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
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.
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.
