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