Academic Staff - Personal Page

Associate Professor ZERRİN IŞIK FACULTY OF ENGINEERING DEPARTMENT OF COMPUTER ENGINEERING COMPUTER SOFTWARES

 zerrin.isik@deu.edu.tr
 +90 232 - 3017413 - 17413

Education/Academic Info
Undergraduate Degree	Dokuz Eylül University Mühendislik Fakültesi Bilgisayar Mühendisliği Bölümü	2001
Master's Degree	Sabancı University . Elektronik Mühendisliği ve Bilgisayar Bilimi	2003
PhD (Doctorate)	Middle East Technical University Fen Bilimleri Enstitüsü Bilgisayar Mühendisliği Anabilim Dalı	2011
Assistant Professor	Dokuz Eylül University Mühendislik Fakültesi	2014
Associate Professor	Dokuz Eylül University Mühendislik Fakültesi Bilgisayar Bilimleri ve Mühendisliği	2020

NO	NAME	YEAR
1	Compound Target Identification in Tissue-Specific Interaction Networks...	2021
2	Akciğer ve Prostat Kanseri için İlaç Yeniden Konumlandırmanın Uygulanması...	2020
3	A machine learning-based recommendation model for bipartite networks...	2020
4	Integrative Biological Network Analysis to Identify Shared Genes in Metabolic Disorders...	2020
5	Applying deep learning models on structural MRI for stage prediction of Alzheimer's disease...	2020
6	Identification of Leukemia Subtypes from Microscopic Images Using Convolutional Neural Network...	2019
7	Ubiquitin-Proteasome Axis, Especially Ubiquitin-Specific Protease-17 ( USP17) Gene Family, is a Pote...	2019
8	Predicting Drug Synergy for Precision Medicine using Network Biology and Machine Learning...	2019
9	Evaluation Machine-Learning Approaches for Classification of Cryotherapy and Immunotherapy Datasets...	2018
10	Kanser Alt-Türlerinin Sınıflandırılması İçin RNA-Sekanslama ve RPPA Verilerinin Karşılaşt...	2018
11	Estimation of Drug Treatment Effects on the Signaling Pathways...	2017
12	Integration of RNA-Seq and RPPA data for survival time prediction in cancer patients...	2017
13	Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state...	2016
14	Drug target prioritization by perturbed gene expression and network information...	2015
15	Network information improves cancer outcome prediction...	2014
16	A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines tran...	2012

