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Serdar Bozdag

Associate Professor

University of North Texas

Department of Computer Science and Engineering

Email: Serdar.Bozdag@unt.edu

Education

  • PhD, University of California, Riverside, 2008
    Major: Computer Science
    Dissertation: Combinatorial Approaches to the Physical Mapping Problem
  • BS, Marmara University, 2002
    Major: Computer Engineering

Professional Memberships

  • Alzheimer's Association. (June 2023 - Present).
  • Association for Computing Machinery. (June 2019 - Present).
  • ACM SIGBioinformatics. (February 2013 - Present).
  • The International Society for Computational Biology. (February 2013 - Present).

Development Activities

  • Conference Attendance, Machine Learning in Computational Biology (MCLB 2023), MLCB. United States of America. (November 2023 - November 2023).
  • Conference Attendance, Festival of Genomics, Front Line Genomics. Boston,MA,United States of America. (October 2022 - October 2023).
  • Conference Attendance, Intelligent Systems for Molecular Biology (ISMB 2023), International Society of Computational Biology. Lyon,France. (July 2023 - July 2023).
  • Conference Attendance, The Alzheimer's Association International Conference, Alzheimer's Association. United States of America. (July 2023 - July 2023).
  • Workshop, NSF-NIH Joint Workshop on Emerging AI in Biology, NSF/NIH. United States of America. (June 2023 - June 2023).
  • Conference Attendance, IEEE International Parallel and Distributed Processing Symposium, IEEE. st. petersburg,florida,United States of America. (May 2023 - May 2023).
  • Workshop, Funding Opportunity Workshop with Dr. Moore -CPRIT Research, Uni. Denton,TX,United States of America. (January 2023 - January 2023).
  • Conference Attendance, IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2022), IEEE. Las Vegas,Nevada,United States of America. (December 2022 - December 2022).
  • Conference Attendance, Tri Omics Summit, Front Line Genomics. Boston,MA,United States of America. (September 2022 - September 2022).
  • Conference Attendance, 2022 ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2022), International Society of Computational Biology. Washington,DC,United States of America. (August 2022 - August 2022).
  • Conference Attendance, Intelligent Systems for Molecular Biology (ISMB 2022), International Society of Computational Biology. Madison,Wisconsin,United States of America. (July 2022 - July 2022).
  • Workshop, NVIDIA Workshop on CUDA Programming in Python, NVIDIA. United States of America. (July 2022 - July 2022).
  • Workshop, Workshop on Future Directions in Network Biology, NSF. Indiana,United States of America. (June 2022 - June 2022).
  • Workshop, Flight Path to Promotion Success: A Midcareer Faculty Workshop, University of North Texas. Denton,TX,United States of America. (March 2022 - March 2022).
  • Conference Attendance, IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2021), IEEE. United States of America. (December 2021 - December 2021).
  • Conference Attendance, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2021), ACM. United States of America. (August 2021 - August 2021).
  • Conference Attendance, Intelligent Systems for Molecular Biology (ISMB 2021), International Society of Computational Biology. United States of America. (July 2021 - July 2021).
  • Conference Attendance, Plant Biology Worldwide Summit 2021, ASBP. United States of America. (June 2021 - July 2021).
  • Conference Attendance, Great Lakes Bioinformatics Conference (GLBIO 2021), International Society of Computational Biology. United States of America. (May 2021 - May 2021).
  • Conference Attendance, IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2020), IEEE. United States of America. (December 2020 - December 2020).
  • Workshop, Faculty Grantsmanship Workshop, University of North Texas. United States of America. (November 2020 - November 2020).
  • Conference Attendance, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2020), ACM. United States of America. (September 2020 - September 2020).
  • Conference Attendance, Intelligent Systems for Molecular Biology (ISMB 2020), International Society of Computational Biology. United States of America. (July 2020 - July 2020).
  • Conference Attendance, Plant Biology Worldwide Summit 2020, ASBP. United States of America. (June 2020 - July 2020).

Teaching

Teaching Experience

    University of North Texas

  • BIOL 4810 - Bioinformatics Algorithms, 4 courses.
  • BIOL 5810 - BioComputing, 4 courses.
  • BIOL 6810 - Advanced Topics in Computational Life Science, 2 courses.
  • CSCE 4110 - Algorithms, 3 courses.
  • CSCE 4810 - Bioinformatics Algorithms, 6 courses.
  • CSCE 4820 - Advances in Bioinformatics, 2 courses.
  • CSCE 5810 - BioComputing, 5 courses.
  • CSCE 5820 - Advances in Bioinformatics, 2 courses.
  • CSCE 5900 - Special Problems, 2 courses.
  • CSCE 5934 - Directed Study, 1 course.
  • CSCE 6810 - Advanced Topics in Computational Life Science, 2 courses.
  • CSCE 6940 - Individual Research, 9 courses.
  • CSCE 6950 - Doctoral Dissertation, 8 courses.
  • MATH 4810 - Bioinformatics Algorithms, 4 courses.
  • MATH 6710 - Topics in Applied Mathematics, 1 course.

