ABOUT ME

I am a Ph.D in the Biostatistics Department at Hacettepe University. My research interests are focused on machine learning, proteomics and computer-aided drug design.

I studied for my MSc in the Biostatistics Department at Ege University from 2009-2011, and the title of my thesis is “The Use of Nonlinear Mixed-Effects Models in Bioequivalence Studies”.

I worked as a visiting scientist at RCSB Protein Data Bank (at University of California, San Diego) and have developed new approaches for the evaluation of biological assemblies and protein-protein interfaces in my PhD thesis under supervision of Prof. Dr. Osman Saraçbaşı and Dr. Peter W. Rose.

Click to access my Google Scholar and GitHub pages.

Last updated: August 2016

MY SKILLS

Python

Html / CSS

Matlab / SAS

Orange / Weka / RapidMiner

PASS / GPower

R / SPSS / Statistica / Minitab / NCSS / MedCalc

EDUCATION

2004 - 2008

Graduated

BACHELOR DEGREE OF STATISTICS

Ege University

I got my bachelor degree from Ege University Department of Statistics.

2009 - 2011

Graduated

MASTER DEGREE OF BIOSTATISTICS

Ege University

I got my master degree from Ege University Department Biostatistics under supervision of Prof. Dr. Mehmet N. Orman.

2012 - 2016

Graduated

PhD DEGREE OF BIOSTATISTICS

Hacettepe University

I got my PhD from Hacettepe University Department of Biostatistics under supervision of Prof. Dr. Osman Saraçbası and Dr. Peter W. Rose.

WORK EXPERIENCE

2009 - 2011

Ege University Rectorate

Statistician

2011 - 2012

Trakya University

Research Assistant

2012 - Now

Hacettepe University

Research Assistant

PUBLICATIONS

Papers in International Journals


1. Goksuluk D, Korkmaz S, Zararsiz G, Karaağaoğlu AE (2016) "easyROC: An Interactive Web-tool for ROC Curve Analysis Using R Language Environment" The R Journal, Accepted/In press.


2. Zararsiz G, Goksuluk D, Korkmaz S, Ozturk A, Akyildiz HY (2016) "Statistical learning approaches in diagnosing patients with nontraumatic acute abdomen" Turkish Journal of Electrical Engineer and Computer Science 24, 3685-3697.


3. Zararsiz G, Korkmaz S, Goksuluk D, Eldem V, Ozturk A (2015) "Diagonal Discriminant Analysis for Gene-Expression Based Tumor Classification" Journal of Advances in Information Technology 6(2): 59-62.


4. Korkmaz S, Zararsiz G and Goksuluk D (2015) "MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development" PLOS ONE 10(4): e0124600.


5. Korkmaz S, Goksuluk D and Zararsiz G (2014) "MVN: An R Package for Assessing Multivariate Normality" The R Journal 6(2), 151-162.


6. Korkmaz S, Zararsiz G and Goksuluk D (2014) "Drug/Nondrug Classification Using Support Vector Machines with Various Feature Selection Strategies" Computer Methods and Programs in Biomedicine 117(2), 51-60.


7. Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Duru İP, Ünver T, Öztürk A (2014) "Classification of RNASeq Data via Bagging Support Vector Machines" bioRxiv.


8. Alkin Z, Perente I, Ozkaya A, Alp D, Agca A, Aygit ED, Korkmaz S, Yazici AT, Demirok A (2014) "Comparison of Efficacy Between Low-fluence and Half-dose Verteporfin Photodynamic Therapy for Chronic Central Serous Chorioretinopathy" Journal of Clinical Ophthalmology 2014(8), 685-690.


9. Korkmaz S and Orman MN (2012) "The Use of Nonlinear Mixed Effects Models in Bioequivalence Studies: A Real Data Application" Journal of Bioequivalence and Bioavailability 512(1): 1-11.


Presentations in International Conferences


1. Zararsiz G, Akyildiz HY, Goksuluk D, Korkmaz S, Ozturk A, Karahan S, Karaismailoglu E "DDNAA: Decision Support System for Differential Diagnosis of Nontraumatic Acute Abdomen", The R User Conference 2015, June 30 - July 3 2015, Aalborg/Denmark.


