Serdar Bozdag BS,PhD
Research Experience
Computational BiologyData MiningMachine LearningModels, StatisticalStatistical DistributionsUnsupervised Machine LearningMethodologies and Techniques
AlgorithmsComputational BiologyDNA Copy Number VariationsDNA MethylationGene ExpressionGene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksMicroRNAsSequence Analysis, DNASoftwareLeadership Positions
Co-director, MS in BioinformaticsProgram Director, Undergraduate Major in BioinformaticsUndergraduate Studies Director, Dept of Computer SciencePublications (27)
GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. (Stamm K, Tomita-Mitchell A, Bozdag S) BMC Bioinformatics 2019 Mar 06;20(1):115 PMID: 30841846 PMCID: PMC6404334 SCOPUS ID: 2-s2.0-85062495607 03/08/2019 4 CitationsCancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. (Do D, Bozdag S) PLoS Comput Biol 2018 Jul;14(7):e1006318 PMID: 30011266 PMCID: PMC6072113 SCOPUS ID: 2-s2.0-85050957092 07/17/2018 18 CitationsMapping the STK4/Hippo signaling network in prostate cancer cell. (Ready D, Yagiz K, Amin P, Yildiz Y, Funari V, Bozdag S, Cinar B) PLoS One 2017;12(9):e0184590 PMID: 28880957 PMCID: PMC5589252 SCOPUS ID: 2-s2.0-85029853212 09/08/2017 19 CitationsProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. (Baur B, Bozdag S) Genomics 2017 Jul;109(3-4):233-240 PMID: 28438487 SCOPUS ID: 2-s2.0-85018352164 04/26/2017 1 CitationGenome resources for climate-resilient cowpea, an essential crop for food security. (Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ) Plant J 2017 Mar;89(5):1042-1054 PMID: 27775877 SCOPUS ID: 2-s2.0-85012879883 10/25/2016 141 CitationsA Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data. (Baur B, Bozdag S) PLoS One 2016;11(2):e0148977 PMID: 26872146 PMCID: PMC4752315 SCOPUS ID: 2-s2.0-84960510969 02/13/2016 24 CitationsSequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. (Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel 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 PM, Lemaux P, Mammadov J, Close TJ) Plant J 2015 Oct;84(1):216-27 PMID: 26252423 PMCID: PMC5014227 SCOPUS ID: 2-s2.0-84942794562 08/08/2015 27 CitationsGene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention? (LaDisa JF Jr, Bozdag S, Olson J, Ramchandran R, Kersten JR, Eddinger TJ) PLoS One 2015;10(7):e0133356 PMID: 26207811 PMCID: PMC4514739 SCOPUS ID: 2-s2.0-84941695738 07/25/2015 6 CitationsA canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data. (Baur B, Bozdag S) J Comput Biol 2015 Apr;22(4):289-99 PMID: 25844668 SCOPUS ID: 2-s2.0-84926655923 04/07/2015 18 CitationsNovel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction. (Pradeep P, Povinelli RJ, Merrill SJ, Bozdag S, Sem DS) Mol Inform 2015 Apr;34(4):236-45 PMID: 27490169 SCOPUS ID: 2-s2.0-84926429047 04/01/2015 10 CitationsCorrection to "master regulators, regulatory networks, and pathways of glioblastoma subtypes". (Bozdag S, Li A, Baysan M, Fine HA) Cancer Inform 2014;13(Suppl 3):91 PMID: 25573794 PMCID: PMC4251187 01/13/2015 Master regulators, regulatory networks, and pathways of glioblastoma subtypes. (Bozdag S, Li A, Baysan M, Fine HA) Cancer Inform 2014;13(Suppl 3):33-44 PMID: 25368508 PMCID: PMC4214595 SCOPUS ID: 2-s2.0-84907877985 11/05/2014 11 CitationsMicro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells. (Baysan M, Woolard K, Bozdag S, Riddick G, Kotliarova S, Cam MC, Belova GI, Ahn S, Zhang W, Song H, Walling J, Stevenson H, Meltzer P, Fine HA) PLoS One 2014;9(4):e94045 PMID: 24728236 PMCID: PMC3984100 SCOPUS