Ali Cakmak, Ph.D.
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Patents:

    • Chakkappen, S. P., Zait, M., Lee, A. W., & Cakmak, A. (2022). U.S. Patent No. 11,403,295. Washington, DC: U.S. Patent and Trademark Office.
    • Delibas, E., Uzun, A., Inan, M. F., Guzey, O., & Cakmak, A. (2019). U.S. Patent Application No. 16/331,744.
    • Cakmak, A., Aytimur, M. (2018). LIKE Selectivity Estimation. International Patent App. No. PCT/TR2018/050366.
    • Cakmak, A., Celik, M.H. (2018). A System for Diagnosing Diseases. International Patent App. No. PCT/TR2019/051101.
    • Chakkappen, S. P., Zait, M., Lee, A. W., & Cakmak, A. (2016). U.S. Patent No. 9,471,631. Washington, DC: U.S. Patent and Trademark Office.


Refereed/Invited Journal Publications:

    • Cakmak, A., Ibrahimzada A. R., Arıkan, S., Ayaz, H., Demirkol, Ş., Sönmez, D., Hakan, M. T., Turan, S. S., Horozoğlu, C., Küçükhüseyin, Ö., Kiran, B., Zeybek, Ş. Ü., Baysan, M., Yaylim, I. (2022). Predicting the Predisposition to Colorectal Cancer based on SNP Profiles of Immune Phenotypes using Supervised Learning Models. Medical & Biological Engineering & Computing (To appear).
    • Cakmak, A., & Celik, M. (2021). Personalized Metabolic Analysis of Diseases. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(3), 1014-1025.
    • Aytimur, M., & Cakmak, A. (2021). Using positional sequence patterns to estimate the selectivity of SQL LIKE queries. Expert Systems with Applications, 165, 113762.
    • Sohsah, G. N., Ibrahimzada, A. R., Ayaz, H., & Cakmak, A. (2020). Scalable classification of organisms into a taxonomy using hierarchical supervised learners. Journal of Bioinformatics and Computational Biology, 18(05), 2050026.
    • Polat, N., Cakmak, A., & Turan, R. (2020). Exploring the power of supervised learning methods for company name disambiguation in microblog posts. Turkish Journal of Electrical Engineering & Computer Sciences, 28(5), 2400-2415.
    • Emrullah D., Uzun, A., Inan, M.F., Guzey, O., Cakmak, A. (2019). Interactive exploratory soccer data analytics. Information Systems and Operational Research, 57(2), 141-164.
    • Cakmak, A., Uzun, A., & Delibas, E. (2018). Computational modeling of pass effectiveness in soccer. Advances in Complex Systems, 21(3-4). doi: 10.1142/S0219525918500108
    • Aytimur, M., Çakmak, A. (2018). Estimating the selectivity of LIKE queries using pattern-based histograms. Turkish Journal of Electrical Engineering & Computer Sciences, 26(6), 3319-3334.
    • Cakmak, A. (2017). Predicting student success in courses via collaborative filtering. International Journal of Intelligent Systems and Applications in Engineering, 5(1), 10-17.
    • Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephan Johnson, Xu Han, Sami Alshalwi, Gultekin Ozsoyoglu. "An Online System for Metabolic Network Analysis ". Database: The Journal of Biological Databases and Curation (Oxford Univ. Press), 2014.
    • X. Qi, S.A. Coskun, A. Cakmak, E. Cheng, E. A. Cicek, M. Das, L. Yang, R. Jadeja, S. Syed, R.K. Dash, N. Lai, G. Ozsoyoglu, Z. M. Ozsoyoglu. “PathCase-SB: Database-Enabled Tools for Regulatory Metabolic Networks”. ACM SIGBioinformatics Record, Volume 2, Issue 3, 2012.
    • Sarp Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu. “PathCase-SB: Integrating Data Sources and Providing Tools for Systems Biology Research”. BMC Systems Biology; 6(1):67, June 2012
    • Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Praskac, Mitchell Drumm, Gultekin Ozsoyoglu. “A New Metabolomics Analysis Technique: Steady-State Metabolic Network Dynamics Analysis”. Journal of Bioinformatics and Computational Biology 10:1, February, 2012.
    • Ali Cakmak, Xinjian Qi, Sarp Coskun, Mitali Das, En Cheng, Ercument Cicek, Nicola Lai, Gultekin Ozsoyoglu, Meral Ozsoyoglu. “PathCase-SB Architecture and Database Design”. BMC Systems Biology, 5:188, November 2011.
    • Ali Cakmak, Gultekin Ozsoyoglu, Richard W. Hanson. "Querying Metabolism under Different Physiological Constraints". Journal of Bioinformatics and Computational Biology, 8:(2) pp. 247-293, April 2010.
    • Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Steve Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu. "PathCase Pathways Database System". Bioinformatics, 24(21):2526-2533, November 2008. [Publisher's Free Access Link]
    • Ali Cakmak, Gultekin Ozsoyoglu. "Discovering Gene Annotations in Biomedical Text Databases". BMC Bioinformatics 2008, 9:143, March 2008.   [Publisher's Free Access Link]
    • Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Ozsoyoglu. "Context-Based Literature Digital Collection Search". VLDB Journal, 2008. (©Springer)
    • Ali Cakmak, Gultekin Ozsoyoglu. "Mining Biological Networks for Unknown Pathways". Bioinformatics 23(20):2775-2783, October 2007.   [Publisher's Free Access Link]
    • Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Ozsoyoglu, Abdullah Al-Hamdani. "Evaluating Publication Similarity Measures". IEEE Data Eng. Bull, 28(4):21-28, December 2005. (Invited paper)(©IEEE)

