Peer-Reviewed Publications

2017

  • [DOI] D. Ready, K. Yagiz, P. Amin, Y. Yildiz, V. Funari, S. Bozdag, and B. Cinar, “Mapping the STK4/Hippo signaling network in prostate cancer cell,” PLoS ONE, vol. 12, iss. 9, pp. 1-26, 2017.
    [Bibtex]
    @article{10.1371/journal.pone.0184590,
        author = {Ready, Damien AND Yagiz, Kader AND Amin, Pooneh AND Yildiz, Yuksel AND Funari, Vincent AND Bozdag, Serdar AND Cinar, Bekir},
        journal = {PLoS ONE},
        publisher = {Public Library of Science},
        title = {Mapping the STK4/Hippo signaling network in prostate cancer cell},
        year = {2017},
        month = {09},
        volume = {12},
        url = {https://doi.org/10.1371/journal.pone.0184590},
        pages = {1-26},
        abstract = {Dysregulation of MST1/STK4, a key kinase component of the Hippo-YAP pathway, is linked to the etiology of many cancers with poor prognosis. However, how STK4 restricts the emergence of aggressive cancer remains elusive. Here, we investigated the effects of STK4, primarily localized in the cytoplasm, lipid raft, and nucleus, on cell growth and gene expression in aggressive prostate cancer. We demonstrated that lipid raft and nuclear STK4 had superior suppressive effects on cell growth in vitro and in vivo compared with cytoplasmic STK4. Using RNA sequencing and bioinformatics analysis, we identified several differentially expressed (DE) genes that responded to ectopic STK4 in all three subcellular compartments. We noted that the number of DE genes observed in lipid raft and nuclear STK4 cells were much greater than cytoplasmic STK4. Our functional annotation clustering showed that these DE genes were commonly associated with oncogenic pathways such as AR, PI3K/AKT, BMP/SMAD, GPCR, WNT, and RAS as well as unique pathways such as JAK/STAT, which emerged only in nuclear STK4 cells. These findings indicate that MST1/STK4/Hippo signaling restricts aggressive tumor cell growth by intersecting with multiple molecular pathways, suggesting that targeting of the STK4/Hippo pathway may have important therapeutic implications for cancer.},
        number = {9},
        doi = {10.1371/journal.pone.0184590}
    }
  • M. Muñoz-Amatria’in, H. Mirebrahim, P. Xu, S. I. Wanamaker, M. Luo, H. Alhakami, M. Alpert, I. Atokple, B. J. Batieno, …, S. Bozdag, and et al., “Genome resources for climate-resilient cowpea, an essential crop for food security,” The Plant Journal, vol. 89, iss. 5, pp. 1042-1054, 2017.
    [Bibtex]
    @article{munoz2017genome,
      title={Genome resources for climate-resilient cowpea, an essential crop for food security},
      author={Mu{\~n}oz-Amatria{\'\i}n, Mar{\'\i}a and Mirebrahim, Hamid and Xu, Pei and Wanamaker, Steve I and Luo, MingCheng and Alhakami, Hind and Alpert, Matthew and Atokple, Ibrahim and Batieno, Benoit J and ... and Bozdag, Serdar and et al.},
      journal={The Plant Journal},
      volume={89},
      number={5},
      pages={1042--1054},
      year={2017}
    }
  • B. Baur and S. Bozdag, “ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer,” Genomics, vol. 109, iss. 3, pp. 233-240, 2017.
    [Bibtex]
    @article{baur2017processdriver,
      title={ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer},
      author={Baur, Brittany and Bozdag, Serdar},
      journal={Genomics},
      volume={109},
      number={3},
      pages={233--240},
      year={2017},
      publisher={Academic Press}
    }

2016

  • B. Baur and S. Bozdag, “A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data,” PLoS ONE, vol. 11, iss. 2, p. e0148977, 2016.
    [Bibtex]
    @article{baur2016feature,
      title={A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data},
      author={Baur, Brittany and Bozdag, Serdar},
      journal={PLoS ONE},
      volume={11},
      number={2},
      pages={e0148977},
      year={2016},
      publisher={Public Library of Science}
    }