ID: 2-s2.0-84899653917 04/15/2014 34 CitationsA graph-theoretical approach to the selection of the minimum tiling path from a physical map. (Bozdag S, Close TJ, Lonardi S) IEEE/ACM Trans Comput Biol Bioinform 2013;10(2):352-60 PMID: 23929859 SCOPUS ID: 2-s2.0-84883015012 08/10/2013 5 CitationsGenomic analysis of stress response against arsenic in Caenorhabditis elegans. (Sahu SN, Lewis J, Patel I, Bozdag S, Lee JH, Sprando R, Cinar HN) PLoS One 2013;8(7):e66431 PMID: 23894281 PMCID: PMC3722197 SCOPUS ID: 2-s2.0-84880800525 07/31/2013 28 CitationsAge-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels. (Bozdag S, Li A, Riddick G, Kotliarov Y, Baysan M, Iwamoto FM, Cam MC, Kotliarova S, Fine HA) PLoS One 2013;8(4):e62982 PMID: 23658659 PMCID: PMC3639162 SCOPUS ID: 2-s2.0-84876895426 05/10/2013 47 CitationsCombinatorial pooling enables selective sequencing of the barley gene space. (Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Bhat PR, Wu Y, Ciardo G, Alsaihati B, Ma Y, Wanamaker S, Resnik J, Bozdag S, Luo MC, Close TJ) PLoS Comput Biol 2013 Apr;9(4):e1003010 PMID: 23592960 PMCID: PMC3617026 SCOPUS ID: 2-s2.0-84876934998 04/18/2013 15 CitationsA Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. (Bozdag S, Close TJ, Lonardi S) IEEE/ACM Trans Comput Biol Bioinform 2013 Mar 26: PMID: 23547006 04/03/2013 Genome-wide associations of signaling pathways in glioblastoma multiforme. (Wuchty S, Vazquez A, Bozdag S, Bauer PO) BMC Med Genomics 2013 Mar 28;6:11 PMID: 23537212 PMCID: PMC3616958 SCOPUS ID: 2-s2.0-84875283630 03/30/2013 3 CitationsG-cimp status prediction of glioblastoma samples using mRNA expression data. (Baysan M, Bozdag S, Cam MC, Kotliarova S, Ahn S, Walling J, Killian JK, Stevenson H, Meltzer P, Fine HA) PLoS One 2012;7(11):e47839 PMID: 23139755 PMCID: PMC3490960 SCOPUS ID: 2-s2.0-84876435048 11/10/2012 32 CitationsInvolvement of microRNA families in cancer. (Wuchty S, Arjona D, Bozdag S, Bauer PO) Nucleic Acids Res 2012 Sep 01;40(17):8219-26 PMID: 22743268 PMCID: PMC3458565 SCOPUS ID: 2-s2.0-84866947636 06/30/2012 21 CitationsGenomic analysis of immune response against Vibrio cholerae hemolysin in Caenorhabditis elegans. (Sahu SN, Lewis J, Patel I, Bozdag S, Lee JH, LeClerc JE, Cinar HN) PLoS One 2012;7(5):e38200 PMID: 22675448 PMCID: PMC3364981 SCOPUS ID: 2-s2.0-84861679962 06/08/2012 39 CitationsGliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes. (Li A, Bozdag S, Kotliarov Y, Fine HA) BMC Med Inform Decis Mak 2010 Jul 15;10:38 PMID: 20633285 PMCID: PMC2912783 SCOPUS ID: 2-s2.0-77954552334 07/17/2010 14 CitationsFastMEDUSA: a parallelized tool to infer gene regulatory networks. (Bozdag S, Li A, Wuchty S, Fine HA) Bioinformatics 2010 Jul 15;26(14):1792-3 PMID: 20513661 PMCID: PMC2894517 SCOPUS ID: 2-s2.0-77954517578 06/02/2010 16 CitationsCNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. (Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA) BMC Med Genomics 2010 Apr 09;3:11 PMID: 20380730 PMCID: PMC2872651 SCOPUS ID: 2-s2.0-77950637906 04/13/2010 3 CitationsDevelopment and implementation of high-throughput SNP genotyping in barley. (Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R) BMC Genomics 2009 Dec 04;10:582 PMID: 19961604 PMCID: PMC2797026 SCOPUS ID: 2-s2.0-73449108400 12/08/2009 502 CitationsA compartmentalized approach to the assembly of physical maps. (Bozdag S, Close TJ, Lonardi S) BMC Bioinformatics 2009 Jul 15;10:217 PMID: 19604400 PMCID: PMC2717093 SCOPUS ID: 2-s2.0-68149182691 07/17/2009 2 Citations Last update: 11/26/2019