Directed Student Learning

  • Dissertation Committee Chair, Computer Science and Engineering. (September 2023).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2023).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2023).
  • Dissertation Committee Member, Computer Science and Engineering. (September 2023).
  • Postdoctoral Research Supervision, Computer Science and Engineering. (August 2023).
  • Postdoctoral Research Supervision, Computer Science and Engineering. (July 2023).
  • Supervised Research, Computer Science and Engineering. (June 2023).
  • Dissertation Committee Chair, Computer Science and Engineering. (January 2023).
  • Dissertation Committee Member, Biological Sciences. (September 2022).
  • Dissertation Committee Chair, Computer Science and Engineering. (August 2022).
  • Supervised Research, Computer Science and Engineering. (June 2022).
  • Dissertation Committee Member, Computer Science and Engineering. (March 2022).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Member, Computer Science and Engineering. (2021).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2020).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2020).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2020).
  • Dissertation Committee Member, Computer Science and Engineering. (July 2022 - 2023).
  • Supervised Research, Computer Science and Engineering. (June 2021 - 2023).
  • Dissertation Committee Chair, Computer Science and Engineering. (September 2020 - 2023).
  • Postdoctoral Research Supervision, Computer Science and Engineering. (July 2022 - January 2023).
  • Supervised Research, Computer Science and Engineering. (August 2022 - December 2022).
  • Supervised Research, Computer Science and Engineering. (August 2022 - December 2022).
  • Supervised Research, Computer Science and Engineering. (June 2022 - December 2022).
  • Supervised Research, Computer Science and Engineering. (October 2021 - December 2022).
  • Supervised Research, Computer Science and Engineering. (October 2021 - December 2022).
  • Dissertation Committee Member, Computer Science and Engineering. (2021 - 2022).
  • Supervised Research, Computer Science and Engineering. (June 2022 - August 2022).
  • Postdoctoral Research Supervision, Computer Science and Engineering. (February 2021 - August 2022).
  • Supervised Research, Computer Science and Engineering. (January 2022 - July 2022).
  • Supervised Research, Computer Science and Engineering. (August 2021 - December 2021).
  • Supervised Research, Computer Science and Engineering. (January 2021 - May 2021).
  • Dissertation Committee Chair, "Identifying Gene-Complex Trait Associations and Chemical-Gene Interactions to Uncover Genotype-Phenotype Relationships," Other - Outside UNT. (2018 - August 2020).
  • Dissertation Committee Chair, "Integration of Multi Omics Data to Compute Gene Regulatory Networks and To Predict Personalized Drug Response In Cancer," Other - Outside UNT. (2017 - August 2020).

Awards and Honors

  • Distinguished Faculty Fellow, College of Engineering, University of North Texas. (May 2023).
  • Best Poster Award, Marquette University. (2019).
  • Best Poster Award, Marquette University. (2018).
  • Way Klingler Young Scholar Award, Marquette University. (2015).
  • Visiting Fellowship, National Institutes of Health. (2008).

Research

Published Intellectual Contributions

    Abstracts and Proceedings

  • Vashishath, Y., Bozdag, S. (2021). GWAS Analysis to Compute Genetic Markers of Progression to Alzheimer's Disease. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 1. New York, NY, USA, Association for Computing Machinery. https://doi.org/10.1145/3459930.3470854
  • Kesimoglu, Z.N., Bozdag, S. (2021). SUPREME: A Cancer Subtype Prediction Methodology Integrating Multiple Biological Datatypes Using Graph Convolutional Neural Networks. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA, Association for Computing Machinery. https://doi.org/10.1145/3459930.3470853