2015

  • P. Pradeep, R. J. Povinelli, S. J. Merrill, S. Bozdag, and D. S. Sem, “Novel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction,” Molecular Informatics, vol. 34, iss. 4, pp. 236-245, 2015.
    [Bibtex]
    @article{pradeep2015novel,
      title={Novel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction},
      author={Pradeep, Prachi and Povinelli, Richard J and Merrill, Stephen J and Bozdag, Serdar and Sem, Daniel S},
      journal={Molecular Informatics},
      volume={34},
      number={4},
      pages={236--245},
      year={2015},
      publisher={WILEY-VCH Verlag}
    }
  • B. Baur and S. Bozdag, “A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data,” Journal of Computational Biology, vol. 22, iss. 4, pp. 289-299, 2015.
    [Bibtex]
    @article{baur2015canonical,
      title={A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data},
      author={Baur, Brittany and Bozdag, Serdar},
      journal={Journal of Computational Biology},
      volume={22},
      number={4},
      pages={289--299},
      year={2015},
      publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
    }
  • J. F. LaDisa Jr, S. Bozdag, J. Olson, R. Ramchandran, J. R. Kersten, and T. J. Eddinger, “Gene expression in experimental aortic coarctation and repair: candidate genes for therapeutic intervention?,” PLoS ONE, vol. 10, iss. 7, p. e0133356, 2015.
    [Bibtex]
    @article{ladisa2015gene,
      title={Gene expression in experimental aortic coarctation and repair: candidate genes for therapeutic intervention?},
      author={LaDisa Jr, John F and Bozdag, Serdar and Olson, Jessica and Ramchandran, Ramani and Kersten, Judy R and Eddinger, Thomas J},
      journal={PLoS ONE},
      volume={10},
      number={7},
      pages={e0133356},
      year={2015},
      publisher={Public Library of Science}
    }
  • M. Muñoz-Amatria’in, S. Lonardi, M. Luo, K. Madishetty, J. T. Svensson, M. J. Moscou, S. Wanamaker, T. Jiang, A. Kleinhofs, …, S. Bozdag, and et al., “Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome,” The Plant Journal, vol. 84, iss. 1, pp. 216-227, 2015.
    [Bibtex]
    @article{munoz2015sequencing,
      title={Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome},
      author={Mu{\~n}oz-Amatria{\'\i}n, Mar{\'\i}a and Lonardi, Stefano and Luo, MingCheng and Madishetty, Kavitha and Svensson, Jan T and Moscou, Matthew J and Wanamaker, Steve and Jiang, Tao and Kleinhofs, Andris and ... and Bozdag, Serdar and et al.},
      journal={The Plant Journal},
      volume={84},
      number={1},
      pages={216--227},
      year={2015}
    }

2014

  • M. Baysan, K. Woolard, S. Bozdag, G. Riddick, S. Kotliarova, M. C. Cam, G. I. Belova, S. Ahn, W. Zhang, H. Song, and et al., “Micro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells,” PLoS ONE, vol. 9, iss. 4, p. e94045, 2014.
    [Bibtex]
    @article{baysan2014micro,
      title={Micro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells},
      author={Baysan, Mehmet and Woolard, Kevin and Bozdag, Serdar and Riddick, Gregory and Kotliarova, Svetlana and Cam, Margaret C and Belova, Galina I and Ahn, Susie and Zhang, Wei and Song, Hua and et al.},
      journal={PLoS ONE},
      volume={9},
      number={4},
      pages={e94045},
      year={2014},
      publisher={Public Library of Science}
    }
  • S. Bozdag, A. Li, M. Baysan, and H. A. Fine, “Master regulators, regulatory networks, and pathways of glioblastoma subtypes,” Cancer Informatics, vol. 13, iss. Suppl 3, p. 33, 2014.
    [Bibtex]
    @article{bozdag2014master,
      title={Master regulators, regulatory networks, and pathways of glioblastoma subtypes},
      author={Bozdag, Serdar and Li, Aiguo and Baysan, Mehmet and Fine, Howard A},
      journal={Cancer Informatics},
      volume={13},
      number={Suppl 3},
      pages={33},
      year={2014},
      publisher={Libertas Academica}
    }