Refereed Conference/Workshop Publications:

    • Tekdogan, T., Cakmak, A. (2021). Benchmarking Apache Spark and Hadoop MapReduce on Big Data Classification. International Conference on Cloud and Big Data Computing. Liverpool, United Kingdom.
    • Cakmak, A., Ibrahimzada, A. R., Arikan, S., Ayaz, H., Demirkol, S. et al. (2019, September). Predicting the Predisposition to Colorectal Cancer based on SNP Profiles of Immune Checkpoints using Supervised Learning Models. 7th International Congress of Molecular Medicine, Istanbul.
    • Cakmak, A., Celik, M.H. (2018). Personalized metabolic analysis of diseases. The International Symposium on Health Informatics and Bioinformatics (HIBIT). Antalya, Turkey.
    • Feruz Davletov, Ali Selman Aydin, Ali Cakmak. "High Impact Academic Paper Prediction Using Temporal and Topological Features". ACM International Conference on Information and Knowledge Management (ACM CIKM 2014), pp. 491-498, November 3-7, Shanghai, China.
Citation Prediction
    • Ahmet Bulut, Tarik Arici, Onur Guzey, Baris Arslan, Ali Cakmak. "Training the Data Scientists of the Future". Big Data and Analytics EdCon, Las Vegas, Nevada, USA, October 25-26, 2014.
Training Data Scientists
    • Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephan Johnson, Xu Han, Sami Alshalwi, Gultekin Ozsoyoglu. "PathCase-MAW: An Online Metabolic Network Analysis Workbench". ACM International Conference on Bioinformatics and Computational Biology (ACM BCB 2013), September 22-25, Washington, DC.
PathCaseMAW.BCB
    • Ali Cakmak, Xinjian Qi, Ercument Cicek, Tekin Ozsoyoglu. "Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis". ACM International Conference on Bioinformatics and Computational Biology (ACM BCB 2011), Aug 1 -3, Chicago, IL.
SMDA.BCB
    • Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Ozsoyoglu. "Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms". ACM International Conference on Bioinformatics and Computational Biology (ACM BCB 2010), Niagara Falls, New York, USA, August 2-4, 2010.
OMA
    • En Cheng, Ali Cakmak, Z. Meral Özsoyoglu. "Efficient query evaluation for DAG -shaped hierarchies". ACM International Conference on Bioinformatics and Computational Biology (ACM BCB 2010), Niagara Falls, New York, USA, August 2-4, 2010 (Short paper).
OMA
    • Brendan Elliott, Steve Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu. "Advanced Querying Interface for Biochemical Network Databases". 25th ACM Symposium On Applied Computing (SAC), Sierre, Switzerland, March 22 - 26, 2010.
AQI
    • Ali Cakmak, Gultekin Ozsoyoglu, Richard W. Hanson. "Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing". 8th International Conference on Computational Systems Bioinformatics (CSB), Stanford, California, August 10-13, 2009.
MQL
    • Ali Cakmak, Mustafa Kirac, Gultekin Ozsoyoglu. "PopulusLog: People Information Database". 24th International Symposium on Computer and Information Sciences (ISCIS), pp. 165-170. Guzelyurt, Northern Cyprus, September 14-16, 2009.
