Arastirmalar

Theses:

2024

Erdem Türk, Ph.D., Advisor: Barış Ethem Süzek, Computational Approaches for Improving Analysis of Diagnostic Next-generation Sequencing
Esra Demiral, MSc, Advisor: Ömür Baysal, Data Mining Studies On The Whole Genome Sequence Data Of Bacillus Amyloliquefaciens (Eu07) In Purpose Of Dsrna Silence Against Phytophthora Infestans
Furkan Kıyıkçı, MSc, Advisor: Ülkü Anık, Creating Viral Enzymatic Reaction Library Using Bioinformatic Databases And Designing A Prototype Biosensor For An Analyte To Be Prioritized

2023

Talip Zengin, Ph.D., Advisor: Tuğba Önal-Süzek, Detection Of Immune Targetable Cancer Biomarkers In The Cancer Genome Atlas Datasets

2021

Başak Abak, MSc, Advisor: Tuğba Önal-Süzek, TCGAnalyzeR: A Web Portal for Visualization of Pan-Cancer Molecular Patient Data

2021
  1. Moustafa Almanla, MSc, Advisor:Ülkü Anık

2020
  1. Ufuk Yenigün, MSc, Advisor: Zeynep Filiz Eren Doğu, Statistical Methods and Tools For Quantitative Mass Spectrometry-based Proteomics
  2. Onur Can Karabulut, MSc, Advisor: Barış Ethem Süzek, A computational approach for predicting host specificity of adenoviruses