    • Conference Proceeding

  • Yang, T., Al-Duailij, M.A., Bozdag, S., Saeed, F. (2022). Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks. 2022 IEEE International Conference on Big Data (Big Data). 3131--3138.
  • Dursun, C., Smith, J.R., Hayman, G.T., Kwitek, A.E., Bozdag, S. (2020). NECo: A node embedding algorithm for multiplex heterogeneous networks. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 146--149.
  • Do, D., Bozdag, S. (2020). CanMod: A computational model to identify co-regulatory modules in cancer. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. (117) 1--10. New York, NY, USA, Association for Computing Machinery. https://doi.org/10.1145/3388440.3415586
  • Bose, B., Bozdag, S. (2020). CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. (7) 1--10. New York, NY, USA, Association for Computing Machinery. https://doi.org/10.1145/3388440.3412456
  • Bose, B., Bozdag, S. (2019). miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 366--375. New York, NY, USA, ACM. http://doi.acm.org/10.1145/3307339.3342172
  • Dursun, C., Shimoyama, N., Shimoyama, M., Schläppi, M., Bozdag, S. (2019). PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 279--288. New York, NY, USA, ACM. http://doi.acm.org/10.1145/3307339.3342155
  • Bozdag, S., Close, T.J., Lonardi, S. (2007). A Compartmentalized Approach to the Assembly of Physical Maps. IEEE International Conference on Bioinformatics and Bioengineering. 218--225.