2013

  • S. Wuchty, A. Vazquez, S. Bozdag, and P. O. Bauer, “Genome-wide associations of signaling pathways in glioblastoma multiforme,” BMC Medical Genomics, vol. 6, iss. 1, p. 11, 2013.
    [Bibtex]
    @article{wuchty2013genome,
      title={Genome-wide associations of signaling pathways in glioblastoma multiforme},
      author={Wuchty, Stefan and Vazquez, Alexei and Bozdag, Serdar and Bauer, Peter O},
      journal={BMC Medical Genomics},
      volume={6},
      number={1},
      pages={11},
      year={2013},
      publisher={BioMed Central}
    }
  • S. Bozdag, T. J. Close, and S. Lonardi, “A graph-theoretical approach to the selection of the minimum tiling path from a physical map,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, iss. 2, pp. 352-360, 2013.
    [Bibtex]
    @article{bozdag2013graph,
      title={A graph-theoretical approach to the selection of the minimum tiling path from a physical map},
      author={Bozdag, Serdar and Close, Timothy J and Lonardi, Stefano},
      journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
      volume={10},
      number={2},
      pages={352--360},
      year={2013},
      publisher={IEEE}
    }
  • S. Lonardi, D. Duma, M. Alpert, F. Cordero, M. Beccuti, P. R. Bhat, Y. Wu, G. Ciardo, B. Alsaihati, …, S. Bozdag, and et al., “Combinatorial pooling enables selective sequencing of the barley gene space,” PLoS Computational Biology, vol. 9, iss. 4, p. e1003010, 2013.
    [Bibtex]
    @article{lonardi2013combinatorial,
      title={Combinatorial pooling enables selective sequencing of the barley gene space},
      author={Lonardi, Stefano and Duma, Denisa and Alpert, Matthew and Cordero, Francesca and Beccuti, Marco and Bhat, Prasanna R and Wu, Yonghui and Ciardo, Gianfranco and Alsaihati, Burair and ... and Bozdag, Serdar and et al.},
      journal={PLoS Computational Biology},
      volume={9},
      number={4},
      pages={e1003010},
      year={2013},
      publisher={Public Library of Science}
    }
  • S. Bozdag, A. Li, G. Riddick, Y. Kotliarov, M. Baysan, F. M. Iwamoto, M. C. Cam, S. Kotliarova, and H. A. Fine, “Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels,” PLoS ONE, vol. 8, iss. 4, p. e62982, 2013.
    [Bibtex]
    @article{bozdag2013age,
      title={Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels},
      author={Bozdag, Serdar and Li, Aiguo and Riddick, Gregory and Kotliarov, Yuri and Baysan, Mehmet and Iwamoto, Fabio M and Cam, Margaret C and Kotliarova, Svetlana and Fine, Howard A},
      journal={PLoS ONE},
      volume={8},
      number={4},
      pages={e62982},
      year={2013},
      publisher={Public Library of Science}
    }
  • S. N. Sahu, J. Lewis, I. Patel, S. Bozdag, J. H. Lee, R. Sprando, and H. N. Cinar, “Genomic analysis of stress response against arsenic in Caenorhabditis elegans,” PLoS ONE, vol. 8, iss. 7, p. e66431, 2013.
    [Bibtex]
    @article{sahu2013genomic,
      title={Genomic analysis of stress response against arsenic in Caenorhabditis elegans},
      author={Sahu, Surasri N and Lewis, Jada and Patel, Isha and Bozdag, Serdar and Lee, Jeong H and Sprando, Robert and Cinar, Hediye Nese},
      journal={PLoS ONE},
      volume={8},
      number={7},
      pages={e66431},
      year={2013},
      publisher={Public Library of Science}
    }

