce) açılması uygun görülmüştür.

26/08/2020 tarihli YÖK Yürütme Kurulu kararı ile ise Biyotıp ve Sağlık Teknolojileri Anabilim Dalı bünyesinde Biyotıp ve Sağlık Teknolojileri Tezli Yüksek Lisans Programı (İngilizce) ile Biyotıp ve Sağlık Teknolojileri Doktora Programı (İngilizce) açılmıştır.

2015 yılında eğitim-öğretim faaliyetlerine başlayan İzmir Uluslararası Biyotıp ve Genom Enstitüsü, giderek artan öğrenci kapasitesi ve akademik faaliyetleriyle çalışmalarını sürdürmektedir.

Kuruluştan Bugün Kadar Görev Yapmış Olan Yöneticiler

Prof.Dr.Şermin GENÇ                       02.09.2025-

Prof.Dr.İ.Mehmet Ali ÖKTEM        25.02.2021-02.09.2025

Prof.Dr.Sefa KIZILDAĞ                    20.02.2018-20.02.2021

Prof.Dr.Mehmet ÖZTÜRK                09.03.2015-14.02.2018

Professor Brian Carr was born in Glasgow, Scotland in 1944 and grew up in London.

He graduated medical school at the University of London in 1967 and worked for several years in medicine and then in medical oncology. He realized that medical oncology was confusing and mainly witchcraft and decided to learn how to do research and was apprenticed at the Imperial Cancer Research Labs, London with Renato Dulbecco. After his molecular biology PhD (5′-mRNA capped ends) he moved after his advisor’s Nobel Prize with him to the USA.

He then repeated a solid tumor clinical Fellowship and simultaneous Post-Doc in chemical hepatocarcinogenesis at the McArdle Labs, Madison, WI. His first staff job was for 10 yr at the City of Hope, LA, first as Assistant and then as Associate Professor of Medicine, continuing to work on rodent hepatocarcinogenesis, with special interest in natural growth inhibitors (TGF beta).

He was then invited to set up the first liver cancer (HCC) group within the Liver Transplant Institute in Pittsburgh and was appointed as full Professor with tenure and worked there for 20 yr, both running the clinical HCC service and his lab working on HCC growth regulation.

His clinical interests have been for a long time in developing new HCC therapies, focussing initially on hepatic chemoembolization and subsequently on Yttrium-90 bead hepatic internal radioembolization and more recently on vitamin K as HCC therapy. Currently, he is analyzing HCC databases involving several thousand patients, to identify HCC phenotypes with differing clinical parameter patterns and prognoses. The main findings are that context is key, and that any given parameter (such as serum bilirubin or tumor mass) can only be understood in its total clinical context.

Scientifically, he spent several yr working on K vitamins, since their aberrant use is a key biochemical characteristic of HCC and helps identify one of the most important HCC tumor markers, DCP or des-gamma-carboxy prothrombin. DCP positive and AFP positive tumor cells have quite different regulation, just as AFP positive and AFP negative HCCs have differing phenotypes and prognosis. Vitamin K1 mediates inhibitory phosphorylation of Raf via PKC. Sorafenib is an FDA-approved HCC multikinase inhibitor working through direct Raf inhibition. Thus, vitamin K enhances Sorafenib-mediated Raf inhibition and thus enhances the HCC cell growth inhibition.

The clinical observations of HCC context, have led to the recent observations that blood platelet levels identify phenotypically different HCC patient subsets. This has been developed further by recently examining the actions of platelet lysates as promoters of HCC growth and invasion. This has been shown to be due in large part to platelet content of epidermal growth factor (EGF) and insulin-like growth factor 1 (IGF-1). These factors also modulate HCC growth sensitivity and resistance to multikinase inhibitors. Therefore, the net effect of these therapies depends in part on the tumor (HCC) microenvironment. Thus, clinical observations led to experimental mechanistic observations, that in turn have led to clinical application: translational work.
He has published 296 papers-mainly on HCC and 4 books, 3 of which are on HCC and one on Psychological Aspects of Cancer and has written the chapter on Liver Tumors for the last 3 editions of: Harrison’s Principles of Internal Medicine (19th edition, April 2015).

Contact Information: brianicarr@hotmail.com

The İzmir International Biomedicine and Genome Institute commenced its activities following the renaming of the Hemodialysis–Transplantation Institute, which had been operating under the Rectorate of Dokuz Eylül University, to the İzmir International Biomedicine and Genome Institute, in accordance with Decision No. 2015/7321 adopted by the Grand National Assembly of Türkiye on 16/02/2015 and published in the Official Gazette of the Republic of Türkiye dated 9 March 2015, No. 29290.

Pursuant to the Senate Decision dated 07/04/2015 and numbered 439, and the decision of the Executive Board of the Council of Higher Education (YÖK) dated 28/04/2015, the Departments of Genome Sciences and Molecular Biotechnology and of Biomedicine and Health Technologies were established.

At the meeting of the YÖK Executive Board held on 10/08/2016, it was approved to open the Molecular Biology and Genetics Master’s Program (with Thesis, English) and the Doctoral Program (English) within the Department of Genome Sciences and Molecular Biotechnology.

By the decision of the YÖK Executive Board dated 26/08/2020, the Master’s Program in Biomedicine and Health Technologies (with Thesis, English) and the Doctoral Program in Biomedicine and Health Technologies (English) were established within the Department of Biomedicine and Health Technologies.

Having started its educational activities in 2015, the İzmir International Biomedicine and Genome Institute continues its operations with a steadily increasing student capacity and expanding academic activities.

Administrators Who Have Served Since the Establishment

Prof. Dr. Şermin GENÇ  02.09.2025 –

Prof. Dr. İ. Mehmet Ali ÖKTEM 25.02.2021 – 02.09.2025

Prof. Dr. Sefa KIZILDAĞ  20.02.2018 – 20.02.2021

Prof. Dr. Mehmet ÖZTÜRK  09.03.2015-14.02.2018

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464.

