Workshop sessions were canceled. 11 speakers from 5 countries have presented their recent findings in cancer to an audience of 88 attendees from 26 countries. For the conference program: https://cancerbioinformatics.mu.edu.tr/en/program-7432
2024
Erdem Türk, Ph.D., Advisor: Barış Ethem Süzek, Computational Approaches for Improving Analysis of Diagnostic Next-generation Sequencing
Furkan Kıyıkçı, MSc, Advisor: Ülkü Anık, Co-Advisor: Barış Ethem Süzek, Creating Viral Enzymatic Reaction Library Using Bioinformatic Databases And Designing A Prototype Biosensor For An Analyte To Be Prioritized
Selahattin Aksoy, MSc, Advisor: Tuğba Önal-Süzek, Co-Advisor: Banu Kılıç, Development of Machine Learning Models for Drug Re-purposing Targeting 18 Cancer-Related Proteins
2023
Barış Ceyhan, Ph.D., Advisor: Tuğba Önal-Süzek, A Smart Wristband Connected Mobile Application For The Management And Machine Learning Based Assesment Of Dementia Symptoms
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
2020
Onur Can Karabulut, MSc, Advisor: Barış Ethem Süzek, A computational approach for predicting host specificity of adenoviruses
2019
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
Talip Zengin, MSc, Advisor: Tuğba Önal-Süzek, Analysis of genomic and transcriptomic variations as the prognostic signature for lung adenocarcinoma
Erdem Türk, MSc,Advisor: Barış Ethem Süzek, An open source proteomics platform for in silico comparative analysis
Suzek Lab holds 11 high capacity Dell workstations. One server has 350GB memory and 40TB hard disk, four servers have 128GB memory, two servers have 64GB memory, and 16TB hard disk, two servers have 32GB memory, and 8TB hard-disk running on Ubuntu managed completely by SuzekLab members. SuzekLab servers are dedicated to SuzekLab members’ research projects and Bioinformatics lectures. All of the 11 workstations are racked at a climate controlled system room at Mugla University Research Laboratories Center and can be accessed via remote access from researchers’ own personal computers.
Software
Orthodontist Web Tool: https://kedi-mobile.com/
Orthodontist Mobile App(IOS): https://apps.apple.com/tr/app/orthodontist/id6444021818
TCGAnalyzeR: Pan-Cancer Cohort-Gene Discovery Web Tool http://tcganalyzer.mu.edu.tr/
CompCorona: Coronaviridae Host-Response Analysis Web Tool: https://compcorona.mu.edu.tr/
2 of our faculty, Baris Ethem Suzek and Tugba Onal-Suzek made to the top-scientist list of Turkey by Webometrics! http://www.webometrics.info/en/node/72
HIBIT2015
Between Oct 16-17 2015, Mugla university hosted the 9th International Symposium on Health Informatics and Bioinformatics !
For conference photos, click here
I.Immunogenomics Workshop
On Dec 5-6 2015, SuzekLab hosted the I.Immunogenomics workshop at Renaissance Izmir Hotel
Bioinformatics Masters Program is jointly offered by Molecular Biology and Genetics, Biology, Medical Biology, Chemistry and Computer Engineering Departments at Muğla Sıtkı Koçman University. http://bioinformatik.fenbilimleri.mu.edu.tr
Program is 100% English and accepts on average 3 students each semester.
Medicine, Engineering and Science students: GPA >2.4, ALES,TUS > 60
Non-Turkish nationals with GPA > 3.0 are accepted.
