2024
Ozdemir C, Olaimat MA, Vashishath Y, Bozdag S, & Alzheimer’s Disease Neuroimaging Initiative. IGCN: Integrative Graph Convolutional Networks for Multi-modal Data. arXiv; 2024 https://doi.org/10.48550/arXiv.2401.17612
Olaimat MA, Bozdag S. & Alzheimer’s Disease Neuroimaging Initiative TA-RNN: an Attention-based Time-aware Recurrent Neural Network Architecture for Electronic Health Records. arXiv; 2024 https://doi.org/10.48550/arXiv.2401.14694
2023
Akhavan Aghdam, M., Bozdag, S., Saeed, F., & Alzheimer’s Disease Neuroimaging Initiative. (2023). PVTAD: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied To White Matter Of T1-Weighted Structural MRI Data. bioRxiv, 2023-11.
Zitnik M, Li MM, Wells A, Glass K, Gysi DM, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline S, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Current and future directions in network biology. arXiv; 2023. http://arxiv.org/abs/2309.08478.
Z. N. Kesimoglu and S. Bozdag, “SUPREME: multiomics data integration using graph convolutional networks,” NAR Genomics and Bioinformatics, vol. 5, no. 2, p. lqad063, Mar. 2023, doi: 10.1093/nargab/lqad063.
S. S. Madugula, S. Pandey, S. Amalapurapu, and S. Bozdag, “NRPreTo: A Machine Learning-Based Nuclear Receptor and Subfamily Prediction Tool,” ACS Omega, May 2023, https://doi.org/10.1021/acsomega.3c00286.
Z. N. Kesimoglu & S. Bozdag (2023). GRAF: Graph Attention-aware Fusion Networks. arXiv preprint arXiv:2303.16781. https://doi.org/10.48550/arXiv.2303.16781
M. Al Olaimat, J. Martinez, F. Saeed, S. Bozdag, and Alzheimer’s Disease Neuroimaging Initiative, “PPAD: a deep learning architecture to predict progression of Alzheimer’s disease,” (ISMB/ECCB 2023) Bioinformatics, vol. 39, no. Supplement_1, pp. i149–i157, Jun. 2023, doi: 10.1093/bioinformatics/btad249.
2022
T. Yang, M. A. Al-Duailij, S. Bozdag and F. Saeed, Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks, 2022 IEEE International Conference on Big Data (Big Data), Osaka, Japan, 2022, pp. 3131-3138, https://doi.org/10.1109/BigData55660.2022.10021070
Bose B, Bozdag S. 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; 2022 https://doi.org/10.1101/2022.12.18.520831
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 ONE, 15(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 . 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. 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 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., … 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 Biology, 14(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 ONE, 12(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. Genomics, 109(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 J, 89(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 One, 11(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 Biology, 22(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 ONE, 10(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, 84.1: 216-227.. 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 Informatics, 34(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 ONE, 9(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 Inform, 13(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 Genomics, 6, 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 ONE, 8(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 Bioinform. https://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 Biol, 9(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 One, 8(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 One, 7(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 One, 7(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 Res, 40(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 Genomics, 3, 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. Bioinformatics, 26(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 Mak, 10, 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 Bioinformatics, 10, 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 Genomics, 10, 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