Publications (Peer-reviewed & Preprint)

2022

Madugula, S. S., Pandey, S., Amalapurapu, S., & Bozdag, S. (2022). NRPreTo: A Machine Learning Based Nuclear Receptor and Subfamily Prediction Tool. bioRxiv.

Kesimoglu ZN, Bozdag S. SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network. bioRxiv; 2022 

Kleven AD, Middleton AH, Kesimoglu ZN, Slagel IC, Creager AE, Hanson R, Bozdag S, Edelstein AI (2022). Do In-Hospital Rothman Index Scores Predict Postdischarge Adverse Events and Discharge Location After Total Knee Arthroplasty?. The Journal of Arthroplasty, 37(4), 668-673. https://doi.org/10.1016/j.arth.2021.12.022

Bose B, Moravec M, Bozdag S. Computing microRNA-gene interaction networks in pan-cancer using miRDriver. Sci Rep. Nature Publishing Group; 2022 Mar 8;12(1):3717. https://doi.org/10.1038/s41598-022-07628-z

Creager, A. E., Kleven, A. D., Kesimoglu, Z. N., Middleton, A. H., Holub, M. N., Bozdag, S., & Edelstein, A. I. (2022). The Impact of Pre-Operative Healthcare Utilization on Complications, Readmissions, and Post-Operative Healthcare Utilization Following Total Joint Arthroplasty. The Journal of Arthroplasty, 37(3), 414-418. https://doi.org/10.1016/j.arth.2021.11.018

2021

Dursun C, Kwitek A, Bozdag S. PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul 20;PP. PMID: 34283720 https://doi.org/10.1109/TCBB.2021.3098278

Kesimoglu ZN, Bozdag S. Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. PLoS One. 2021;16(5):e0251399. PMCID: PMC8118266 https://doi.org/10.1371/journal.pone.0251399

2020

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 ONE15(6), e0234557. https://doi.org/10.1371/journal.pone.0234557

Dursun C, Smith JR, Hayman GT, Kwitek AE, Bozdag S. NECo: A node embedding algorithm for multiplex heterogeneous networks. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2020. p. 146–149. https://doi.org/10.1109/BIBM49941.2020.9313595

Do D, Bozdag S. 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 [Internet]. New York, NY, USA: Association for Computing Machinery; 2020. p. 1–10. https://doi.org/10.1145/3388440.3415586

Bose B, Bozdag S. 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 [Internet]. New York, NY, USA: Association for Computing Machinery; 2020. p. 1–10.  https://doi.org/10.1145/3388440.3412456

2019

Stamm, K., Tomita-Mitchell, A., & Bozdag, S. (2019). GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. BMC Bioinformatics20(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., … 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. https://doi.org/10.1101/582676

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. https://doi.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. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (pp. 279–288). New York, NY, USA: ACM. https://doi.org/10.1145/3307339.3342155

2018

Do, D., & Bozdag, S. (2018). Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PLoS Computational Biology14(7), e1006318. https://doi.org/10.1371/journal.pcbi.1006318

2017

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 ONE12(9). https://doi.org/10.1371/journal.pone.0184590

Baur, B., & Bozdag, S. (2017). ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. Genomics109(3–4), 233–240. https://doi.org/10.1016/j.ygeno.2017.04.004

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 J89(5), 1042–1054. https://doi.org/10.1111/tpj.13404

2016

Baur, B., & Bozdag, S. (2016). A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data. PloS One11(2), e0148977. https://doi.org/10.1371/journal.pone.0148977

2015

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 Biology22(4), 289–299. https://doi.org/10.1089/cmb.2014.0296

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 ONE10(7). https://doi.org/10.1371/journal.pone.0133356

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. https://doi.org/10.1111/tpj.12959

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 Informatics34(4), 236–245. https://doi.org/10.1002/minf.201400168

2014

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 ONE9(4). https://doi.org/10.1371/journal.pone.0094045

Bozdag, S., Li, A., Baysan, M., & Fine, H. A. (2014). Master regulators, regulatory networks, and pathways of glioblastoma subtypes. Cancer Inform13(Suppl 3), 33–44. https://doi.org/10.4137/CIN.S14027

2013

Wuchty, S., Vazquez, A., & Bozdag, S. (2013). Genome-wide associations of signaling pathways in glioblastoma multiforme. BMC Medical Genomics6, 11. https://doi.org/10.1186/1755-8794-6-11

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 ONE8(4). https://doi.org/10.1371/journal.pone.0062982

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 Bioinformhttps://doi.org/B886D413-EA51-4D69-9095-CC2D5FEF04AB

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 Biol9(4), e1003010. https://doi.org/10.1371/journal.pcbi.1003010

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 One8(7), e66431. https://doi.org/10.1371/journal.pone.0066431

2012

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 One7(11), e47839. https://doi.org/10.1371/journal.pone.0047839

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 One7(5), e38200. https://doi.org/10.1371/journal.pone.0038200

Wuchty, S., Arjona, D., Bozdag, S., & Bauer, P. O. (2012). Involvement of microRNA families in cancer. Nucleic Acids Res40(17), 8219–8226. https://doi.org/10.1093/nar/gks627

2010

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 Genomics3, 11. https://doi.org/10.1186/1755-8794-3-11

Bozdag, S., Li, A., Wuchty, S., & Fine, H. A. (2010). FastMEDUSA: a parallelized tool to infer gene regulatory networks. Bioinformatics26(14), 1792–1793. https://doi.org/10.1093/bioinformatics/btq275

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 Mak10, 38. https://doi.org/10.1186/1472-6947-10-38

2009

Bozdag, S., Close, T. J., & Lonardi, S. (2009). A compartmentalized approach to the assembly of physical maps. BMC Bioinformatics10, 217. https://doi.org/10.1186/1471-2105-10-217

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 Genomics10, 582. https://doi.org/10.1186/1471-2164-10-582

2008

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.

2007

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). https://doi.org/10.1109/BIBE.2007.4375568