Serhat Tozburun, Cedric Blatter, Meena Siddiqui, Eelco F. J. Meijer, and Benjamin J. Vakoc. Phase-stable Doppler OCT at 19 MHz using a stretched-pulse mode-locked laser. Biomedical Optics Express 2018; 9(3): 952-961. doi: 10.1364/BOE.9.000952.

Meena Siddiqui, Ahhyun S. Nam, Serhat Tozburun*, Norman Lippok, Cedric Blatter & Benjamin J. Vakoc. High-speed optical coherence tomography by circular interferometric ranging. Nature Photonics 2018 Jan 26; 12: 111–116. doi: 10.1038/s41566-017-0088-x.

Brian I. Carr, Hikmet Akkiz, Oguz Üsküdar et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464. doi: 10.4172/clinical-practice.1000393.

Sag D, Özkan M, Kronenberg M, Wingender G. Improved Detection of Cytokines Produced by Invariant NKT Cells. Sci Rep 2017 Nov 30; 7(1):16607. doi: 10.1038/s41598-017-16832-1.

U. Blache, J. Guerrero, S. Güven, A.S. Klar, A. Scherberich. Microvascular Networks and Models, In vitro Formation, in: W. Holnthoner, A. Banfi, J. Kirkpatrick, H. Redl (Eds.),. Vascularization for Tissue Engineering and Regenerative Medicine. Springer International Publishing Cham, 2017, pp. 1-40.

Cigdem Ozen, Meltem Ceylan Unlusoy, Nazanin Aliary, Mehmet Ozturk, Oya Bozdag Dundar. Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives. J Pharm Pharm Sci 2017 Nov; 20 (1): 415-427. doi:10.18433/J38P9R.

Gökhan Karakülah. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics 2017 Nov; 17. doi:10.1016/j.ygeno.2017.11.002.

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Oct 31;32(4):e391-e396. doi:10.5301/ijbm.5000300.

Refolo MG, D’Alessandro R, Lippolis C, Carella N, Cavallini A, Messa C, Carr BI. IGF-1R tyrosine kinase inhibitors and Vitamin K1 enhance the antitumor effects of Regorafenib in HCC cell lines. Oncotarget 2017 Sep 30; 8(61):103465-103476. doi:10.18632/oncotarget.21403.

Onur Tokel, Ahmet Turnalı, Ghaith Makey, et al. In-chip microstructures and photonic devices fabricated by nonlinear laser lithography deep inside silicon. Nature Photonics 2017 Sep; 11: 639–645. doi:10.1038/s41566-017-0004-4.

Ozen C, Ceylan-Unlusoy M, Ozturk M, Bozdag-Dundar O. A novel chromonyl thiohydantoin with anti-proliferative action on primary hepatocellular carcinoma cells. Med Chem Res 2017 Sep; 1-8. doi:10.1007/s00044-017-2037-0.

Yuqing Zhu, Vahid Serpooshan, Sean Wu, Utkan Demirci, Pu Chen, Sinan Güven. Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly. In: Methods in Molecular Biology. Humana Press 2017 Sep; 1-12. doi: 10.1007/7651_2017_68.

Lina Zelinger, Gökhan Karakülah*, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J. Brooks, Anand Swaroop. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative Ophthalmology & Visual Science 2017 Sep; 58: 4422-4435. doi: 10.1167/iovs.17-21805.

Ozturk M, Batur T, Ekin U, Erdogan A, İscan E, Keles U, Oz O, Ozen C. Molecular Pathogenesis of Liver Cancer. J Gastrointest Cancer. 2017 Jul 17 (Review). doi: 10.1007/s12029-017-9957-2. [Epub ahead of print].

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Aug 28. doi: 10.5301/ijbm.5000300.

Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017 Aug; 95(4):491-499. doi: 10.1139/bcb-2016-0190.

Yılmaz Y, Güneş A, Topel H, Atabey N. Signaling Pathways as Potential Therapeutic Targets in Hepatocarcinogenesis. J Gastrointest Cancer 2017 Aug 18. doi: 10.1007/s12029-017-9958-1.

Carr BI, Guerra V. Validation of a Liver Index and Its Significance for HCC Aggressiveness. J Gastrointest Cancer 2017 Jun 20. doi: 10.1007/s12029-017-9971-4.

Ezgi Karaca*, João P.G.L.M. Rodrigues, Andrea Graziadei, Alexandre M.J.J. Bonvin, Teresa Carlomagno. M3: an integrative framework for structure determination of molecular machines. Nature Methods 2017. doi: 10.1038 / nmeth.4392.

Alural B, Ayyildiz ZO, Tufekci KU, Genc S, Genc K. Erythropoietin Promotes Glioblastoma via miR-451 Suppression. Vitam Horm. 2017;105:249-271. doi: 10.1016/bs.vh.2017.03.002. Epub 2017 Apr 19. PubMed PMID: 28629521.

Gökhan Karakülah. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 (in press), doi: 10.1515/jib-2017-0009.

Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J. 2017 Aug; 284(15): 2513-2526. doi: 10.1111/febs.14139.

Akyerli C., Yuksel S., Can O., Erson-Omay Z., Oktay Y.*, Cosgun E., Ulgen E., Erdemgil Y., San A., von Deimling A., Gunel M., Yakicier C., Pamir M.N., Ozduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. Journal of Neurosurgery. 2017 Jun; 16:1-13. doi: 10.3171/2016.11.

Schneider F, Waithe D, Clausen MP, Galiani S, Koller T, Ozhan G, Eggeling C, Sezgin E. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS. Mol Biol Cell. 2017 Jun 1;28(11): 1507-1518. doi: 10.1091/mbc.E16-07-0536.