    • Ali Cakmak, Arun Dsouza, Richard W. Hanson, Meral Ozsoyoglu, Gultekin Ozsoyoglu. "A Web-Based Data Source for Metabolomics". 24th International Symposium on Computer and Information Sciences (ISCIS), pp 454-459. Guzelyurt, Northern Cyprus, September 14-16, 2009.
    • Ali Cakmak, Gultekin Ozsoyoglu. "Taxonomy-Superimposed Graph Mining". 11th International Conference on Extending Database Technology (EDBT), Vol. 261, pp. 217-228. Nantes, France, March 25-30, 2008. (©ACM)
    • Ali Cakmak, Mustafa Kirac, Marc Reynolds, Meral Ozsoyoglu, Gultekin Ozsoyoglu. "Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways". 19th International Conference on Scientific and Statistical Databases (SSDBM), Banff, Calgary, Canada, July 9-11, 2007. (©IEEE Computer Society)
    • Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Ozsoyoglu. "Evaluating Different Ranking Functions for Context-Based Literature Search". ICDE Workshop on Ranking in Databases (DBRANK), pp. 261-268, Istanbul, Turkey, April 16, 2007. (©IEEE Computer Society)
as
    • Ali Cakmak, Gultekin Ozsoyoglu. "Annotating Genes Using Textual Patterns". 12th Pacific Symposium on Biocomputing (PSB), pp. 221-232, Maui, Hawaii, USA, January 3-7, 2007. (©World Scientific)
    • Mustafa Kirac, Ali Cakmak, Gultekin Ozsoyoglu. "Task-Oriented Integrated Use of Biological Web Data Sources". 18th International Conference on Scientific and Statistical Databases (SSDBM), pp. 81-90, Vienna, Austria, July 3-5, 2006. (©IEEE Computer Society)
    • Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Ozsoyoglu. "On Data and Visualization Models for Signaling Pathways". 18th International Conference on Scientific and Statistical Databases (SSDBM), pp. 133-142, Vienna, Austria, July 3-5, 2006. (©IEEE Computer Society)
    • Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Ozsoyoglu. "Evaluating Score and Publication Similarity Functions in Digital Libraries". 8th International Conference on Asian Digital Libraries (ICADL), Lecture Notes in Computer Science, Vol. 3815, pp. 483-485, Bangkok, Thailand, December 12-15, 2005. (Published as a short paper)(©Springer)
Research Posters in Conferences:
    • Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Ozsoyoglu, Gultekin Ozsoyoglu. "Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms". Metabolomics 2008, 4th International Conference, Boston, Massachusetts, USA, September 2-6, 2008.
    • Ali Cakmak, Gultekin Ozsoyoglu. "Mining Biological Networks for Unknown Pathways". 5th International Conference on Pathways, Networks, and Systems (PNAS), Porto Heli, Greece, June 24-29, 2007.
    • Meral Ozsoyoglu, Gultekin Ozsoyoglu, Joseph Nadeau, Brendan Elliott, Ali Cakmak, Mustafa Kirac, Fatih Akgul, Gokhan Yavas, Greg Strnad, Marc Reynolds, Michael Starke, Brandon Evans, Murat Tasan. "PathCase: Biological Pathways Database System". 12th Pacific Symposium on Biocomputing (PSB), Maui, Hawaii, USA, January 3-7, 2007.


Books:

    • Ali Cakmak. "Mining Metabolic Networks and Biomedical Literature: Knowledge Discovery and Analysis". VDM Verlag, Saarbrücken, Germany, ISBN: 978-3639229127, January 2010. (Adapted from my doctoral dissertation)