2012

  • S. N. Sahu, J. Lewis, I. Patel, S. Bozdag, J. H. Lee, J. E. LeClerc, and H. N. Cinar, “Genomic analysis of immune response against Vibrio cholerae hemolysin in Caenorhabditis elegans,” PLoS ONE, vol. 7, iss. 5, p. e38200, 2012.
    [Bibtex]
    @article{sahu2012genomic,
      title={Genomic analysis of immune response against Vibrio cholerae hemolysin in Caenorhabditis elegans},
      author={Sahu, Surasri N and Lewis, Jada and Patel, Isha and Bozdag, Serdar and Lee, Jeong H and LeClerc, Joseph E and Cinar, Hediye Nese},
      journal={PLoS ONE},
      volume={7},
      number={5},
      pages={e38200},
      year={2012},
      publisher={Public Library of Science}
    }
  • S. Wuchty, D. Arjona, S. Bozdag, and P. O. Bauer, “Involvement of microRNA families in cancer,” Nucleic Acids Research, vol. 40, iss. 17, pp. 8219-8226, 2012.
    [Bibtex]
    @article{wuchty2012involvement,
      title={Involvement of microRNA families in cancer},
      author={Wuchty, Stefan and Arjona, Dolores and Bozdag, Serdar and Bauer, Peter O},
      journal={Nucleic Acids Research},
      volume={40},
      number={17},
      pages={8219--8226},
      year={2012},
      publisher={Oxford University Press}
    }
  • M. Baysan, S. Bozdag, M. C. Cam, S. Kotliarova, S. Ahn, J. Walling, J. K. Killian, H. Stevenson, P. Meltzer, and H. A. Fine, “G-cimp status prediction of glioblastoma samples using mRNA expression data,” PLoS ONE, vol. 7, iss. 11, p. e47839, 2012.
    [Bibtex]
    @article{baysan2012g,
      title={G-cimp status prediction of glioblastoma samples using mRNA expression data},
      author={Baysan, Mehmet and Bozdag, Serdar and Cam, Margaret C and Kotliarova, Svetlana and Ahn, Susie and Walling, Jennifer and Killian, Jonathan K and Stevenson, Holly and Meltzer, Paul and Fine, Howard A},
      journal={PLoS ONE},
      volume={7},
      number={11},
      pages={e47839},
      year={2012},
      publisher={Public Library of Science}
    }

2010

  • S. Bozdag, A. Li, S. Wuchty, and H. A. Fine, “FastMEDUSA: a parallelized tool to infer gene regulatory networks,” Bioinformatics, vol. 26, iss. 14, pp. 1792-1793, 2010.
    [Bibtex]
    @article{bozdag2010fastmedusa,
      title={FastMEDUSA: a parallelized tool to infer gene regulatory networks},
      author={Bozdag, Serdar and Li, Aiguo and Wuchty, Stefan and Fine, Howard A},
      journal={Bioinformatics},
      volume={26},
      number={14},
      pages={1792--1793},
      year={2010},
      publisher={Oxford University Press}
    }
  • A. Li, S. Bozdag, Y. Kotliarov, and H. A. Fine, “GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes,” BMC Medical Informatics and Decision Making, vol. 10, iss. 1, p. 38, 2010.
    [Bibtex]
    @article{li2010gliomapredict,
      title={GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes},
      author={Li, Aiguo and Bozdag, Serdar and Kotliarov, Yuri and Fine, Howard A},
      journal={BMC Medical Informatics and Decision Making},
      volume={10},
      number={1},
      pages={38},
      year={2010},
      publisher={BioMed Central}
    }
  • Y. Kotliarov, S. Bozdag, H. Cheng, S. Wuchty, J. Zenklusen, and H. A. Fine, “CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations,” BMC Medical Genomics, vol. 3, iss. 1, p. 11, 2010.
    [Bibtex]
    @article{kotliarov2010cnareporter,
      title={CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations},
      author={Kotliarov, Yuri and Bozdag, Serdar and Cheng, Hangjiong and Wuchty, Stefan and Zenklusen, Jean-Claude and Fine, Howard A},
      journal={BMC Medical Genomics},
      volume={3},
      number={1},
      pages={11},
      year={2010},
      publisher={BioMed Central}
    }