Oktay Y., Boylu C.A., Özduman K. Gliom Gelişiminde Genetik Yatkınlığın Rolü. Türk Nöroşirürji Dergisi. 2017 May; 27(2): 122-130.

Gökhan Karakülah, Aslı Suner. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 (in press), doi:10.1016/j.ygeno.2017.05.008.

Bağırsakçı E., Şahin E., Atabey N., Erdal E. & Carr B.I. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology. 2017 May 10. doi:10.1159/000471807.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar 30; 7:45661. doi:10.1038/srep45661.

Marino IR, Carr B.I. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15(Suppl 2):1-6.

Alural B, Genc S, Haggarty S. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biology Psychiatry. 2017 Feb; 6;73:87-103 doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Pinato D., Sharma R., Allara E., Yen C., Arizumi T., Kubota K., Bettinger D., Jang J.W., Smirne C., Kim Y.W., Kudo M., Howell J., Ramaswami R., Burlone M.E., Guerra V., Thimme R., Ishizuka M., Stebbing J., Pirisi M. & Carr B.I. The ALBI grade provides objective hepatic reserve estimation across each BCLC stage of hepatocellular carcinoma. J. Hepatology, 2017 Feb; 66(2): 338-346. doi:http://dx.doi.org/10.1016/j.jhep.2016.09.008.

van Waalwijk van Doorn LJ, Gispert JD, Kuiperij HB, et al. Improved Cerebrospinal Fluid-Based Discrimination between Alzheimer’s Disease Patients and Controls after Correction for Ventricular Volumes. J Alzheimers Dis. 2017 Jan 24; 56(2):543-555. doi: 10.3233/JAD-160668

Park CG, Park Y & Suh BC. The HOOK region of voltage-gated Ca2+ channel β subunits senses and transmits PIP2 signals to the gate. J Gen Physiol. 2017 Jan 13. doi:10.1085/jgp.201611677.

Arslan N, Guzel O, Kose E, Yılmaz U, Kuyum P, Aksoy B, Çalık T. Is ketogenic diet treatment hepatotoxic for children with intractable epilepsy? Seizure. 2016 Dec; 43: 32-38. doi:10.1016/j.seizure.2016.10.024.

Ebru Diler, Turgay Unver & Gökhan Karakülah. Differential Expression of Hyperhydricity Responsive Peach miRNAs. Journal of Integrative Bioinformatics. 2016 Dec; 13(5): 308. doi:10.2390/biecoll-jib-2016-308.

İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14; 1-12. doi:10.1007/s12079-016-0368-0.

Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLoS ONE. 2016 Dec 9; 11(12): e0167698. doi:10.1371/journal.pone.0167698.

Calibasi Kocal G, Güven S, Foygel K, Goldman A, Chen P, Sengupta S, Paulmurugan R, Baskin Y, Demirci U. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow. Sci Rep. 2016 Dec 2; 6:38221. doi: 10.1038/srep38221.

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah*, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Reports. 2016 Nov 22; 17(9): 2460-2473. doi:http://dx.doi.org/10.1016/j.celrep.2016.10.074.

Arslan N, Kose E, Guzel O. The Effect of Ketogenic Diet on Serum Selenium Levels in Patients with Intractable Epilepsy. Biol Trace Elem Res. 2016 Nov 21. doi:10.1007/s12011-016-0897-7.

Erbayraktar Z, Alural B, Erbayraktar RS, Erkan EP. Cell division cycle 7-kinase inhibitor PHA-767491 hydrochloride suppresses glioblastoma growth and invasiveness. Cancer Cell Int. 2016 Nov 18;16:88. eCollection 2016. doi:10.1186/s12935-016-0364-8.

Muhammad Ayaz Mustufa, Cigdem Ozen, Imran Ali Hashmi, Afshan Aslam, Jameel Ahmed Baig, Gokhan Yildiz, Shoaib Muhammad, Imam Bakhsh Solangi, Naim ul Hasan Naqvi, Mehmet Ozturk and Firdous Imran Ali. Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma. BMC Cancer. 2016, Nov 14; 16: 883. doi:10.1186/s12885-016-2942-5.

Büyüköz M, Erdal E, Alsoy Altinkaya S. Nanofibrous gelatin scaffolds integrated with NGF-loaded alginate microspheres for brain tissue engineering. J Tissue Eng Regen Med. 2016 Nov 12. doi: 10.1002/term.2353.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A. Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma. OncoTargets and Terapy. 2016, Nov 9; 9: 6843—6855. doi:10.2147/OTT.S117743.

Carr B.I., Guerra V., Giannini E.G. et al. A Liver Index and its Relationship to Indices of HCC Aggressiveness. J Integr Oncol. 2016 Oct;5(4). pii: 178. doi: 10.4172/2329-6771.1000178.

Erkan D, Kayali HA. Replacement of Soybean Meal with Animal Origin Protein Meals Improved Ramoplanin A2 Production by Actinoplanes sp. ATCC 33076. Appl Biochem Biotechnol. 2016 Sep;180(2):306-21. doi:10.1007/s12010-016-2100-1.

Hani Alotaibi, Nese Atabey, Kasım Diril, Esra Erdal, Mehmet Ozturk. Molecular Mechanisms of Hepatocellular Carcinoma, Chapter Hepatocellular Carcinoma Part of the series Current Clinical Oncology. Springer. 2016, Aug 27; 43-63. doi:10.1007/978-3-319-34214-6_3.

Alagoz Y., Gurkok T.,  Zhang B. & Unver T. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology. Sci Rep. 2016 Aug 3; 6:30910. doi: 10.1038/srep30910.

Bakır Y., Eldem V., Zararsız G. & Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. Plant Genome. 2016 Jul; 9(2). doi:10.3835/plantgenome2015.09.0080.

