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Serdar Bozdag BS,PhD

Serdar Bozdag BS,PhD profile photo picture

Assistant Professor, Director of Bioinformatics Lab

Institution: Marquette University
Department: Dept. of Mathematics, Statistics and Computer Science

Member of the Genomic Sciences and Precision Medicine Center (GSPMC)

I am willing to collaborate on research projects.

Research Experience

  • Computational Biology
  • Data Mining
  • Machine Learning
  • Models, Statistical
  • Statistical Distributions
  • Unsupervised Machine Learning
  • Methodologies and Techniques

  • Algorithms
  • Computational Biology
  • DNA Copy Number Variations
  • DNA Methylation
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks
  • MicroRNAs
  • Sequence Analysis, DNA
  • Software
  • Leadership Positions

  • Co-director, MS in Bioinformatics
  • Program Director, Undergraduate Major in Bioinformatics
  • Undergraduate Studies Director, Dept of Computer Science
  • Publications (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       1 Citation
  • Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. (Do D, Bozdag S) PLoS Comput Biol 2018 07;14(7):e1006318 PMID: 30011266 PMCID: PMC6072113 07/17/2018       7 Citations
  • Mapping 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 09/08/2017       7 Citations
  • ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. (Baur B, Bozdag S) Genomics 2017 07;109(3-4):233-240 PMID: 28438487 04/26/2017       1 Citation
  • Genome 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 10/25/2016       60 Citations
  • A 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 02/13/2016       16 Citations
  • Sequencing 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 08/08/2015       23 Citations
  • Gene 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 07/25/2015       3 Citations
  • A 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 04/07/2015       15 Citations
  • Novel 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 04;34(4):236-45 PMID: 27490169 04/01/2015       5 Citations
  • Correction 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 11/05/2014    
  • Micro-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 04/15/2014       24 Citations
  • A 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-Apr;10(2):352-60 PMID: 23929859 08/10/2013       5 Citations
  • Genomic 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 07/31/2013    
  • Age-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 05/10/2013       32 Citations
  • Combinatorial 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 04/18/2013       14 Citations
  • A 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 03/30/2013       3 Citations
  • G-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 11/10/2012       23 Citations
  • Involvement 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 06/30/2012       15 Citations
  • Genomic 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 06/08/2012       27 Citations
  • GliomaPredict: 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 07/17/2010       13 Citations
  • FastMEDUSA: 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 06/02/2010       15 Citations
  • CNAReporter: 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 04/13/2010       3 Citations
  • Development 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 12/08/2009       445 Citations
  • A 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 07/17/2009       2 Citations
  • Last update: 11/26/2019
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