Serdar Bozdag
University of North Texas
Computer Science and Engineering
Email:

Professional Memberships

Association for Computing Machinery. (June 2019 – Present).

ACM SIGBioinformatics. (February 2013 – Present).

The International Society for Computational Biology. (February 2013 – Present).

Teaching

Teaching Experience

University of North Texas
BIOL 4810, BioComputing, 2 courses.
BIOL 5810, BioComputing, 2 courses.
BIOL 6810, Advanced Topics in Computational Life Science, 1 course.
CSCE 4110, Algorithms, 2 courses.
CSCE 4810, BioComputing, 4 courses.
CSCE 5810, BioComputing, 3 courses.
CSCE 6810, Advanced Topics in Computational Life Science, 1 course.
CSCE 6940, Individual Research, 3 courses.
CSCE 6950, Doctoral Dissertation, 1 course.
MATH 4810, Biocomputing, 2 courses.

Directed Student Learning

Postdoctoral Research Supervision, Computer Science and Engineering. (February 2021 – Present).

Supervised Research, Computer Science and Engineering. (January 2021 – Present).

Dissertation Committee Chair, Computer Science and Engineering. (September 2020 – Present).

Dissertation Committee Chair, Computer Science and Engineering. (September 2020 – Present).

Dissertation Committee Chair, Computer Science and Engineering. (September 2020 – Present).

Dissertation Committee Chair, Computer Science and Engineering. (September 2020 – Present).

Research

Published Intellectual Contributions

Conference Proceeding
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
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.
Kesimoglu, Z. N., Bozdag, S. (2020). Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. Other. 2020.06.18.160408. https://www.biorxiv.org/content/10.1101/2020.06.18.160408v2
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.

Contracts, Grants and Sponsored Research

Grant - Research
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. (September 1, 2020June 30, 2024).

Service

University Service

Committee Member, PhD in Math Program Reform Ad-Hoc Committee. (October 2020 – Present).

Committee Member, Executive Committee. (September 2020 – Present).

Committee Member, Faculty Search Committee. (September 2020May 2021).

Professional Service

Session Chair, International Conference on Bioinformatics and Biomedicine (BIBM). (December 2020 – 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, Great Lakes Bioinformatics Conference Organization Committee. (November 2020May 2021).

Reviewer, Conference Paper, Great Lakes Bioinformatics Conference. (February 2021March 2021).

Reviewer, Conference Paper, 13th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. (April 2020October 2020).

Workshop Organizer, 2nd International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data. (May 2020September 2020).

Reviewer, Grant Proposal, NSF. (December 2019January 2020).