Marsano A, Medeiros da Cunha CM, Ghanaati S, Gueven S, Centola M, Tsaryk R, Barbeck M, Stuedle C, Barbero A, Helmrich U, Schaeren S, Kirkpatrick JC, Banfi A, Martin I. Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling. Stem Cells Transl Med. 2016 Jul 26. doi: 10.5966/sctm.2015-0321.

Pavlopoulou A., Oktay Y., Vougas K., Louka M., Vorgias C.E., Georgakilas A.G. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 2016, Jul 19; 380(2):485-493. doi: 10.1016/j.canlet.2016.07.018.

Carr B.I., Guerra V., Giannini E.O. et al. An HCC Aggressiveness Index and Blood GTP, Blirubin and Platelet Levels. J. Integrative Oncology. 2016 Jun 20; 5:172. doi: 10.4172/2329-6771.1000172.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N. & Özduman K. IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Sci Rep. 2016 Jun 10; 6: 27569. doi: 10.1038/srep27569.

Yilmaz Y, Atabey N, Erdal E & Brian I. Carr. Platelets, Microenvironment and Hepatocellular Carcinoma. Biochemistry & Analytical Biochemistry, 2016 June 29; 5:281 (Review). doi:10.4172/2161-1009.1000281.

Antonio Mazzoccaa, Giovanni Ferrarob, Giovanni Misciagnac, Brian I. Carr. A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm. Medical Hypotheses, 2016, Aug; 93: 132-137. doi:10.1016/j.mehy.2016.05.027.

Karakülah G, Karakuş M, Suner A, Demir S, Arserim SK, Töz S, Özbel Y. sandflyDST: a dynamic web-based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe, and user study. Medical and Veterinary Entomology, 2016 June 24. doi:10.1111/mve.12182.

Can Küçük, Xiaozhou Hu, Qiang Gong, Bei Jiang, Adam Cornish, Philippe Gaulard, Timothy McKeithan, Wing C. Chan. Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. The American Journal of Pathology, 2016 June; 186(6): 1435-1441. doi:10.1016/j.ajpath.2016.02.011.

Zeynep Firtina Karagonlar, Doğukan Koç, Eren Şahin, Sanem Tercan Avci, Mustafa Yilmaz, Neşe Atabey, Esra Erdal. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and Biophysical Research Communications, 2016 June 3; 474(3): 482-490. doi:10.1016/j.bbrc.2016.04.137.

Yakup Bakır, Vahap Eldem, Gökmen Zararsız, Turgay Unver. Global Transcriptome Analysis Reveals Significant Differences in Gene Expression Patterns Between The Non-Hyperhydric and Hyperhydric Leaves of Prunus persica. The Plant Genome, 2016, May; 9(2): 1-9.

Salimi R, Yener N, Safari R. Use and Evaluation of Newly Synthesized Fluorescence Probes to Detect Generated OH• Radicals in Fibroblast Cells. J Fluoresc. 2016 May; 26(3):919-24. doi: 10.1007/s10895-016-1780-9.

Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated hepatocyte growth factor expression as an autocrine c‐Met activation mechanism in acquired resistance to sorafenib in hepatocellular carcinoma cells. Cancer Sci. 2016 Apr; 107(4):407-416 doi: 10.1111/cas.12891.

Carr BI & Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and Its Relationship to Liver Enzyme Levels. Oncology 2016 Mar 15; 90(4). doi: 10.1159/000444394.

Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites. Am J Surg Pathol, 2016 Mar 11. doi: 10.1097/PAS.0000000000000634.

Carr BI & Guerra V. Low Alpha-Fetoprotein Levels Are Associated with Improved Survival in Hepatocellular Carcinoma Patients with Portal Vein Thrombosis. Digestive Diseases and Sciences, 2016 Feb 26; 61(3):937-947. doi: 10.1007/s10620-015-3922-3.

Ferroudj S, Yildiz G, Bouras M, Iscan E, Ekin U, Ozturk M. Role of fanconi anemia/BRCA pathway genes in hepatocellular carcinoma chemoresistance. Hepatol Res. 2016 Feb 16. doi: 10.1111/hepr.12675.

Carr BI & Guerra V. Hepatocellular Carcinoma Extrahepatic Metastasis in Relation to Tumor size and Alkaline Phosphatase Levels. Oncology 2016 Feb 12; 90(3):1-7. doi: 10.1159/000443480.

Durmaz I, Guven EB, Ersahin T, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine. 2016 Jan 15; 23(1):42-51. doi: 10.1016/j.phymed.2015.11.012.

Wingender G. From the deep sea to everywhere? Environmental antigens for iNKT cells. Arch Immunol Ther Exp, 2015 Dec 24 (Review). doi: 10.1007/s00005-015-0381-7.

Güzel O, Yılmaz U, Uysal U, Arslan N. The effect of olive oil-based ketogenic diet on serum lipid levels in epileptic children. Neurol Sci. 2015 Dec 23; 1-6. doi: 10.1007/s10072-015-2436-2.

Namkoong B, Guven S, Ramesan S, Liaudanskaya V, Abzhanov A, Demirci U. Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomaterialia, 2015 Dec 07. doi: 10.1016/j.actbio.2015.12.004.

Hanna RN, Cekic C, Sag D, Tacke R, Thomas GD, Nowyhed H, Herrley E, Rasquinha N, McArdle S, Wu R, Peluso E, Metzger D, Ichinose H, Shaked I, Chodaczek G, Biswas SK, Hedrick CC. Patrolling Monocytes Control Tumor Metastasis to the Lung. Science. 2015, Nov 20; 350(6263): 985-90.

Wingender G & Kronenberg M. Characterization of human T cell subsets via surface markers. Cytometry A, 2015, Oct 27; 87A; 1067-1069.

