2024

Ferreira SS, Pandey S, Hemminger J, Bozdag S, Antunes MS. Early changes in microRNA expression in Arabidopsis plants infected with the fungal pathogen Fusarium graminearum bioRxiv; 2024 https://www.biorxiv.org/content/10.1101/2024.05.29.596347v1

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

Al Olaimat M, Bozdag S, & Alzheimer’s Disease Neuroimaging Initiative. TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records. Bioinformatics. 2024 Jun 28; 40(Supplement_1):i169–i179. https://doi.org/10.1093/bioinformatics/btae264

M. A. Aghdam, S. Bozdag and F. Saeed, "Pvtad: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural Mri Data," 2024 IEEE International Symposium on Biomedical Imaging (ISBI), Athens, Greece, 2024, pp. 1-4, doi: 10.1109/ISBI56570.2024.10635541.

Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T M Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z Chen, Lenore Cowen, Kapil Devkota, Anthony Gitter, Sara J C Gosline, Pengfei Gu, Pietro H Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R Pico, Nataša Pržulj, Teresa M Przytycka, Benjamin J Raphael, Anna Ritz, Roded Sharan, Yang Shen, Mona Singh, Donna K Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković, Current and future directions in network biology, Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae099, https://doi.org/10.1093/bioadv/vbae099

Bose, B., Bozdag, S. Identifying cell lines across pan-cancer to be used in preclinical research as a proxy for patient tumor samples. Commun Biol 7, 1101 (2024). https://doi.org/10.1038/s42003-024-06812-3

2023

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

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