Please refer to Bioinformatics program web site for more information:
http://biyoinformatik.fenbilimleri.mu.edu.tr/en
Classes offered are:
Principal Investigator
Kurşun D, Principal Investigator,Önal-Süzek T, Home Lab Advisor, Van den Heynden J, Host Lab Advisor, EMBO Staf Exchange Grant
Machine Learning-Based Feature Extraction for Predicting Pan-Cancer Therapy Response Using Immune Signatures and Molecular Subtypes
1 May 2025- 1 Aug 2025
€9,000
Önal-Süzek T, Principal Investigator(Consortium Partner-Turkey), Zengin T, Researcher, Küçük C, Researcher, Karpuzcu BA, Technician, EU Cofund Transcan-3 , PerImmune
Intraperitoneal Immune Modulation for Colorectal Peritoneal Metastases
1 Feb 2023-March 2026
€39,000
Kılıç B , Principal Investigator, Önal-Süzek T,Co-Principal Investigator, Kılıç Ö, Researcher, Horizon European Innovation Ecosystems Framework, WomenTech EU
Early Detection and Prediction of Skeletal Orthodontic Malocclusions from Profile Photos with Deep Learning
May 2023-May 2024
€75,000
Önal-Süzek T, Principal Investigator,Kılıç B, Researcher/Partner, Sakman MC, Researcher, İbrahim AH, Researcher, Turkish Ministry of Industry and Technology, İstanbul Boğaziçi KOSGEB, SBIR Grant Program
Early Diagnosis of Skeletal Syndromes from Mobile Profile Photos using Artificial Intelligence
March 2022-March 2023
€11,000
Önal-Süzek T, Principal Investigator,Kılıç B, Researcher/Partner, Demircan GS, Researcher, Aksoy S, Researcher, Turkish National Science Foundation (NSF) SBIR- Multi-phase Entrepreneurship Grant Program , Early Diagnosis of Class III Malocclusion from Mobile Profile Photos using Artificial Intelligence
August 1st 2021-Oct 31st 2022
€19,370
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
Önal-Süzek T, Principal Investigator, Zengin T,Researcher, Abak B,Researcher, Kurşun D, Researcher, Aksoy S, Researcher, Turkish Health Institutes (NIH) Grant
Development of a personalized drug re-purposing web platform for cancer cohorts created using genetic, transcriptomic and survival data
May 1 2020-Nov 31st 2022
$41,000
Önal-Süzek T, Principal Investigator, Salihoglu R, Researcher, Turkish National Science Foundation (NIH) STAR COVID-19
Development of a COVID-19 web platform
June 1st 2020-Feb,2021
€6,000
Önal-Süzek T, Principal Investigator, Kurşun D, Researcher, Turkish Council of Higher Education 100/2000 Bioinformatics/Biostatistics
Mar 1 2021-Mar,2025
€11,000
Önal-Süzek T, Principal Investigator, Salihoglu R, Researcher, Turkish Council of Higher Education 100/2000 Bioinformatics/Biostatistics
Mar 1 2020-Mar,2024
€11,000
Süzek BE, Principal Investigator, Turk E, Researcher, Turkish National Science Foundation (NSF) 1002
Development of an Open Source Proteomics Platform for in-silico comparative analysis, Sep 15 2017-Sep 15 2018
$9000
Önal-Süzek T, Principal Investigator, Mugla University Intramural Research-Development Grant
In silico identification of the immune response biomarker candidates predicting the response to bacterial immune therapy for melanoma
Sep 1 2016-Oct 19,2017
$9,000
Önal-Süzek T, Principal Investigator, Turkish National Science Foundation (NSF) Reintegration Grant 2232
Development of Text Mining techniques for extracting keywords from the Cheminformatics database
23 October 2013-23 October 2015
$40,000
Süzek BE, Principal Investigator,Turkish National Science Foundation (NSF) Reintegration Grant 2232
İnsan Proteinleri için En Doğru Çoklu Dizi Hizalamalarının Hesaplanması ve Hastalığa Neden Olan Bilinen Tek Amino Asit Polimorfizmleri (SAP) Tahmini
23 October 2013-23 October 2015