D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015 Oct 19; 16(18):1-8. doi: 10.1517/14656566.2015.1101065.

Wingender G, Sag D, Kronenberg M. NKT10 cells: a novel iNKT cell subset. Oncotarget. 2015 Sept 29; 6(29): 26552-26553 (Review). doi: 10.18632/oncotarget.5270.

Wingender G, Birkholz A, Sag D, Farber E, Chitale S, Howell AR, Kronenberg M. Selective conditions are required for the induction of iNKT cell hypo-responsiveness by antigenic stimulation. The Journal of Immunology. 2015 Sept 9; 195: 3838-3848. doi: 10.4049/jimmunol.1500203.

Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. Journal of Experimental & Clinical Cancer Research. 2015 Sept 2; 34(1):90. doi: 10.1186/s13046-015-0210-1.

Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Seminars in Oncology. 2015 Aug; 42(4):672-678. doi: 10.1053/j.seminoncol.2015.05.004.

Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. The International Journal of Biochemistry & Cell Biology. 2015 Aug; 65:169-181. doi: 10.1016/j.biocel.2015.05.025.

Hu X, Chan WC, Kücük C. Generation of a genetically engineered aggressive nk-cell leukemia cell line with stable IL2 expression. Acta Medica International. 2015 Jul; 2(2):78-84. doi: 10.5530/ami.2015.3.6.

Ozhan G and Weidinger G. Wnt/β-catenin signaling in heart regeneration. Cell Regen (Lond). 2015 Jul 8; 4(1):3. doi: 10.1186/s13619-015-0017-8

Alotaibi H, Basilicata MF, Shehwana H, Kosowan T, Schreck I, Braeutigam C, Konu O, Brabletz T, Stemmler MP. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2015 June; 1849(6):731-742. doi: 10.1016/j.bbagrm.2015.01.005.

Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28; 9:209. doi: 10.3389/fncel.2015.00209.

Dilek Cevik, Gokhan Yıldız & Mehmet Ozturk. Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations. World J Gastroenterol. 2015 Jan 7; 21(1): 311–317. doi: 10.3748/wjg.v21.i1.311.

Alural B, Duran GA, Tufekci KU, Allmer J, Onkal Z, Tunali D, Genc K, Genc S. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells. Frontiers in Immunology. 2014 Sep 30; 5:475. doi: 10.3389/fimmu.2014.00475.

* Current address IBG.

The Hybridoma and Monoclonal Antibody Production Core Facility will provide service for researchers and biotechnology companies. The aim is to establish an efficient and affordable production of antibodies and other biological materials. Our service covers the whole process from antigen immunization in mice, rat or rabbit to production of purified monoclonal antibodies. We use hybridoma technology that includes generation of hybrid cell lines or hybridomas by fusing an antibodyproducing B cell with an immortal myeloma cell. The facility produces both monoclonal and polyclonal antibodies and provides antibody purification service using different benchtop chromatography techniques. Following purification of the antibody, the IgG type can also be characterized on request. Furthermore, the facility offers consultation service on all aspects of monoclonal antibody production.

SCOPE
Advanced animal models of human diseases continue to expand their use for both descriptive basic research as well as applied preclinical research. In this program, we focus on preclinical research with a clear emphasis on functional drug screening and validation. Our ultimate goal will be the translation of these preclinical results on disease intervention into clinical trials. For this, we will use existing animal models and where appropriate; we will design novel, better-suited models. In vitro drug screen assays typically rely on simple interactions of chemicals with a drug target, such as receptor binding or enzyme activity inhibition. However, in vitro results often poorly correlate with in vivo results because of the complicated physiological environment is absent in the in vitro testing system. Although cell-based assays can provide some information, cultured cells still do not provide physiological conditions and complex interactions among different cell types and tissues. Therefore, results in animal studies are essential to validate high – throughput screening (HTS) hits and exclude compounds with unfavorable absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, which are responsible for more than half of compound attrition in costly clinical trials. Currently, in vivo assays are not usually performed until or after the lead optimization stage. This is partly due to the low speed and high cost of conventional animal models (typically rodents) and the relatively high number of preliminary hits from HTS. With alternative small-animal models, however, it is now possible to perform in vivo testing earlier in the development process. Thus, researchers have developed systems using both vertebrates (e.g. zebrafish) and invertebrates (e.g. the fruit fly Drosophila melanogaster) for drug screening. The small size, high fecundity, and experimental tractability of these animals enable costeffective and rapid screening of numerous compounds. The experimental animal facility at iBG-izmir maintains and utilizes the whole breath of animal model systems, namely: Drosophila, zebrafish and rodents (mice/rats)

FOCUS AREAS AND MILESTONES
The emphasis of each model system will be:
• Drosophila: Drosophila is being used frequently in high impact studies to model, for example, cancer and diabetes, because of the simple ability to perform genome-wide modifier and drug compound screens. Simple phenotypes associated with human mutations in conserved disease orthologs can be examined. We will establish novel animal models of diseases in the Drosophila system, to uncover genetic disease mechanism involving loss and gain of known pathway function. Furthermore, we will screen for pathway modifications by genetic and pharmacological modifiers. To best complement our work on wound healing, high priority will be placed on exploring the interactions between epithelial healing mechanisms and metabolic disorders, such as diabetes.

