Faculty Profile

Serdar Bozdag

Title
Associate Professor
Department
Computer Science and Engineering
College
College of Engineering

    

Current Scheduled Teaching*

BIOL 6810.002, Advanced Topics in Computational Life Science, Fall 2021
CSCE 6810.002, Advanced Topics in Computational Life Science, Fall 2021
BIOL 4810.001, BioComputing, Fall 2021 Syllabus
BIOL 5810.001, BioComputing, Fall 2021
CSCE 4810.001, BioComputing, Fall 2021 Syllabus
CSCE 5810.001, BioComputing, Fall 2021
MATH 4810.001, Biocomputing, Fall 2021 Syllabus
CSCE 6950.706, Doctoral Dissertation, Fall 2021
CSCE 6940.706, Individual Research, Fall 2021

* Texas Education Code 51.974 (HB 2504) requires each institution of higher education to make available to the public, a syllabus for undergraduate lecture courses offered for credit by the institution.

Previous Scheduled Teaching*

CSCE 4110.002, Algorithms, Spring 2021 Syllabus SPOT
CSCE 4110.005, Algorithms, Spring 2021 Syllabus SPOT
CSCE 6940.706, Individual Research, Spring 2021
BIOL 4810.001, BioComputing, Fall 2020 Syllabus SPOT
BIOL 5810.001, BioComputing, Fall 2020 Syllabus SPOT
CSCE 4810.001, BioComputing, Fall 2020 Syllabus SPOT
CSCE 4810.004, BioComputing, Fall 2020
CSCE 4810.281, BioComputing, Fall 2020 Syllabus SPOT
CSCE 5810.001, BioComputing, Fall 2020 Syllabus SPOT
CSCE 5810.600, BioComputing, Fall 2020 SPOT
MATH 4810.001, Biocomputing, Fall 2020 Syllabus SPOT
CSCE 6940.706, Individual Research, Fall 2020 Syllabus

* Texas Education Code 51.974 (HB 2504) requires each institution of higher education to make available to the public, a syllabus for undergraduate lecture courses offered for credit by the institution.