2009

  • T. J. Close, P. R. Bhat, S. Lonardi, Y. Wu, N. Rostoks, L. Ramsay, A. Druka, N. Stein, J. T. Svensson, …, S. Bozdag, and et al., “Development and implementation of high-throughput SNP genotyping in barley,” BMC Genomics, vol. 10, iss. 1, p. 582, 2009.
    [Bibtex]
    @article{close2009development,
      title={Development and implementation of high-throughput SNP genotyping in barley},
      author={Close, Timothy J and Bhat, Prasanna R and Lonardi, Stefano and Wu, Yonghui and Rostoks, Nils and Ramsay, Luke and Druka, Arnis and Stein, Nils and Svensson, Jan T and ... and Bozdag, Serdar and et al.},
      journal={BMC Genomics},
      volume={10},
      number={1},
      pages={582},
      year={2009},
      publisher={BioMed Central}
    }
  • S. Bozdag, T. J. Close, and S. Lonardi, “A compartmentalized approach to the assembly of physical maps,” BMC Bioinformatics, vol. 10, iss. 1, p. 217, 2009.
    [Bibtex]
    @article{bozdag2009compartmentalized,
      title={A compartmentalized approach to the assembly of physical maps},
      author={Bozdag, Serdar and Close, Timothy J and Lonardi, Stefano},
      journal={BMC Bioinformatics},
      volume={10},
      number={1},
      pages={217},
      year={2009},
      publisher={BioMed Central}
    }

2008

  • [DOI] S. Bozdag, T. J. Close, and S. Lonardi, “Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming,” in Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings, K. A. Crandall and J. Lagergren, Eds., Berlin, Heidelberg: Springer Berlin Heidelberg, 2008, pp. 148-161.
    [Bibtex]
    @Inbook{Bozdag2008,
    author="Bozdag, Serdar
    and Close, Timothy J.
    and Lonardi, Stefano",
    editor="Crandall, Keith A.
    and Lagergren, Jens",
    title="Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming",
    bookTitle="Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings",
    year="2008",
    publisher="Springer Berlin Heidelberg",
    address="Berlin, Heidelberg",
    pages="148--161",
    abstract="We study the problem of selecting the minimal tiling path (MTP) from a set of clones arranged in a physical map. We formulate the constraints of the MTP problem in a graph theoretical framework, and we derive an optimization problem that is solved via integer linear programming. Experimental results show that when we compare our algorithm to the commonly used software FPC, the MTP produced by our method covers a higher portion of the genome, even using a smaller number of MTP clones. These results suggest that if one would employ the MTP produced by our method instead of FPC's in a clone-by-clone sequencing project, one would reduce by about 12{\%} the sequencing cost.",
    isbn="978-3-540-87361-7",
    doi="10.1007/978-3-540-87361-7_13",
    url="https://doi.org/10.1007/978-3-540-87361-7_13"
    }

2007

  • [DOI] S. Bozdag, T. J. Close, and S. Lonardi, “A Compartmentalized Approach to the Assembly of Physical Maps,” in IEEE International Conference on Bioinformatics and Bioengineering, Boston, MA, 2007, pp. 218-225.
    [Bibtex]
    @inproceedings{4237808,
      author = {Bozdag, Serdar  and Close, Timothy J.  and Lonardi, Stefano},
      booktitle = {IEEE International Conference on Bioinformatics and Bioengineering},
      title = {A Compartmentalized Approach to the Assembly of Physical Maps},
      uuid = {87D1B21D-0F66-4DD5-B581-8DBC0FA5EB93},
      pages = {218-225},
      address = {Boston, MA},
      year = {2007},
      doi = {10.1109/BIBE.2007.4375568}
    }