• Zebrafish: Wnt/β-catenin signaling pathway components are considered as preferred targets for drug development as malfunctioning of the pathway is associated with human diseases including cancer. Unfortunately, targeted treatment of the underlying cause of these diseases is currently not possible, since very few compounds are known to specifically inhibit β-catenin signaling. In the coming years, we aim to perform a drug screen for Wnt-related cancers using zebrafish, which has become an attractive model for high-throughput drug screening. Zebrafish embryos offer a unique system where pharmacological molecules can directly be added to the embryo water and become readily absorbed. They allow for direct observation of phenotypic hallmarks of cancer, such as enhanced cell proliferation and angiogenesis, reduced apoptosis, abnormal activation of oncogenes, repression of tumor suppressor genes and changes in cell migratory behavior. Compounds can be identified via embryonic screens and further validated in adults for their molecular mechanisms to pinpoint them as a target for a specific cancer type. For this purpose, we aim to exploit zebrafish as a drug discovery model and a biopharmaceutical service by collaborating with pharmaceutical companies to identify novel drug candidates. Another strength of the zebrafish system is that it represents an exclusive example of a highly regenerative vertebrate model, due to its distinct regenerative capacity in various organs and tissues including the heart, pancreas, liver, muscle, skin, blood and pigment cells, fins and the CNS. Here, we aim to establish part of the zebrafish facility as a unit that can serve to collaborate for the regeneration-related research projects of internal and external laboratories that would like to benefit from this unique regeneration model.

• Rodents (rats/mice): At iBG-izmir we will make use of well-established mouse models of cancer and metastasis (mainly liver and lung cancer), diabetes, obesity, experimental allergic encephalomyelitis (EAE), viral and bacterial infections, using wild-type and humanized mice. Some congenic rat strains for diabetes and obesity research will also be used. However, genetically modified mice strains will be the most suitable models for e.g. cancer and some other diseases. Our fully integrated transgenic core facility will not only enable us to adapt existing models but also to design new ones. Such advanced genetically modified mice will make use of state-of-the-art technologies, including Cre/lox, Flp/frt conditional alleles or Tet/on-off inducible transgenes. In this way we, will have accurate somatic mouse models for diseases that are ideally suited to test drug candidates for targeted therapy against defined molecular pathway(s). As described above, mice models are not practical for HTS of drugs, but rather will be used for preclinical therapy testing. For example, mice strains that express luciferase and fluorescent protein reporter alleles will enable us to follow disease interventions in real time by non-invasive in vivo imaging at our core facility. We will establish and maintain the essential number of genetically modified mice strains for the various diseases of interest. The core will also become a member of the European consortium for Mouse Phenotyping and Archiving Research Infrastructure (INFRAFRONTIER) to become the central facility for Turkey. Thereby, we will be access and participate in the large non-profit genetically modified mice repository, the European Mouse Mutant Archive (EMMA). These cooperations will greatly enhance the interaction with our European partners and our access to funding.

• Lastly, we will set up Patient Derived Xenotransplant (PDX) models for lung cancer. These PDX models recapitulate the heterogeneity of human cancer, to a much higher extend than conventional mouse models do. Recent experiments with severe immune compromised NOD-SCID-Gamma (NSG) recipient mice have shown very promising results in maintaining human primary tumor tissue characteristics after transplantation. PDX models are thus a very important supplement to our preclinical drug testing capacity. Here too we initiated participation efforts to become member of the EUROPDX consortium for mutual use and exchange of PDX cancer models between European partner institutes.

• Development and testing of drug HTS in both Drosphila and zebrafish systems. Here our focus will be on small molecule drug testing. Our minimal goals are the development of one or more candidates during the first 3 years, and the validation of at least one molecule after preclinical testing to allow its use for follow-up clinical trials. The funding will be obtained from TUBITAK and industrial partners.

• Development and optimization of genetically modified mice models for lung and liver cancer, as well as of PDX models for lung cancer. These models will be used to test preclinical and targeted be specific monoclonal antibodies, small molecules, or biosimilars. Our minimal goals during the first 3 years are the establishment and functional characterization of the mouse models, together with conclusive validation results for the candidate drug. Our mouse model should then be ready as a tool for preclinical testing to make candidate drugs ready for clinical trials. Funding will be obtained from TUBİTAK, European consortia (Infrafrontier), EU research funds and industrial partners.

SCOPE
Medical diagnostics is the key element for providing the right therapeutic approach to curing diseases. Finding, describing and correlating the chemical and physical symptoms of diseases demands devices equipped with highly precise and accurate sensors. Modern clinical approaches utilize different methods for diagnostics such as using specific biomarkers, hi-tech imaging systems, genomic analysis methods, high-throughput screening and point of care technologies. Bio-microdevices are miniaturized technologically engineered platforms that provide high and precise control over environmental variables and mimic the native physiological conditions of living organisms. Biosensor-supplied microdevices are excellent tools for diagnostics, as they minimize the sample volumes, analysis time and cost of tests. In the Program for Diagnostics and Medical Microdevices at iBG-izmir, we formed a multidisciplinary research team of bioengineers, molecular biologists, physicists, chemists and clinicians to develop micro- and nano-devices for diagnostics. With close clinical collaborations, we will implement the most current analytical techniques (such as next generation sequencing) and design biosensors for detection of diagnostic markers from patient samples (such as body fluids, circulating tumor cells or solid tissues). Cancer, infectious agents, metabolic, autoimmune and neurological diseases are in the scope of the program. For these we aim to generate reliable, rapid and cost effective micro- and nano-diagnostic devices. The minimal success criterion of the program is to bring an innovative, micro-/nanodiagnostic device on the medical market. iBG-izmir and this Innovation Program will advance the medical R&D activities in the region and will be a key component providing competitive products to the healthcare market. Furthermore, Dokuz Eylul University also hosts the BioIzmir initiative and DEPARK (Dokuz Eylul Technology Development Zone), which both focus on the industrial translation of medical innovations. The cooperation with these organizations will further increase the impact of this Innovation Program.

The program is going to obtain substantial funds from TÜBITAK, EU research funds, NIH partnerships, private and industrial funding.

FOCUS AREAS AND MILESTONES
• Develop and validate at least one reliable, rapid, low cost, easy to operate and cost-efficient diagnostic device.

• Apply for a patent of the developed device and its technology.

• Validation and commercialization of the device.