$43,000
Researcher
Kılıç Ö, Principal Investigator, Önal-Süzek T, Researcher, Kılıç B, Researcher/Partner, Turkish National Science Foundation (NSF) SBIR- Multi-phase Entrepreneurship Grant Program
Early Prediction of Skeletal Syndromes from Profile Profile using Artificial Intelligence – A Mobile Application
Jan 2025-July 2026
€22,000
Oktay Y, Principal Investigator, Süzek BE, Researcher,Önal-Süzek T,Researcher, Zengin T, PhD student, Türk E, Ph.D. student, Ahmed Hassan Mohammed Hussein, PhD student, Karaca-Uluoğlu I, MSc Student-Turkish National Science Foundation (NSF) Center of Excellence
Development of Next Generation Sequencing-Based Genetic Analysis Kit for CAR-T Cell Therapies in acute lymphoblastic leukemia
October 2021-October 2025
€60,000
Kılıç Eren M, Principal Investigator, Önal-Süzek T, Researcher, COST Action CA21140-Interception of oral cancer development; INTERCEPTOR
2023-2026
$55,000
Kılıç Eren M, Principal Investigator, Önal-Süzek T, Researcher, Turkish National Science Foundation (NSF)
Investigating the Tumor Suppressant Role of ARID1A in Burkitt Lymphoma
2023-2026
$73,000
Tokgün O, Principal Investigator, Önal-Süzek T, Researcher, Kurşun D, Ph.D. Student, 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
Kılıç B, Principal Investigator, Önal-Süzek T, Researcher, Turkish National Science Foundation (NSF) 1001
Orthodontics, 119S125, Turkish National Science Foundation,May 1st 2019-Dec 31st 2021,
$45,000
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
Önal-Süzek T, Researcher, Principal Investigator is Dr.Kemal Ergin, Turkish National Science Foundation (NSF) 1001, Investigation of cell death after in vitro and in vivo silencing of pancreatic cancer elongation initiation factor 2 alpha (eIF2-A) siRNA
Oct 2014- Mar 2017
$111,000
Onur Can Karabulut, Ph.D. candidate, Research Assistant, YOK 100/2000 & TUBITAK scholar
Betül Asiye Karpuzcu, Ph.D. candidate, EU Transcan & TUBITAK scholar
Ahmed H. İbrahim, Ph.D. Candidate TUBITAK scholar
İrem Karaca Uluoğlu, MSc, Research Assistant, TUBITAK Scholar
Çilem Özdemir Ph.D. Candidate, EU Transcan & TÜBİTAK scholar
Abdulahad Bayraktar,Assistant Professor at Istanbul University, MSc, PhD (London King’s College)
Esra Esmeray, MSc, Ph.D. IBG, İzmir, Küçük Lab
Doreen Mokeira Kebande,Software Engineer at DHL,KEMRI-Wellcome Trust Scholar, Kenya
Fatih Saraçoğlu, Software Engineer at TUBITAK
Gaye Çolakoğlu, MSc student at Zurich University, TÜBİTAK STAR scholar
Başak Abak Masud, MSc, TUSEB scholar, Software Engineer at TUBITAK
İlayda Betül Uçar,Software Engineer at Amadeus
Erdem Türk , Ph.D., Assistant Professor at Mugla University, TUBITAK scholar
Barış Ceyhan, Ph.D., Dr. Lecturer at Yasar University, TUSEB scholar,Sr.Software Engineer at Infor
SCI Publications
Zengin, T.; Masud, B.A.; Önal-Süzek, T. TCGAnalyzeR: An Online Pan-Cancer Tool for Integrative Visualization of Molecular and Clinical Data of Cancer Patients for Cohort and Associated Gene Discovery. Cancers 2024, 16, 345. https://doi.org/10.3390/cancers16020345
Sali̇hoğlu, Rana; Saraçoğlu, Fati̇h; Si̇bai̇, Mustafa; Zengi̇n, Tali̇p; Abak Masud, Başak; Karasoy, Onur; and Önal Süzek, Tuğba (2023) “CompCorona: A web application for comparative transcriptome analyses of coronaviruses reveals SARS-CoV-2-specific host response,” Turkish Journal of Biology: Vol. 47: No. 6, Article 5. https://doi.org/10.55730/1300-0152.2673 (2023) “CompCorona: A web application for comparative transcriptome analyses of coronaviruses reveals SARS-CoV-2-specific host response,” Turkish Journal of Biology: Vol. 47: No. 6, Article 5. https://doi.org/10.55730/1300-0152.2673