Published Publications

Published Intellectual Contributions

Conference Proceeding
Dursun, C., Smith, J. R., Hayman, G. T., Kwitek, A. E., Bozdag, S. (2020). NECo: A node embedding algorithm for multiplex heterogeneous networks. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 146--149.
Do, D., Bozdag, S. (2020). 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. (117), 1--10. New York, NY, USA: Association for Computing Machinery. https://doi.org/10.1145/3388440.3415586
Bose, B., Bozdag, S. (2020). 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. (7), 1--10. New York, NY, USA: Association for Computing Machinery. https://doi.org/10.1145/3388440.3412456
Bose, B., Bozdag, S. (2019). miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 366--375. New York, NY, USA: ACM. http://doi.acm.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. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 279--288. New York, NY, USA: ACM. http://doi.acm.org/10.1145/3307339.3342155
Bozdag, S., Close, T. J., Lonardi, S. (2007). A Compartmentalized Approach to the Assembly of Physical Maps. IEEE International Conference on Bioinformatics and Bioengineering. 218--225.
Journal Article
Milali, M. P., Kiware, S. S., Govella, N. J., Okumu, F., Bansal, N., Bozdag, S., Charlwood, J. D., Maia, M. F., Ogoma, S. B., Dowell, F. E., Corliss, G. F., Sikulu-Lord, M. T., 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.
Kesimoglu, Z. N., Bozdag, S. (2020). Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. Other. 2020.06.18.160408. https://www.biorxiv.org/content/10.1101/2020.06.18.160408v2
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., Pleiss, S. S., Murphy, C. C., Casnar, C. L., Potts, S., Cibich, D., Nelsen-Freund, K., Fernandez, D., Hernandez, I., Hecke, A. 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. Other. 582676. https://www.biorxiv.org/content/10.1101/582676v2
Do, D., Bozdag, S. (2018). Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PLOS Computational Biology. 14(7), e1006318.
Muñoz-Amatriaín, M., Mirebrahim, H., Xu, P., Wanamaker, S. I., Luo, M., Alhakami, H., Alpert, M., Atokple, I., Batieno, B. J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J. D., Farmer, A., Fatokun, C., Gu, Y. Q., Guo, Y. N., Huynh, B. L., Jackson, S. A., Kusi, F., Lawley, C. T., Lucas, M. R., Ma, Y., Timko, M. P., Wu, J., You, F., Barkley, N. A., Roberts, P. A., Lonardi, S., Close, T. J. (2017). Genome resources for climate-resilient cowpea, an essential crop for food security.. Other. 89(5), 1042--1054.
Baur, B., Bozdag, S. (2017). ProcessDriver: A computational pipeline to identify copy number drivers and associated disrupted biological processes in cancer. Other. 109(3-4), 233--240.
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589252/
Baur, B., Bozdag, S. (2016). A Feature Selection Algorithm to Compute Gene Centric Methylation from Probe Level Methylation Data. PLOS One. 11(2), e0148977.
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.
Muñoz-Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G. J., Wise, R. P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bhat, P. R., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H. N., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., \textbackslashu Simková, Hana,, Doleel, 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, P. M., Lemaux, P., Mammadov, J., Close, T. J. (2015). Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Other. n/a--n/a.
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514739/
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. Other. 22(4), 289--299.
Bozdag, S., Li, A., Baysan, M., Fine, H. A. (2014). Master regulators, regulatory networks, and pathways of glioblastoma subtypes.. Other. 13(Suppl 3), 33--44.
Baysan, M., Woolard, K., Bozdag, S., Riddick, G., Kotliarova, S., Cam, M. C., Belova, G. I., Ahn, S., Zhang, W., Song, H., Walling, J., Stevenson, H., Meltzer, P., 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984100/
Bozdag, S., Close, T. J., Lonardi, S. (2013). A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map.. Other.
Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Bhat, P. R., Wu, Y., Ciardo, G., Alsaihati, B., Ma, Y., Wanamaker, S., Resnik, J., Bozdag, S., Luo, M. C., Close, T. J. (2013). Combinatorial pooling enables selective sequencing of the barley gene space.. Other. 9(4), e1003010.
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.
Bozdag, S., Li, A., Riddick, G., Kotliarov, Y., Baysan, M., Iwamoto, F. M., Cam, M. C., Kotliarova, S., Fine, H. A. (2013). Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels. PLOS One. 8(4), . https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639162/
Wuchty, S., Vazquez, A., Bozdag, S. (2013). Genome-wide associations of signaling pathways in glioblastoma multiforme. Other. 6, 11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616958/
Baysan, M., Bozdag, S., Cam, M. C., Kotliarova, S., Ahn, S., Walling, J., Killian, J. K., Stevenson, H., Meltzer, P., Fine, H. A. (2012). G-cimp status prediction of glioblastoma samples using mRNA expression data.. PLOS One. 7(11), e47839.
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.
Wuchty, S., Arjona, D., Bozdag, S., Bauer, P. O. (2012). Involvement of microRNA families in cancer.. Other. 40(17), 8219--26.
Bozdag, S., Li, A., Wuchty, S., Fine, H. A. (2010). FastMEDUSA: a parallelized tool to infer gene regulatory networks.. Other. 26(14), 1792--3.
Li, A., Bozdag, S., Kotliarov, Y., Fine, H. A. (2010). GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes.. Other. 10, 38.
Kotliarov, Y., Bozdag, S., Cheng, H., Wuchty, S., Zenklusen, J., Fine, H. A. (2010). CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. Other. 3, 11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872651/
Bozdag, S., Close, T. J., Lonardi, S. (2009). A compartmentalized approach to the assembly of physical maps.. BMC Bioinformatics. 10, 217.
Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J. T., Wanamaker, S., Bozdag, S., Roose, M. L., Moscou, M. J., Chao, S., Varshney, R. K., Szucs, P., Sato, K., Hayes, P. M., Matthews, D. E., Kleinhofs, A., Muehlbauer, G. J., DeYoung, J., Marshall, D. F., Madishetty, K., Fenton, R. D., Condamine, P., Graner, A., Waugh, R. (2009). Development and implementation of high-throughput SNP genotyping in barley.. BMC Genomics. 10, 582.
Bozdag, S., Close, T., Lonardi, S. (2008). Computing the minimal tiling path from a physical map by integer linear programming. Other. 148--161.

Awarded Grants

Contracts, Grants and Sponsored Research

Grant - Research
Bozdag, S., "Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response," Sponsored by National Institutes of Health, Federal, $1191286 Funded. (September 1, 2020June 30, 2024).
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Overall
Summative Rating
Challenge and
Engagement Index
Response Rate

out of 5

out of 7
%
of
students responded
  • Overall Summative Rating (median):
    This rating represents the combined responses of students to the four global summative items and is presented to provide an overall index of the class’s quality. Overall summative statements include the following (response options include a Likert scale ranging from 5 = Excellent, 3 = Good, and 1= Very poor):
    • The course as a whole was
    • The course content was
    • The instructor’s contribution to the course was
    • The instructor’s effectiveness in teaching the subject matter was
  • Challenge and Engagement Index:
    This rating combines student responses to several SPOT items relating to how academically challenging students found the course to be and how engaged they were. Challenge and Engagement Index items include the following (response options include a Likert scale ranging from 7 = Much higher, 4 = Average, and 1 = Much lower):
    • Do you expect your grade in this course to be
    • The intellectual challenge presented was
    • The amount of effort you put into this course was
    • The amount of effort to succeed in this course was
    • Your involvement in course (doing assignments, attending classes, etc.) was
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