NO	NAME	DATE
1	Algorithm-based approach to uncover potential microRNAs related to cancers of the gastrointestinal t...	09/09/2021 - 11/09/2021
2	Evaluation of Link Prediction Methods on Temporal Networks...	02/06/2021 - 05/06/2021
3	Can the proton pump be used as a target for diagnosis and treatment of cancer?...	16/04/2021 - 18/04/2021
4	Network-Based Integrative Analysis of Breast Cancer and Lung Cancer for Identifying Common Functiona...	16/04/2021 - 18/04/2021
5	Meme ve Cilt Kanserleri için Ağ Benzerliğine Dayalı İlaç Yeniden Konumlandırma Yaklaşımı...	24/03/2021 - 27/03/2021
6	Integrative analysis of DNA methylation and RNA-sequencing data for identifying diagnostic cancer ma...	22/10/2020 - 23/10/2020
7	Derin Öğrenme Ile Hisse Senedi Fiyat Analizi Ve Öngörüsü...	05/10/2020 - 07/10/2020
8	Kolon kanserinde alt tip transkriptom veri analizi...	16/01/2020 - 18/01/2020
9	Sentiment Analysis in Turkish Text with Machine Learning Algorithms...	31/10/2019 - 02/11/2019
10	Predicting Personality with Twitter Data and Machine Learning Models...	31/10/2019 - 02/11/2019
11	Stock Market Forecasting Using Machine Learning Models...	31/10/2019 - 02/11/2019
12	Supervised Link Prediction Developed For Bipartite Social Networks...	26/10/2019 - 28/10/2019
13	Review of Drug Repositioning With Network Analysis In Cancer...	17/10/2019 - 19/10/2019
14	Characterization of Cancer Types by Applying Machine Learning Methods on Blood RNA-Sequencing Data...	11/10/2019 - 13/10/2019
15	Developing Combinatorial Therapies Towards Gliomas by Network-Based Analysis of Whole Transcriptome ...	27/09/2019 - 29/09/2019
16	Subtype analysis of ovarian cancer in RNA sequencing data...	01/03/2019 - 03/03/2019
17	Ubiquitin-Proteasome Axis is a Potential Target for Epithelial-Mesenchymal Transition in High-Grade ...	21/11/2018 - 25/11/2018
18	Understanding lower-grade glioma progression by integrative analysis of glioblastoma recurrence...	25/10/2018 - 27/10/2018
19	Gene co-expression network analysis to identify shared disease genes in metabolic syndrome, type 2 d...	25/10/2018 - 27/10/2018
20	Graph-Based Data Mining for Compound Target Identification...	20/09/2018 - 24/09/2018
21	Investigation of potential therapeutic targets by using in silico methods in glioblastoma...	30/06/2018 - 03/07/2018
22	Classification of CAD Dataset by Using Principal Component Analysis and Machine Learning Approaches...	03/05/2018 - 05/05/2018
23	Doğal İmgelerde Çizge Tabanlı Gösterimle Karakter Bölütlenmesi...	02/05/2018 - 05/05/2018
24	Demans ve Alzheimer Teşhisinde Yapay Sinir Ağlarının Uygulanması...	02/05/2018 - 05/05/2018
25	A Hybrid Movie Recommendation System Using Graph-Based Approach...	26/04/2018 - 27/04/2018
26	Ubiquitin specific-17 (USP17) related genes are potential targets for epithelial mesenchymal transit...	04/11/2017 - 07/11/2017
27	Makine Öğrenmesi Yöntemleriyle Daha Etkili İlaç Tedavilerinin Kestirilmesi...	13/10/2017 - 15/10/2017
28	Yüksek dereceli seröz over tümörlerinin peritoneal metastazlarında epitelyal mezenkimal tranzis...	19/05/2017 - 23/05/2017
29	Destek Vektör Makineleriyle İlaç Birleşimlerinin Etkilerinin Sınıflandırılması ...	15/05/2017 - 18/05/2017
30	Classification of Breast Cancer Subtypes By Using TCGA Data...	26/10/2016 - 28/10/2016
31	Survival time prediction by integrating RNA-sequencing and RPPA data...	08/07/2016 - 12/07/2016
32	Breast cancer subtype prediction by using RNA-sequencing data and machine learning methods...	16/10/2015 - 17/10/2015
33	Akıllı Obje Sistemi ile Zihinsel Engelli Bireylerin Eğitimi ve Rehabilitasyonu...	04/02/2015 - 06/02/2015
34	Integration of gene expression data and biological networks for predicting cancer outcomes...	19/10/2014 - 22/10/2014
35	Can specific transcriptional regulators assemble a Universal Cancer Signature?...	27/11/2013 - 29/11/2013
36	Evaluation of cyclic pathway activities by signal transduction score flow algorithm...	21/07/2013 - 23/07/2013
37	Privacy-Preserving Cloud Computing for Biomedical Research...	09/07/2013 - 10/07/2013
38	Assessment of network data on outcome prediction of cancer patients...	11/09/2012 - 14/09/2012
39	Integrated Transcriptome Data Unified into the En Route of the Cell Signaling Pathways...	20/04/2010 - 22/04/2010
40	Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data...	05/09/2009 - 06/09/2009
41	Integration of ChIP-seq and microarray gene expression data...	16/04/2009 - 18/04/2009
42	Progressive Clustering by Integration of Heterogenous Data From Multiple Sources for Target Gene Ide...	13/09/2008 - 14/09/2008
43	Short Time Series Microarray Data Analysis for Resistance to Selenium Deficiency...	18/05/2008 - 20/05/2008
44	Short Time Series Microarray Data Analysis and Biological Annotation...	20/04/2008 - 22/04/2008
45	A Hybrid Method For The Identification of Expression Patterns From Microarray Data...	21/07/2007 - 25/07/2007
46	MLC1 structure prediction...	30/04/2007 - 02/05/2007
47	Genetic Algorithm for Protein Threading...	01/11/2002 - 03/11/2002