2019
  1. Abdulahad Bayraktar, MSc, Advisor: Ömür Baysal, Co-advisor: Tuğba Önal-Süzek, Understanding neurodegeneration: Pathway analysis of neurodegenerative disorders by merged and meta-analyzed gene expression data
  2. Talip Zengin, MSc, Advisor: Tuğba Önal-Süzek, Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Projects
  1. Süzek TO, Principal Investigator,ICGEB Cancer Bioinformatics Workshop,Marion-Ramirez L, Lecturer, Süzek BE,Lecturer, Zengin T,Lecturer, Türk E, Lecturer, Dec 2021, €15,000
  2. Tokgün O, Principal Investigator, Önal-Süzek T, Researcher, Turkish National Science Foundation (NSF)
    Determining the Role of Exosomal RNA Content in Cancer Development in Common and Limited Stage Small Cell Lung Carcinoma, 2021-2022,$77,000
  3. Süzek BE, Principal Investigator, Turkish National Science Foundation (NSF) Career Grant
    Development of a bioinformatics system for predicting Adenovirus host specificity and cross-species transmission events
    June 1st 2020-Dec,2022,$50,000
  4. Süzek TO, Principal Investigator, Zengin T,Researcher, Abak B,Researcher, Turkish Health Institutes (NIH) Grant
    Development of a personalized drug repurposing web platform for cancer cohorts created using genetic, transcriptomic and survival data, May 1 2020-Sep 1st 2022, $41,000
  5. Süzek TO, Principal Investigator, Salihoglu R, Researcher, Saraçoğlu F, Researcher, Turkish National Science Foundation (NIH) STAR COVID-19, Development of a COVID-19 web platform,June 1st 2020-Feb,2021,$6,500
  6. Süzek TO, Principal Investigator, Salihoglu R, Researcher, Turkish Council of Higher Education 100/2000 Bioinformatics/Biostatistics,Mar 1 2020-Mar,2024, $17,000
  7. Demircan T, Principal Investigator, Süzek BE, Researcher, Turkish Health Institutes Grant Detection of Candidate Target Epitranscriptomic Pathway Genes in Cancer Treatment by Bioinformatic Methods and In-Vitro Validation by CRISPR Method, Mar 1 2020-Mar,2020, $49,000
  8. Kılıç B, Principal Investigator, Süzek TO, Researcher, Turkish National Science Foundation (NSF) 1001 Orthodontics, 119S125, Turkish National Science Foundation,May 1st 2019-Dec 31st 2021, $45,000
  9. Süzek BE, Principal Investigator, TUBITAK 1002,  Development of an Open Source Proteomics Platform for in-silico comparative analysis, Sep 15 2017-Sep 15 2018, 
  10. Süzek TO, Principal Investigator,TUBITAK 2232,Development of text mining techniques for extracting keywords from the Cheminformatics database,23 October 2013-23 October 2015
  11. Süzek BE, Principal Investigator,TUBITAK 2232, Classification and Prediction of Disease-causing Single Amino Acid Polymorphisms (SAPs) for Multiple Sequence Alignment Computations, 23 October 2013-23 October 2015
  12. Süzek TO, Researcher, Principal Investigator is Dr.Kemal Ergin, TUBITAK 1001, Investigation of cell death after in vitro and in vivo silencing of pancreatic cancer elongation initiation factor 2 alpha (eıf2 A) siRNA, 11 August 2014-11 August 2016
  13. Süzek TO, Principal Investigator,TUBITAK 2223D,NIH-Mugla University collaboration,I.Immunogenomics Workshop, 18 Oct 2015
SCI Journal Publications (2013-2021)
  1. Zengin, T.; Önal-Süzek, T. Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. J. Pers. Med. 2021, 11, 154. https://doi.org/10.3390/jpm11020154
  2. Salihoğlu, R ; Önal-Süzek, T.  Tissue Microbiome Associated With Human Diseases by Whole Transcriptome Sequencing and 16S Metagenomics. Front. Genet. 2021, 12:585556. doi:  10.3389/fgene.2021.585556
  3. Hatipoğlu Tevfik,Esmeray Esra,Hu Xiaozhou, Yuan Hongling, Danyeli Ayça Erşen, Şeyhanlı Ahmet, Önal-Süzek Tuğba, Zhang Weiwei, Olgun Aybüke,Akman Burcu, Özkal Şermin, You Hua, Alacacıoğlu İnci, Özcan Mehmet Ali,Kucuk Can, Ultra-Deep Targeted Sequencing Reveals Cancer-Associated, Prognostically Significant Mutations in Circulating Cell-Free DNA in Treatment-Naive Patients with Follicular Lymphoma, 2020, Blood , 136 (Supplement 1): 20–21.
  4. Demircan Turan, Hacıbektaşoğlu Harbiye, Sibai Mustafa, Fesçioğlu Ece Cana, Altuntaş Ebru, Öztürk Gürkan, Süzek Barış Ethem, 2020. Preclinical Molecular Signatures of Spinal Cord Functional Restoration: Optimizing the Metamorphic Axolotl (Ambystoma mexicanum) Model in Regenerative Medicine. OMICS: A Journal of Integrative Biology
  5. Samy Asmaa, Süzek Barış Ethem, Özdemir Mehmet Kemal, Şensoy Özge, 2020. In Silico Analysis of a Highly Mutated Gene in Breast Cancer ProvidesInsight Into Abnormal mRNA Splicing: Splicing Factor 3B Subunit 1-K700E Mutant. Biomolecules
  6. Zengin Talip, Önal-Süzek Tuğba, 2020,Analysis of Genomic and Transcriptomic Variations as Prognostic Signature for Lung Adenocarcinoma,  BMC Bioinformatics,10.1186/s12859-020-03691-3 ,2020
  7. Sibai Mustafa, Altuntaş Ebru, Süzek Barış Ethem, Şahin Betül, Parlayan Cüneyd, Öztürk Gürkan, Baykal Ahmet Tarık, Demircan Turan, 2019. Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl. Biochemical and Biophysical Research Communications
  8. Bakar Dertlioğlu Selma, Edgünlü Tuba, Şen Deniz, Süzek Tuğba, 2019. Extracellular Matrix Protein 1 Gene Mutations In Turkish Patients With Lipoid Proteinosis. Indian Journal of Dermatology
  9. Suzek TO, “ Using Latent Semantic Analysis for automated keyword extraction from large document corpora”, Turkish Journal Electrical Engineering Computer Sciences, DOI:10.3906/elk-1511-203
  10. Suzek BE, Wang Y, Huang H, McGarvey P, Mazumder R, Wu CH and the UniProt Consortium. UniRef Clusters: A comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics. November 13,2014 doi:10.1093/bioinformatics/btu739
  11. McGarvey PB,Suzek BE, Baraniuk JB, Rao S,Conkright B,Lababidi S,Sutherland A,Forshee R, Madhavan S. In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases, BMC Immunology, 2014 Dec 2 – 2014
  12. Poux S, Magrane M, Arighi CN, Bridge A, O’Donovan C, Laiho K; UniProt Consortium (Suzek BE co-author) . Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016.
  13. Wang Y, Suzek TO, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant H, PubChem BioAssay: 2014 update, Nucleic Acids Research,2014 Jan;42 (Database issue):D1075-82
  14. Chen C, Li Z, Huang H, Suzek BE, Wu CH; UniProt Consortium. A fast Peptide Match service for UniProt Knowledgebase. Bioinformatics. 2013 Nov 1;29(21):2808-9. doi: 10.1093/bioinformatics/btt484. Epub 2013 Aug 19.
  15. Buckler AJ, Ouellette M, Danagoulian J, Wernsing G, Liu TT, Savig E, Suzek BE, Rubin DL, Paik D. Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers. J Digit Imaging. 2013 Aug;26(4):630-41. doi: 10.1007/s10278-013-9599-2.
  16. Buckler AJ, Paik D, Ouellette M, Danagoulian J, Wernsing G,Suzek BE. A novel knowledge representation framework for the statistical validation of quantitative imaging biomarkers. J Digit Imaging. 2013 Aug;26(4):614-29. doi:10.1007/s10278-013-9598-3.