    • Journal Article

  • Aghdam, M., Bozdag, S., Saeed, F. (2023). PVTAD: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied To White Matter Of T1-Weighted Structural MRI Data. https://www.biorxiv.org/content/10.1101/2023.11.17.567617v1
  • Zitnik, M., Li, M.M., Wells, A., Glass, K., Gysi, D.M., Krishnan, A., Murali, T.M., Radivojac, P., Roy, S., Baudot, A., Bozdag, S., Chen, D.Z., Cowen, L., Devkota, K., Gitter, A., Gosline, S., Gu, P., Guzzi, P.H., Huang, H., Jiang, M., Kesimoglu, Z.N., Koyuturk, M., Ma, J., Pico, A.R., Pržulj, N., Przytycka, T.M., Raphael, B.J., Ritz, A., Sharan, R., Shen, Y., Singh, M., Slonim, D.K., Tong, H., Yang, X.H., Yoon, B., Yu, H., Milenković, T. (2023). Current and future directions in network biology. arXiv. http://arxiv.org/abs/2309.08478
  • Al Olaimat, M., Martinez, J., Saeed, F., Bozdag, S., Initiative, A.D. (2023). PPAD: a deep learning architecture to predict progression of Alzheimer's disease. Other. 39 (39 Suppl 1) i149--i157.
  • Kesimoglu, Z.N., Bozdag, S. (2023). SUPREME: multiomics data integration using graph convolutional networks. Other. 5 (2) lqad063.
  • Madugula, S.S., Pandey, S., Amalapurapu, S., Bozdag, S. (2023). NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool. ACS Omega. 8 (23) 20379--20388. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10268018/
  • Kesimoglu, Z.N., Bozdag, S. (2023). GRAF: Graph Attention-aware Fusion Networks. arXiv. http://arxiv.org/abs/2303.16781
  • Bose, B., Bozdag, S. (2022). Finding the best cell lines across pan-cancer to use in pre-clinical research as a proxy for patient tumor samples considering immune cells, multi-omics, and cancer pathways. bioRxiv. https://www.biorxiv.org/content/10.1101/2022.12.18.520831v1
  • Bose, B., Moravec, M., Bozdag, S. (2022). Computing microRNA-gene interaction networks in pan-cancer using miRDriver. Scientific Reports. 12 (1) 3717. https://www.nature.com/articles/s41598-022-07628-z
  • Kleven, A.D., Middleton, A.H., Kesimoglu, Z.N., Slagel, I.C., Creager, A.E., Hanson, R., Bozdag, S., Edelstein, A.I. (2021). Do In-Hospital Rothman Index Scores Predict Postdischarge Adverse Events and Discharge Location After Total Knee Arthroplasty?. Other. https://api.elsevier.com/content/abstract/scopus_id/85122795806
  • Creager, A.E., Kleven, A.D., Kesimoglu, Z.N., Middleton, A.H., Holub, M.N., Bozdag, S., Edelstein, A.I. (2021). The Impact of Pre-Operative Healthcare Utilization on Complications, Readmissions, and Post-Operative Healthcare Utilization Following Total Joint Arthroplasty.. Other.
  • Dursun, C., Kwitek, A., Bozdag, S. (2021). PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. Other. IEEE.
  • Kesimoglu, Z.N., Bozdag, S. (2021). Crinet: A computational tool to infer genomewide competing endogenous RNA (ceRNA) interactions. PLOS One. 16 (5 May) https://api.elsevier.com/content/abstract/scopus_id/85105825465
  • Milali, M.P., Kiware, S.S., Govella, N.J., Okumu, F., Bansal, N., Bozdag, S., Charlwood, J.D., Maia, M.F., Ogoma, S.B., Dowell, F.E., Corliss, G.F., Sikulu-Lord, M.T., Povinelli, R.J. (2020). An autoencoder and artificial neural network-based method to estimate parity status of wild mosquitoes from near-infrared spectra. PLOS One. 15 (6) e0234557.
  • Stamm, K., Tomita-Mitchell, A., Bozdag, S. (2019). GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. BMC Bioinformatics. 20 (1) 115. https://doi.org/10.1186/s12859-019-2697-5
  • Jain, N., Ahamed, S.I., Bozdag, S., Dolan, B.K., McVey, A.J., Willar, K.S., Pleiss, S.S., Murphy, C.C., Casnar, C.L., Potts, S., Cibich, D., Nelsen-Freund, K., Fernandez, D., Hernandez, I., Hecke, A.V. (2019). Have It, Know It, but Don’t Show It: Examining Physiological Arousal, Anxiety, and Facial Expressions over the Course of a Social Skills Intervention for Autistic Adolescents. Other. 582676. https://www.biorxiv.org/content/10.1101/582676v2
  • Do, D., Bozdag, S. (2018). Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PLOS Computational Biology. 14 (7) e1006318.
  • Muñoz-Amatriaín, M., Mirebrahim, H., Xu, P., Wanamaker, S.I., Luo, M., Alhakami, H., Alpert, M., Atokple, I., Batieno, B.J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J.D., Farmer, A., Fatokun, C., Gu, Y.Q., Guo, Y.N., Huynh, B.L., Jackson, S.A., Kusi, F., Lawley, C.T., Lucas, M.R., Ma, Y., Timko, M.P., Wu, J., You, F., Barkley, N.A., Roberts, P.A., Lonardi, S., Close, T.J. (2017). Genome resources for climate-resilient cowpea, an essential crop for food security.. Other. 89 (5) 1042--1054.
  • Baur, B., Bozdag, S. (2017). ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. Other. 109 (3-4) 233--240.
  • Ready, D., Yagiz, K., Amin, P., Yildiz, Y., Funari, V., Bozdag, S., Cinar, B. (2017). Mapping the STK4/Hippo signaling network in prostate cancer cell. PLOS One. 12 (9) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589252/
  • Baur, B., Bozdag, S. (2016). A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data. PLOS One. 11 (2) e0148977.
  • Pradeep, P., Povinelli, R.J., Merrill, S.J., Bozdag, S., Sem, D.S. (2015). Novel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction. Molecular Informatics. 34 (4) 236--245.
  • Muñoz-Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J.T., Moscou, M.J., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G.J., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bhat, P.R., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H.N., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., \textbackslashu Simková, Hana, Doleel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P.M., Lemaux, P., Mammadov, J., Close, T.J. (2015). Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Other. n/a--n/a.
  • LaDisa, J.F., Bozdag, S., Olson, J., Ramchandran, R., Kersten, J.R., Eddinger, T.J. (2015). Gene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention?. PLOS One. 10 (7) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514739/
  • Baur, B., Bozdag, S. (2015). A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data. Other. 22 (4) 289--299.
  • Bozdag, S., Li, A., Baysan, M., Fine, H.A. (2014). Master regulators, regulatory networks, and pathways of glioblastoma subtypes.. Other. 13 (Suppl 3) 33--44.
  • Baysan, M., Woolard, K., Bozdag, S., Riddick, G., Kotliarova, S., Cam, M.C., Belova, G.I., Ahn, S., Zhang, W., Song, H., Walling, J., Stevenson, H., Meltzer, P., Fine, H.A. (2014). Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells. PLOS One. 9 (4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984100/
  • Bozdag, S., Close, T.J., Lonardi, S. (2013). A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map.. Other.
  • Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Bhat, P.R., Wu, Y., Ciardo, G., Alsaihati, B., Ma, Y., Wanamaker, S., Resnik, J., Bozdag, S., Luo, M.C., Close, T.J. (2013). Combinatorial pooling enables selective sequencing of the barley gene space.. Other. 9 (4) e1003010.
  • Sahu, S.N., Lewis, J., Patel, I., Bozdag, S., Lee, J.H., Sprando, R., Cinar, H.N. (2013). Genomic analysis of stress response against arsenic in Caenorhabditis elegans.. PLOS One. 8 (7) e66431.
  • Bozdag, S., Li, A., Riddick, G., Kotliarov, Y., Baysan, M., Iwamoto, F.M., Cam, M.C., Kotliarova, S., Fine, H.A. (2013). Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels. PLOS One. 8 (4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639162/
  • Wuchty, S., Vazquez, A., Bozdag, S. (2013). Genome-wide associations of signaling pathways in glioblastoma multiforme. Other. 6 11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616958/
  • Baysan, M., Bozdag, S., Cam, M.C., Kotliarova, S., Ahn, S., Walling, J., Killian, J.K., Stevenson, H., Meltzer, P., Fine, H.A. (2012). G-cimp status prediction of glioblastoma samples using mRNA expression data.. PLOS One. 7 (11) e47839.
  • Sahu, S.N., Lewis, J., Patel, I., Bozdag, S., Lee, J.H., LeClerc, J.E., Cinar, H.N. (2012). Genomic analysis of immune response against Vibrio cholerae hemolysin in Caenorhabditis elegans.. PLOS One. 7 (5) e38200.
  • Wuchty, S., Arjona, D., Bozdag, S., Bauer, P.O. (2012). Involvement of microRNA families in cancer.. Other. 40 (17) 8219--26.
  • Bozdag, S., Li, A., Wuchty, S., Fine, H.A. (2010). FastMEDUSA: a parallelized tool to infer gene regulatory networks.. Other. 26 (14) 1792--3.
  • Li, A., Bozdag, S., Kotliarov, Y., Fine, H.A. (2010). GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes.. Other. 10 38.
  • Kotliarov, Y., Bozdag, S., Cheng, H., Wuchty, S., Zenklusen, J., Fine, H.A. (2010). CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. Other. 3 11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872651/
  • Bozdag, S., Close, T.J., Lonardi, S. (2009). A compartmentalized approach to the assembly of physical maps.. BMC Bioinformatics. 10 217.
  • Close, T.J., Bhat, P.R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J.T., Wanamaker, S., Bozdag, S., Roose, M.L., Moscou, M.J., Chao, S., Varshney, R.K., Szucs, P., Sato, K., Hayes, P.M., Matthews, D.E., Kleinhofs, A., Muehlbauer, G.J., DeYoung, J., Marshall, D.F., Madishetty, K., Fenton, R.D., Condamine, P., Graner, A., Waugh, R. (2009). Development and implementation of high-throughput SNP genotyping in barley.. BMC Genomics. 10 582.
  • Bozdag, S., Close, T., Lonardi, S. (2008). Computing the minimal tiling path from a physical map by integer linear programming. Other. 148--161.