SCOPE
The incidence of many rare diseases is much higher in Turkey due to the high rate of relative (consanguineous) marriages. The clinical presentation of such rare diseases is highly heterogeneous, and therefore the proper diagnosis and treatment of these diseases is currently challenging. Additionally, the genetic background of most of these diseases is poorly defined. However, the identification of the underlying genetic aberrations will likely lead to the development of better diagnostic, prognostic and therapeutic strategies. Recently, the discovery of nextgeneration sequencing (NGS)-based methodologies rendered it possible to identify disease-associated mutations with a genome-wide scope. The work within this program will apply whole-exome sequencing (WES) to identify specific mutations associated with rare diseases, with the aim to generate unique diagnostic panels. Moreover, we will identify driver mutations with the potential to function as novel therapeutic targets. Specifically, we plan to focus on rare diseases of the nervous system, such as epilepsy syndromes and neurodegenerative diseases.

FOCUS AREAS AND MILESTONES
5 year goals:
• Establish at least one multi-disciplinary consortium that involves pathologists, clinicians, genome and bioinformatics scientists.

• To collect and store all relevant rare disease-specific clinical and histopathological data in a central database for at least three rare disease types.

• To generate a NGS-based disease panel for at least two rare disease groups. Funding options: TUBITAK (1001, 1003, 1007 grant programs), Izmir Agency of Development (IZKA), and EU funding programs (Horizon 2020 etc).

Success criteria (3rd and 5th years):
• Exome and/or targeted sequencing and bioinformatic analysis of at least 300 patients within three years and of at least 500 patients within five years.

• Identification and validation of all mutations necessary for proper diagnosis in at least one rare disease within three years and of at least two rare disease within five years.

• Development of at least 2 NGS panels for 2 different rare diseases (5th year).

SCOPE
Neurological disorders include Alzheimer disease and other dementias, stroke, multiple sclerosis, Parkinson’s disease, brain tumors, traumatic disorders of the nervous system such as brain trauma, epilepsy and migraine. Hundreds of millions of people worldwide are affected by neurological disorders. For example, stroke is the third most common cause of death worldwide. Alzheimer’s disease is the most common type of dementia, affecting 35 million individuals in the world, with an expected threefold increase by 2050. Furthermore, multiple sclerosis, an inflammatory demyelinating disease of the brain and the spinal cord, affects two million people globally, with rates varying widely in different regions and populations. However, many aspects of etiology, genetics and pathogenesis of neurological disorders are still not clearly defined. In addition, for many of these diseases, no good predictive or diagnostic test is available. Finally, and most importantly, for many neurological disorders the current treatments are largely symptomatic and no final cure can be achieved. For these reasons, neurological disorders have become a major health problem for many countries, whose burden is expected to rise with the aging of the population. Turkey’s Science and Technology High Council declared ‘Neuroscience’ as one of the priority areas of health and technology. The Neurological Disorders Program at iBG-izmir aims to identify novel genes/mutations responsible for familial and non-familial neurological disorders, to discover new biomarkers and to develop novel therapeutic tools and approaches for the treatment of these disorders. To this end, we will study a wide range of patient samples, as well as established and newly generated in vitro and in vivo animal models of neurological disorders. The funding will be obtained from TUBITAK, Ministry of Health, industrial partners and EU research funds.

FOCUS AREAS AND MILESTONES
The focus areas and 5 years goals with milestones of the Program are as follows:

• Development of in vitro and in vivo models: 3D cultures of induced pluripotent stem cells to study differentiation
to neural stem cells, current type neural or glial cells. In addition to in vitro models, we aim to develop new transgenic animal models of neurological disorders. Our minimal goals are the development of one novel in vitro or in vivo model during the first 3 years, and another one within 5 years.

• Discovery of novel predictive genes/mutations: Many neurological disorders have a genetic etiology. We will investigate familial and non-familial forms of neurological disorders to find disease causing novel genes/mutations by whole exome sequencing. Our minimal goals are biobanking of at least 30 families during the first 3 years, and whole exome sequencing within 5 years.

• Biomarker discovery and development of diagnostic tools: Circulating serum micro RNAs (miRNAs), and other possible biomarkers will be investigated to find novel biomarkers for neurological novel mutations will be developed. Additionally, these biomarkers and novel driver mutations in neurological cancers could be possible targets for treatment. Our minimal goals are to identify one novel biomarker or target molecule during the first 3 years, and finish preclinical validation within 5 years.

SCOPE
Immunotherapy is the treatment of diseases via the alteration of the immune system. This can be achieved by inducing, enhancing or suppressing immune responses, depending on the context. Current approaches in immunotherapy are heavily biased to the adaptive immune system by targeting or utilizing conventional T and B cells. However, the innate immune system, and innate like T cells are known to be crucially involved in most, if not all, inflammatory responses. This is particular relevant for chronic inflammatory diseases. Nonetheless, only few immunotherapies based on the innate and innate-like immune system are currently under development. Recognizing the great potential for novel and innovative therapeutic approaches, this program focuses on these aspects, with a particular emphasis on macrophages and innate like T cells.

FOCUS AREAS AND MILESTONES
• Macrophage polarization as therapeutic target: Pro-inflammatory macrophages, which promote inflammation, are called M1 macrophages. In contrast, anti-inflammatory macrophages, which decrease inflammation and support tissue repair, are called M2 macrophages. How environmental factors influence this M1/M2 – balance is poorly defined. Recent intriguing findings by one program member demonstrated that the activity of a cholesterol transporter strongly influences this M1/M2 – balance. This altered macrophage balance had profound impact on tumor immunity. By linking cholesterol transporters to tumor immunity, this finding provides an unprecedented link between the metabolism and chronic inflammatory diseases, including cancer. The intermediate 3 years goal of this project is to find and characterize small molecules and/or monoclonal antibodies to modulate the activity of cholesterol transporters. The long-term 5 years goal is to utilize these reagents as therapeutic approach to alter macrophage polarization for cancer immunotherapy and potentially for metabolic/inflammatory diseases.

