Publications (Peer-reviewed & Preprint)

Kesimoglu, Z. N., & Bozdag, S. (2020). Inferring competing endogenous RNA (ceRNA) interactions in cancer. BioRxiv, 2020.06.18.160408.
Milali, M. P., Kiware, S. S., Govella, N. J., Okumu, F., Bansal, N., Bozdag, S., … 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.
Dursun, C., Smith, J. R., Hayman, G. T., & Bozdag, S. (2020). Gene Embeddings of Complex network (GECo) and hypertension disease gene classification. BioRxiv, 2020.06.15.149559.
Bose, B., & Bozdag, S. (2020). CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer. BioRxiv, 2020.06.13.149666.
Jain, N., Ahamed, S. I., Bozdag, S., Dolan, B. K., McVey, A. J., Willar, K. S., … Hecke, A. V. 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. BioRxiv, 582676.
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.
Dursun, C., Shimoyama, N., Shimoyama, M., Schläppi, M., & Bozdag, S. (2019). PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (pp. 279–288). New York, NY, USA: ACM.
Bose, B., & Bozdag, S. (2019). miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (pp. 366–375). New York, NY, USA: ACM.
Do, D., & Bozdag, S. (2018). Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PLoS Computational Biology, 14(7), e1006318.
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).
Baur, B., & Bozdag, S. (2017). ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. Genomics, 109(3–4), 233–240.
Muñoz-Amatriaín, M., Mirebrahim, H., Xu, P., Wanamaker, S. I., Luo, M., Alhakami, H., … Close, T. J. (2017). Genome resources for climate-resilient cowpea, an essential crop for food security. Plant J, 89(5), 1042–1054.
Baur, B., & Bozdag, S. (2016). A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data. PloS One, 11(2), e0148977.
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).
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. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 22(4), 289–299.
Muñoz-Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., … Close, T. J. (2015). Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal, n/a-n/a.
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.
Baysan, M., Woolard, K., Bozdag, S., Riddick, G., Kotliarova, S., Cam, M. C., … 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).
Bozdag, S., Li, A., Baysan, M., & Fine, H. A. (2014). Master regulators, regulatory networks, and pathways of glioblastoma subtypes. Cancer Inform, 13(Suppl 3), 33–44.
Bozdag, S., Li, A., Riddick, G., Kotliarov, Y., Baysan, M., Iwamoto, F. M., … Fine, H. A. (2013). Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels. PLoS ONE, 8(4).
Wuchty, S., Vazquez, A., & Bozdag, S. (2013). Genome-wide associations of signaling pathways in glioblastoma multiforme. BMC Medical Genomics, 6, 11.
Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Bhat, P. R., … Close, T. J. (2013). Combinatorial pooling enables selective sequencing of the barley gene space. PLoS Comput Biol, 9(4), e1003010.
Bozdag, S., Close, T. J., & Lonardi, S. (2013). A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. IEEE/ACM Trans Comput Biol Bioinform.
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.
Wuchty, S., Arjona, D., Bozdag, S., & Bauer, P. O. (2012). Involvement of microRNA families in cancer. Nucleic Acids Res, 40(17), 8219–8226.
Baysan, M., Bozdag, S., Cam, M. C., Kotliarova, S., Ahn, S., Walling, J., … 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.
Kotliarov, Y., Bozdag, S., Cheng, H., Wuchty, S., Zenklusen, J.-C., & Fine, H. A. (2010). CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Medical Genomics, 3, 11.
Bozdag, S., Li, A., Wuchty, S., & Fine, H. A. (2010). FastMEDUSA: a parallelized tool to infer gene regulatory networks. Bioinformatics, 26(14), 1792–1793.
Li, A., Bozdag, S., Kotliarov, Y., & Fine, H. A. (2010). GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes. BMC Med Inform Decis Mak, 10, 38.
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., … 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. Algorithms in Bioinformatics, 148–161.
Bozdag, S., Close, T. J., & Lonardi, S. (2007). A Compartmentalized Approach to the Assembly of Physical Maps. In IEEE International Conference on Bioinformatics and Bioengineering (pp. 218–225).