Kılıç Banu, İbrahim Ahmed Hassan, Aksoy Selahattin, Sakman Mehmet Cihan, Demircan Gül Sude, Süzek Tuğba, 2023. A family-centered orthodontic screening approach using a machine learning-based mobile application. Journal of Dental Sciences: Vol.19 (2024),186-195, https://doi.org/10.1016/j.jds.2023.05.001
Hatipoğlu T, Esmeray Sönmez E, Hu X, Yuan H, Danyeli AE, Şeyhanlı A, Önal-Süzek T, Zhang W, Akman B, Olgun A, Özkal S, Alacacıoğlu İ, Özcan MA, You H and Küçük C (2022) Plasma Concentrations and Cancer-Associated Mutations in Cell-Free Circulating DNA of Treatment-Naive Follicular Lymphoma for Improved Non-Invasive Diagnosis and Prognosis. Front. Oncol. 12:870487. https://10.3389/fonc.2022.870487
Karabulut OC, Karpuzcu BA, Türk E, Ibrahim AH, Süzek BE. ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor. Front Mol Biosci. 2021 May 7;8:647424. doi: 10.3389/fmolb.2021.647424. PMID: 34026828; PMCID: PMC8139618.
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
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
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.
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
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
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
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
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,
Onal-Suzek T . 2017, Using Latent Semantic Analysis for automated keyword extraction from large document corpora. Turkish Journal Electrical Engineering Computer Sciences
UniProt Consortium(coauthor Suzek BE). UniProt: A hub for protein information. Nucleic Acids Research, 2015 Jan;43(Database issue):D204-12. doi: 10.1093/nar/gku989
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
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
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.
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
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.
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.
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.
Conference Publications
Bayraktar, Abdulahad; Onal-Suzek, Tugba; Ethem Suzek, Baris; Baysal, Omur, Meta-analysis of Gene Expression in Neurodegenerative Diseases Reveals Patterns in GABA Synthesis and Heat Stress Pathways, CNB-MAC 2019, Sep 2019, Niagara Falls, USA, Oral Presentation & Poster
Yousef Malik, Khaelifa Walid, Süzek Tuğba, 2019. In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features. BIOSTEC 2019 Proceedings of the12th International Joint Conference on Biomedical Engineering Systems and Technologies, Oral Presentation
Turk E, Suzek BE, Leveraging Taxonomic Ranks for Improving MirrorTree-based Protein Interaction Prediction, HIBIT2017, Jun 2017, METU NCC, Northern Cyprus, Oral Presentation
Onal-Suzek T, “Using Latent Semantic Analysis for Automated Keyword Extraction from Large Document Corpora”, ISMB2016, July 8-12th, 2016, Orlando, Florida, Poster Presentation
Turk E, Suzek BE, “Assessing Impact of Taxonomic Diversity and Sequence Conservation-based Filters on Mirrortree Method”, ISMB2016,July 8-12th, 2016,Orlando,Florida
Onal-Suzek T,Wang Y, “Text-mining based evaluation of NIH Chemical Probes”, The 3rd Biomedical Informatics Symposium at Georgetown University,Oct 2nd 2014, Washington DC, Poster Presentation
Suzek, BE, “Where are the disease-associated single amino acid polymorphisms located on proteins?”,The 3rd Biomedical Informatics Symposium at Georgetown University,Oct 2nd 2014, Washington DC
Suzek Lab 