Presentations Given

    Invited Talk

  • Bozdag, S. (Author & Presenter), 9th Turkish Medical World Congress and Aziz Sancar Science, Service and Encouragement Awards Ceremony, Declined the invitation due to a schedule conflict., Ministry of Health of Turkey, Istanbul, Turkey, Turkey. (2023).
  • Bozdag, S. (Author & Presenter), Festival of Genomics, Predicting Drug Side Effects via Multi-Modal Graph Representation Learning, Front Line Genomics Limited, Boston, United States of America. (2023).
  • Bozdag, S. (Author & Presenter), Multi-Omics Workshop, Integrating multi-omics datasets using network biology, Front Line Genomics Limited, Boston, United States of America. (2023).
  • Bozdag, S. (Author & Presenter), Bioinfocongress IV, Integrating Multi-omics datasets using graph representation learning, Bioinforange, Virtual, Turkey. (2023).
  • Bozdag, S. (Author & Presenter), Leaders & Innovators Seminar Series, Harnessing machine learning and graph representation learning to integrate multimodal datasets for predicting disease subtypes, Department of Electrical and Computer Engineering (ECE), TAMU, Texas A&M University, United States of America. (2023).
  • Dursun, C. (Author), Smith, J.R. (Author), Haymen, G.T. (Author), Kwitek, A.E. (Author), Bozdag, S. (Author & Presenter), Tri-Omics Summit, Disease-associated gene prioritization using multiplex heterogeneous networks, Front Line Genomics Limited, Boston, United States of America. (2022).
  • Kesimoglu, Z. (Author), Bozdag, S. (Author & Presenter), MLN-DIVE (MultiLayer Network Community Infrastructure for Data, Interaction, Visualization, and Software) Seminar Series, SUPREME: A Cancer subtype Prediction Methodology Integrating Multiomics Data using Graph Convolutional Neural Network, University of Texas Arlington, Virtual, United States of America. (2022).