2. Goksuluk D, Korkmaz S, Zararsiz G, Karahan S, Karaagaoglu AE "easyROC: an interactive web-tool for ROC analysis", The R User Conference 2015, June 30 - July 3 2015, Aalborg/Denmark.


3. Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Duru IP, Unver T, Ozturk A "MLSeq: Machine Learning Interface for RNA-Seq Data", The R User Conference 2015, June 30 - July 3 2015, Aalborg/Denmark.


4. Goksuluk D, Zararsiz G, Korkmaz S, Karaagaoglu E "Negative Binomial Linear Discriminant Analysis For The Classification Of Rna-Seq Data", 8th conference of the Eastern Mediterranean Region of the International Biometric Society (EMR-IBS), 11-15 May 2015 Nevsehir, Turkey.

5. Zararsiz G, Akyildiz HY, Goksuluk D, Korkmaz S, Ozturk A "Statistical Learning Approaches In Diagnosing Patients With Nontraumatic Acute Abdomen", 8th conference of the Eastern Mediterranean Region of the International Biometric Society (EMR-IBS), 11-15 May 2015, Nevsehir, Turkey.

6. Zararsiz G, Eldem V, Korkmaz S, Göksülük D, Duru IP, Unver T, Karabulut E, Öztürk A "Diagonal Discriminant Analysis For Gene-Expression Based Tumor Classification", International Conference on Bioinformatics and Computational Biology (ICBCB 2015), 12-13 March 2015 Hong Kong.

7. Korkmaz S, Zararsiz G, Goksuluk D, Saracbasi O, “Homology Modeling Using Machine Learning Approach”, XXVII International Biometric Conference, 6-11 July 2014, Florence, Italy.


8. Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Unver T, Ozturk A “Classification of RNASeq Data via Bagging Support Vector Machines”, XXVII International Biometric Conference, 6-11 July 2014, Florence, Italy.


9. Goksuluk D, Korkmaz S, Zararsiz G, Karaagaoglu E, “Ensemble Machine Learning Approach for Biomarker Discovery using Mass-Spectrometry based Proteomics Data”, XXVII International Biometric Conference, 6-11 July 2014, Florence, Italy.


10. Korkmaz S, Zararsız G and Dalkara S “Drug/Non-Drug Classification Using Machine Learning” International Multidisciplinary Symposium on Drug Research and Development, 28-30 November 2013, Antalya, Turkey.


11. Korkmaz S, Göksülük, D and Zararsız G “bbRVM: an R package for Ensemble Classification Approaches of Relevance Vector Machines” The R User Conference 2013, 9-12 July 2013, Albacete/Spain.


12. Arslankoz S, Korkmaz S, Netto GJ and Baydar DE “Immunoexpression of mTOR Pathway Members in Non-Invasive Papillary Urothelial Neoplasms of Bladder” Annual Meeting Abstracts, February 2013, USA.


13. Korkmaz S and Orman MN “The Use of Nonlinear Mixed Effects Models in Bioequivalence Studies: A Real Data Application” 26th International Biometric Conference, 26-31 August 2012, Kobe, Japan.


14. Korkmaz S and Orman MN “A Simulation Study Based on Nonlinear Mixed Effects Models” 6th EMR-IBS Conference, 8-12 May 2011, Crete, Greece.


Presentations in National Conferences


1. Korkmaz S, Göksülük D, Zararsız G “MVN: Çok Değişkenli Normal Dağılıma Uygunluğun Belirlenmesi için Bir R Paketi” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey (link) .


2. Korkmaz S, Göksülük D, Zararsız G “MVN-web: Çok Değişkenli Normal Dağılıma Uygunluğun Belirlenmesi için Bir Web Uygulaması” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey (link) .


3. Korkmaz S, Zararsız G, Göksülük D, Saraçbaşı O “Makine Öğrenimi Yaklaşımı ile Homolog Protein Tespiti” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey (link) .