NO	CHAPTER TITLE	YEAR
1	Graph Theory Based Classification of Brain Connectivity Network for Autism Spectrum DisorderBioinformatics and Biomedical Engineering...	2018
2	GeneCloud: Secure Cloud Computing for Biomedical ResearchTrusted Cloud Computing...	2014
3	Data and Model Driven Hybrid Approach to Activity Scoring of Cyclic PathwaysComputer and Information Sciences - ISCIS 2010...	2011
4	Protein Structural Class Determination Using Support Vector MachinesComputer and Information Sciences - ISCIS 2004...	2004

NO	NAME	DATE
1	Kanserde İmmunoterapi Etkinliğinin İyileştirilmesine Yönelik Makine Öğrenmesine Dayalı Yeni Gen Keşfi ve İlaç Yeniden Konumlandırma Platformunun Geliştirilmesi (TÜBİTAK-1003)...	1/2020 - 1/2023
2	TÜSEB Ağ-tabanlı bir sistem biyolojisi yaklaşımı ile kolorektal kanseri gelişiminde ve karaciğer metastazında etkili olan yolakların ve biyo-belirteçlerin tespiti...	4/2020 - /
3	TUBİTAK 1003 Kanserde İmmunoterapi Etkinliğinin İyileştirilmesine Yönelik Makine Öğrenmesine Dayalı Yeni Gen Keşfi ve İlaç Yeniden Konumlandırma Platformunuın Geliştirilmesi...	12/2019 - /
4	Sağlık hizmet sunucularında tahmin ve planlama sistemleri kapsamında tedarik zincir yönetim sistemi ürünü geliştirilmesi...	11/2019 - 6/2021
5	Gliom Oluşumunda Rol Oynayan Kalıcı Epigenomik Değişimlerin IDH1-TERT-MYC Ekseninde Karakterizasyonu...	6/2018 - /
6	İlaç hedeflerinin dokuya özel etkileşim ağlarında keşfedilmesi (2017.KB.FEN.037)...	12/2017 - 12/2018
7	TÜBİTAK Kanser hastalarının yaşam süresi ve kanser alt-kategorisinin akıllı biyomarkerlar ile tahmin edilmesi...	2/2015 - 2/2017
8	Cloud Computing in der Medikamentenentwicklung fur kleine und mittlere Unternehmen...	11/2011 - 11/2014

NO	NAME	DATE
1	Doktora - Ders Performans Ödülü...	2007
2	Konferans Katılım Desteği...	2009
3	Lisans - Bölüm Birinciliği Ödülü...	2001
4	En Başarılı Konferans Makalesi Ödülü...	2013
5	TÜBİTAK Yayın Teşvik Ödülü...	2016
6	TÜBİTAK Yayın Teşvik Ödülü...	2021
7	Toplum ve Sağlık Projeleri Yarışması / İkincilik Ödülü...	2021
8	Akademik Bilişim Projeleri Yarışması / İkincilik Ödülü...	2019
9	Bilgisayar Mühendisleri Odası Özgür Yazılım Kategorisi Ödülü...	2020
10	TÜBİTAK Yayın Teşvik Ödülü...	2019

NO NAME YEAR

1 Doktora Eğitim Bursu - TÜBİTAK 2007

2 Y. Lisans Eğitim Bursu - Sabancı Üniversitesi 2001

NO	Responsibility
1	Faculty of Engineering Department of Computer Engineering , Vice Director of Department, December 2020- August 2023
2	Application and Research Center of Informatics Teknologies , Member of The Central Board, November 2020- August 2023
3	Faculty of Engineering Department of Computer Engineering , Vice Director of Department, August 2017- July 2019
4	Faculty of Engineering Department of Computer Engineering , Vice Director of Department, August 2016- August 2017

NO	NAME	YEAR
1	Doktora Eğitim Bursu - TÜBİTAK	2007
2	Y. Lisans Eğitim Bursu - Sabancı Üniversitesi	2001