    • Oral Presentation

  • Kesimoglu, Z. (Author), Bozdag, S. (Author & Presenter), CSE Seminar Series, Machine learning on Heterogeneous Graphs, Department of CSE, UNT, UNT, United States of America. (2023).
  • Al Olaimat, M. (Author), Martinez, J. (Author), Saeed, F. (Author), Bozdag, S. (Author & Presenter), ISMB Conference, PPAD: a deep learning architecture to predict progression of Alzheimer’s disease, ISCB, Lyon, France, United States of America. (2023).
  • Rifat, J. (Author & Presenter), Bozdag, S. (Author), BioDiscovery Institute Seminar Series, Clustering Single Cells with Transformer Autoencoder, BioDiscovery Institute, Denton, TX, United States of America. (2022).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), BioDiscovery Institute Seminar Series, SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network, BioDiscovery Institute, Denton, TX, United States of America. (2022).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), ISMB Conference, SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network, ISCB, Madison, WI, United States of America. (2022).
  • Vashishath, Y. (Author & Presenter), Bozdag, S. (Author), High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD), GWAS Analysis to Compute Genetic Markers of Progression toAlzheimer's Disease, The 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Virtual, United States of America. (2021).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD), SUPREME: A Cancer Subtype Prediction Methodology IntegratingMultiple Biological Datatypes Using Graph Convolutional Neural Networks, The 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Virtual, United States of America. (2021).
  • Do, D. (Author & Presenter), Bozdag, S. (Author), High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD), CanMod: A computational model to identify co-regulatory modules in cancer, The 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Virtual, United States of America. (2020).

    • Panel Presentation

  • Bozdag, S. (Author & Presenter), International Workshop on Computational Network Biology: Modeling, Analysis, and Control, Declined due to a schedule conflict., Houston, United States of America. (2023).
  • Bozdag, S. (Panelist), NSF-NIH Joint Workshop on Emerging AI in Biology, Emerging AI in Biology, NSF/NIH, Virtual, United States of America. (2023 - 2023).
  • Bozdag, S. (Author & Presenter), Workshop on Future Directions in Network Biology, Machine learning on networks, NSF, University of Notre Dame, United States of America. (2022).

    • Poster

  • Ozdemir, C. (Author & Presenter), Rahman, M. (Author), Rebello, E. (Author), Vashishath, Y. (Author), Bozdag, S. (Author), UNT Research Day, Disease Risk Prediction with Graph Representation Learning, UNT, Denton, TX, United States of America. (2023).
  • Vashishath, Y. (Author & Presenter), Bozdag, S. (Author), UNT Research Day, Integrating Multi-Omics Data for Predicting Mild Cognitive Impairment Conversion to Alzheimer’s Disease, UNT, Denton, TX, United States of America. (2023).
  • Al Olaimat, M. (Author & Presenter), Bozdag, S. (Author), UNT Research Day, PPAD: a deep learning architecture to predict progression of Alzheimer’s disease, UNT, Denton, TX, United States of America. (2023).
  • Pandey, S. (Author & Presenter), Bozdag, S. (Author), UNT CSE Research Showcase, Inference of dynamic gene regulatory network post stimulation of ABA hormone in Arabidopsis plant, UNT, Denton, TX, United States of America. (2023).
  • Vashishath, Y. (Author & Presenter), Bozdag, S. (Author), UNT CSE Research Showcase, Integrating Multi-Omics Data for Predicting Mild Cognitive Impairment Conversion to Alzheimer’s Disease, UNT, Denton, TX, United States of America. (2023).
  • Rifat, J. (Author & Presenter), Bozdag, S. (Author), UNT CSE Research Showcase, Prediction of Single Cell types using Transformer encoder, UNT, Denton, TX, United States of America. (2023).
  • Al Olaimat, M. (Author & Presenter), Bozdag, S. (Author), ISMB Conference, Predicting Alzheimer’s disease progression using a Bidirectional Gated Recurrent Unit-based architecture, ISCB, Madison, WI, United States of America. (2022).
  • Vashishath, Y. (Author & Presenter), Bozdag, S. (Author), UNT Research Showcase, Predicting Mild Cognitive Impairment conversion to Alzheimer's Disease based on genetic markers, College of Engineering, UNT, Denton, TX, United States of America. (2022).
  • Al Olaimat, M. (Author & Presenter), Bozdag, S. (Author), UNT Research Showcase, Prediction of Alzheimer’s Disease Progression Based on Recurrent Neural Networks, College of Engineering, UNT, Denton, TX, United States of America. (2022).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), UNT Research Showcase, SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network, College of Engineering, UNT, Denton, TX, United States of America. (2022).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), UNT Research Showcase, SUPREME: A cancer subtype prediction methodology using Graph Convolutional Networks, College of Engineering, UNT, Denton, TX, United States of America. (2022).
  • Vashishath, Y. (Author & Presenter), Bozdag, S. (Author), BDI Retreat, Predicting Mild Cognitive Impairment conversion to Alzheimer's Disease based on genetic markers, BioDiscovery Institute, Denton, TX, United States of America. (2022).
  • Al Olaimat, M. (Author & Presenter), Bozdag, S. (Author), BDI Retreat, Prediction of Alzheimer’s Disease Progression Based on Recurrent Neural Networks, BioDiscovery Institute, Denton, TX, United States of America. (2022).
  • Madugula, S. (Author & Presenter), Amalapurapu, S. (Author), Bozdag, S. (Author), BDI Retreat, Prediction of Novel Drug-Target Interactions For Drug Repurposing Using Graph-Based Machine Learning, BioDiscovery Institute, Denton, TX, United States of America. (2022).
  • Kesimoglu, Z. (Author & Presenter), Bozdag, S. (Author), BDI Retreat, SUPREME: A cancer subtype prediction methodology using Graph Convolutional Networks, BioDiscovery Institute, Denton, TX, United States of America. (2022).