• iNKT cell based cell therapy: Innate T cells are a unique subset of T cells that combine features of innate NK cells and of adaptive memory T cells. The most prominent member of innate T cells are invariant Natural Killer (iNKT) cells. Following antigenic stimulation, iNKT cells rapidlyproduce copious amounts of various cytokines and thereby can have a pronounced effect on the immune system. They are known to impact an impressive variety of different immune reactions, ranging from chronic and acute inflammatory processes, including responses to pathogens and tumors, to autoimmune responses. As all humans share basically identical iNKT cells, their therapeutic potential is great. Recently, program members characterized a novel iNKT cell subset with potent IL-10-dependent regulatory function, which were termed NKT10 cells. These, NKT10 cells could impair anti-tumor immune responses and protect mice against experimental autoimmune encephalomyelitis (EAE), a
mouse model of multiple sclerosis. The intermediate 3 years goal of this project is to better characterize the regulatory mechanisms of NKT10 cells and to optimize their expansion in vitro and in vivo. The long-term 5 years goal is to utilize NKT10 cells as cell therapy for EAE and for obesity related metabolic diseases.

For both projects funding by one major national or international grant should be obtained within 3 years. We expect for both projects to acquire proof-of-concept preclinical in vivo data in wild type and humanized animals within a 5 years period.

SCOPE
Regenerative medicine is one of the most promising and rapidly advancing areas of modern medicine, as it focuses on innovative approaches to repair and replace cells, tissues and organs. Cell therapies implement patient oriented approaches, and provide novel venues for personalized medicine. At iBG-izmir, we will establish an internationally accredited cGMP facility for the production of therapeutic grade cells and tissues for humans. Our program brings together basic research scientists and clinicians focused on utilizing cells and stem cells in the reconstruction of tissues and organs, as well as engineering cells for therapeutic approaches. Cell therapies and regenerative medicine have already been applied in clinics as experimental and alternative methods. With this program we aim to develop and translate cell-based approaches as validated standard treatment method for clinicians. In this regard, we focus on basic and translational medical sciences utilizing cell therapies, design clinical trials and set new therapeutic standards. Achieving the goals of the program is strongly coupled with innovative thinking and creating value in therapeutic medicine.

FOCUS AREAS AND MILESTONES
• Developing cell based pre-clinical in vitro and in vivo disease models underlining the mechanisms of regeneration.
• Generating autologous and allogeneic adult mesenchymal stem cells from bone marrow, adipose tissue and dental pulp; or from specialized cells, like limbal stem cells, chondrocytes and hepatocytes. Implementing their use for cancer, trauma, plastic and reconstructive surgery, ophthalmology and dental applications.
• Developing and translating cell based therapy methods from Bench-to-Bedside in accordance with national and international guidelines.
• Design and start a clinical trial for cell-based therapy. Funding of the program will be obtained from TUBITAK, Ministry of Health, EU research funds and the Dokuz Eylul University Hospital.

SCOPE
Targeted therapeutics are drugs or other substances such as antibodies acting on specific molecules (“molecular targets”) that are involved in the pathogenesis or complications of a disease. Targeted therapeutics are also called “precision medicines”. Most of targeted therapeutics approved by FDA or EMEA are used against cancer, but their field of application is rapidly spreading to other diseases such as autoimmune and rare diseases. The process of targeted therapeutics development usually starts by the discovery of a critical molecular target, followed by the choice of appropriate targeting molecules, in vitro and in vivo validation studies, production under cGMP conditions and clinical trials.

Many of the currently available targeted therapeutics are “biopharmaceuticals” with expired patents. Consequently, there is a growing interest in Turkey and other countries in the manufacturing of their generic forms called “biosimilars” as they are more affordable. Considering global trends and local needs, iBG-izmir decided to invest its scientific and technological means to cover a broad area of application starting from production of biosimilars and leading towards the development of innovative biopharmaceuticals. Investigation of innovative targeted drugs such as small chemical inhibitors will also be covered by the program. Accordingly, iBG-izmir is building a GMP facility accompanied by quality control, animal toxicology and pharmacology units, dedicated to biosimilar production, as well as state-of-the-art “drug discovery” facilities.

FOCUS AREAS AND MILESTONES
• Development and manufacturing of biosimilars: humanized monoclonal antibodies (Mabs) and antibodylike molecules are the initial focus area. Our minimal goals are the development of one of more biosimilar master cell banks during the first 3 years, and the production of at least one biosimilar molecule ready for initial clinical trials. The funding will be obtained from TUBITAK and industrial partners.

• Development of “biobetter” and innovative Mabs: A “biobetter Mab” is a novel antibody acting on a known target by a different mechanism for example via a different epitope. Several projects on anti-cancer Mab development against validated and novel target molecules will be launched. Our minimal goals are the development of one of more humanized Mab master cell banks during the first 3 years, and preclinical validation within 5 years. The funding will be obtained from TUBITAK, EU research funds and industrial partners.

• Development and validation generic small molecule inhibitors for combined therapy against refractory or relapsed cancer. Patient-derived (chemo)therapy naïve primary tumors together with their refractory or relapsed tumors can be used to screen anti-cancer small molecules efficacy against validated and novel targets from activated molecular pathways. Our minimal goals are the collection and availability of distinct sets of generic small molecules that will be tested in (primary) tumor cultures. This will be followed within 5 years by preclinical validation in our patient-derived-xenotransplant (PDX) models and our advanced, genetically modified animal models.

Funding will be obtained through TUBITAK, EU framework collaborations and industrial partners.

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Enstitü Sekreterliği

İdari Birimler

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