4. Göksülük D, Zararsız G, Korkmaz S, Eldem V, Duru İP “RNA-Dizileme Verilerinde Kullanılan Anlamlılık Testlerine İlişkin Hesaplama Sürelerinin Karşılaştırılması” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.


5. Zararsız G, Eldem V, Korkmaz S, Göksülük D, Duru İP, Ünver T, Öztürk A “De-Brujin Grafikleri ile De-Novo Genom Dizileme Analizleri” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.


6. Zararsız G, Korkmaz S, Göksülük D, Eldem V, Öztürk A “RNA Dizileme Verilerinin İstatistiksel Değerlendirilmesi” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.


7. Zararsız G, Göksülük D, Korkmaz S, Eldem V, Duru İP, Ünver T, Öztürk A “RNA-Dizileme Verileri ile Gen Ekspresyonuna Dayalı Sınıflandırmada Yeni Bir Yaklaşım ve MLSeq R/BIOCONDUCTOR Yazılımı” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.


8. Göksülük D, Korkmaz S, Zararsız G, Karaağaoğlu E “Kütle-Spektrometresine Dayalı Proteomik Verilerinin Ensemble Veri Madenciliği Yöntemleri İle Sınıflandırılması” 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.


9. Yamasan BE, Gülyaşar T, Sipahi T, Korkmaz S, and Palabıyık O “Koroner Arter Hastalığında Anjiyotensinojen M235T ve T174M Gen Polimorfizimlerinin Araştırılması Ve Risk Faktörlerinin Belirlenmesi” 25th National Biophisics Congress, 24-27 September 2013, Trabzon, Turkey.


10. Korkmaz S, Zararsız G, Coşgun E, Dalkara S and Saraçbaşı O “Drug/Non-Drug Classification Using Support Vector Machines with Various Feature Selection Strategies” 15th National Biostatistics Congress, 20-23 August 2013, Aydın, Turkey.


11. Korkmaz S and Süt N “Dört Gözlü Kontenjans Tablolarında Yates Düzeltmeli Ki-Kare Testinin İncelenmesi: Simülasyon Çalışması”. 14th National Biostatistics Congress, 4-7 September 2012, Kayseri, Turkey.


12. Korkmaz S and Orman MN “Doğrusal Olmayan Karma Etki Modelleri Üzerine Bir Simülasyon Çalışması”. 12th National Biostatistics Congress, 28 June - 1 July 2010, Van, Turkey.



PROCESS

IDEA

CONCEPT

DESIGN

DEVELOP

TEST

LAUNCH

PROJECTS


1. Biosoft Project is dedicated to develop free web applications for various fields of science using the R language environment. We aim to develop user-friendly, easy-to-use, up-to-date and comprehensive tools for the science community. The project is started in 2014 at Hacettepe University Department of Biostatistics.


2. TUBITAK Project “A Novel Method for Prediction of Biological Assemblies and Protein-Protein Interfaces”, University of California San Diego, Supercomputer Center. Project coordinator: Peter W. Rose. 2015. (12 months).


3. Erciyes University Scientific Research Project “Novel Machine Learning Approaches for Classification of RNA-Seq Data”, ID:5468. Project coordinator: Ahmet Ozturk. 2015. (24 months).

AWARDS


1. Young Statistician’s Showcase Prize: Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Unver T, Ozturk A “Classification of RNASeq Data via Bagging Support Vector Machines”, XXVII International Biometric Conference, 6-11 July 2014, Florence, Italy.


2. Gevher Nesibe Research Award: Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Unver T, Ozturk A “Yeni Nesil Dizileme Sistemleri için Veri Madenciliği Aracı” 2014.


3. Best oral presentation: Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Unver T, Ozturk A “RNA-Dizileme Verileri ile Gen Ekspresyonuna Dayalı Sınıflandırmada Yeni Bir Yaklaşım ve MLSeq R/BIOCONDUCTOR Yazılımı”, 16th National Biostatistics Congress, 10-12 September 2014, Antalya, Turkey.



REVIEWING MANUSCRIPTS FOR JOURNALS


1. Journal of Chemical Information and Modeling


2. PLOS ONE



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