Contracts, Grants, Sponsored Research

    Grant - Research

  • Bozdag, S. (Principal), "Integrating multiple biomedical data modalities to predict disease diagnosis," sponsored by NIH, Federal, $111375 Funded. (2022 - 2024).
  • Bozdag, S., "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," sponsored by National Institutes of Health, Federal, $1191286 Funded. (2020 - 2024).
  • Bozdag, S. (Principal), "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," sponsored by NIH, Federal, $320473 Funded. (2023 - 2024).
  • Bozdag, S. (Principal), "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," sponsored by NIH, Federal, $8825 Funded. (2023 - 2024).
  • Antunes, M.S. (Principal), Bozdag, S. (Co-Principal), "Identification of early-response small-RNA signatures of biotic stress in plants," sponsored by UNT CENG, COS and VPRI, University of North Texas, $10000 Funded. (2023 - 2024).
  • Bozdag, S. (Principal), "Travel: NSF Student Travel Grant for 2023 Great Lakes Bioinformatics Conference (GLBIO)," sponsored by NSF, Federal, $10000 Funded. (2023 - 2024).
  • Bozdag, S. (Principal), "TACC Computer Server Allocation (Project Name: "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response")," University of North Texas, $10000 Funded. (2022 - 2023).
  • Bozdag, S., "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," sponsored by National Institutes of Health, Federal, Funded. (2020 - 2024).
  • Bozdag, S. (Principal), "Integrating multi-omcs datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," sponsored by National Institutes of Health, FED, Funded. (2020 - 2022).

Service

University Service

  • Committee Member, Faculty Council. (September 2023 - Present).
  • Committee Member, Education Committee, BioDiscovery Institute. (August 2022 - Present).
  • Committee Member, Executive Committee, BioDiscovery Institute. (August 2022 - Present).
  • Faculty Mentor, Faculty Mentor. (2022 - Present).
  • Other (Course Coordinator), Course Coordinator. (October 2021 - Present).
  • Committee Member, PhD in Math Program Reform Ad-Hoc Committee. (October 2020 - Present).
  • Committee Member, Promotion and Tenure Committee. (September 2020 - Present).
  • Committee Member, Qualifying Exam Committee (Applied Math). (September 2023 - May 2024).
  • Committee Member, Search Committee for BioDiscovery Institute Director. (September 2023 - May 2024).
  • Committee Member, Computational Informatics Core Facility Research Scientist Search. (August 2022 - 2023).
  • Attendee, Meeting, BioDiscovery Institute Retreat. (November 2023 - November 2023).
  • Committee Chair, Ad-hoc Committee for CS + Math program. (August 2022 - May 2023).
  • Attendee, Meeting, BDI PI Meeting. (August 2022 - May 2023).
  • Attendee, Meeting, Department Meeting. (August 2022 - May 2023).
  • Attendee, Meeting, Department Retreat. (August 2022 - August 2022).
  • Attendee, Meeting, BDI Advisory Board Meeting. (May 2022 - May 2022).
  • Committee Member, Biodiscovery Institute Ad hoc grad student milestone monitoring attainment working group. (February 2022 - May 2022).
  • Committee Chair, Computational Informatics Core Facility Director Search Committee. (November 2021 - May 2022).
  • Committee Member, Department Chair Search Committee. (September 2021 - May 2022).
  • Committee Chair, Personal Affairs Committee. (September 2021 - May 2022).
  • Attendee, Meeting, BDI PI Meeting. (August 2021 - May 2022).
  • Attendee, Meeting, Department Meeting. (August 2021 - May 2022).
  • Attendee, Meeting, Faculty Search. (August 2021 - May 2022).
  • Committee Member, Executive Committee. (September 2020 - May 2022).
  • Attendee, Meeting, BioDiscovery Institute Retreat. (February 2022 - February 2022).
  • Attendee, Meeting, Department Retreat. (August 2021 - August 2021).
  • Committee Member, Faculty Search Committee. (September 2020 - May 2021).
  • Attendee, Meeting, BDI PI Meeting. (August 2020 - May 2021).
  • Attendee, Meeting, Department Meeting. (August 2020 - May 2021).

Professional Service

  • Other (Steering Committee Member), Great Lakes Bioinformatics Conference Organization Committee. (September 2023 - Present).
  • Editorial Review Board Member, Scientific Reports. (May 2023 - Present).
  • Editorial Review Board Member, Frontiers in Bioinformatics. (October 2020 - Present).
  • Editorial Review Board Member, Plos ONE. (December 2018 - Present).
  • Editorial Review Board Member, Cancer Informatics. (June 2016 - Present).
  • Other (Mentor), 2023 UR2PhD Mentoring Program. (September 2023 - May 2024).
  • Reviewer, Conference Paper, 32nd Conference on Intelligent Systems on Molecular Biology. (January 2024 - April 2024).
  • Reviewer, Grant Proposal, NSF. (December 2023 - January 2024).
  • Reviewer, Grant Proposal, NIH Director's New Innovator Award Program. (September 2023 - January 2024).
  • Reviewer, Grant Proposal, NSF. (September 2023 - January 2024).
  • Other (Coach), 2023 CSGrad4US Mentoring Program. (July 2023 - January 2024).
  • Other (Guest Editor), Plos Computational Biology. (January 2023 - January 2024).
  • Other (PC Member), SIAM International Conference on Data Mining (SDM 2024). (September 2023 - December 2023).
  • Reviewer, Conference Paper, 15th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. (September 2023 - November 2023).
  • Reviewer, Conference Paper, IEEE BIBM. (August 2023 - October 2023).
  • Other (PC Member), Learning on Graphs 2023. (August 2023 - October 2023).
  • Other (Proceedings Chair), 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). (May 2023 - September 2023).
  • Reviewer, Conference Paper, BIOKDD 2022. (May 2023 - June 2023).
  • Reviewer, Journal Article, Bioinformatics Advances. (May 2023 - May 2023).
  • Reviewer, Conference Paper, 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. (February 2023 - May 2023).
  • Other (Program Chair), 23rd IEEE International Workshop on High Performance Computational Biology. (January 2023 - May 2023).
  • Workshop Organizer, 22nd IEEE International Workshop on High Performance Computational Biology. (September 2022 - May 2023).
  • Other (Travel Fellowship Chair), Great Lakes Bioinformatics Conference Organization Committee. (September 2022 - May 2023).
  • Other (External Examiner for PhD dissertation), University of Windsor. (April 2023 - April 2023).
  • Reviewer, Conference Paper, 31st Conference on Intelligent Systems on Molecular Biology. (January 2023 - April 2023).
  • Reviewer, Conference Paper, Great Lakes Bioinformatics Conference. (February 2023 - March 2023).
  • Other (Coach), 2022 CSGrad4US Mentoring Program. (July 2022 - January 2023).
  • Other (Guest Editor), Plos Computational Biology. (January 2022 - January 2023).
  • Workshop Organizer, 4th International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data. (May 2022 - December 2022).
  • Reviewer, Conference Paper, 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. (September 2022 - October 2022).
  • Reviewer, Conference Paper, IEEE BIBM. (August 2022 - October 2022).
  • Mentor, CAHSI (Computing Alliance of Hispanic-Serving Institutions) Local REU program. (June 2022 - August 2022).
  • Reviewer, Conference Paper, BIOKDD 2022. (May 2022 - June 2022).
  • Reviewer, Conference Paper, 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. (February 2022 - May 2022).
  • Reviewer, Conference Paper, 30th Conference on Intelligent Systems on Molecular Biology. (January 2022 - April 2022).
  • Reviewer, Journal Article (Guest Editor), IEEE TCBB (Transactions on Computational Biology and Bioinformatics). (February 2022 - February 2022).
  • Other (Guest Editor), Plos Computational Biology. (January 2021 - January 2022).
  • Workshop Organizer, 3rd International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data. (May 2021 - September 2021).
  • Reviewer, Grant Proposal, National Institutes of Health. (May 2021 - July 2021).
  • Session Chair, Great Lakes Bioinformatics Conference. (May 2021).
  • Other (Travel Fellowship Chair), Great Lakes Bioinformatics Conference Organization Committee. (November 2020 - May 2021).
  • Reviewer, Conference Paper, Great Lakes Bioinformatics Conference. (February 2021 - March 2021).
  • Session Chair, International Conference on Bioinformatics and Biomedicine (BIBM). (December 2020).
  • Reviewer, Conference Paper, 13th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. (April 2020 - October 2020).
  • Workshop Organizer, 2nd International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data. (May 2020 - September 2020).
  • Reviewer, Grant Proposal, NSF. (December 2019 - January 2020).