Ali Çakmak

Assistant Professor

PhD, Case Western Reserve University

alicakmak@sehir.edu.tr

Office: East Campus, Room 106

Phone: +90 216 559 9000

Personal Website

CV:

Bio: Ali Cakmak received his B.Sc. degree in 2003 from the Computer Engineering Department at Bilkent University, and his Ph.D. degree in 2008 from the Electrical Engineering and Computer Science Department at Case Western Reserve University. After completing his Ph.D., he worked as a post-doctoral research associate for a year in the same department. Then, he moved to the Silicon Valley, and worked as an R&D engineer as part of the Query Optimization Group at Oracle, Inc. In Fall 2013, he joined Istanbul Sehir University as a faculty member in the Department of Computer Science. His research interests include bioinformatics, data mining, data management, databases, query optimization, data science, information retrieval, information extraction, big data, and digital libraries. Dr. Cakmak is a recipient of TUBITAK Career Grant (2014).

Research Interests: Bioinformatics, Data Mining, Databases, Data Management, Digital Libraries, Information Retrieval

Funded projects:

Member of research Groups:

Publications:
  • 1. Ali Cakmak: Predicting Student Success in Courses via Collaborative Filtering. International Journal of Intelligent Systems and Applications in Engineering 5(1):10-17 (2017).
  • 2. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating hybrid and top-frequency histograms - US Patent App 15/295,539 2016.
  • 3. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating and using data that indicates misestimates of actual costs - US Patent 9471631 2016. [1 Citation]
  • 4. Emrullah Delibas, Ali Uzun, M. Fatih Inan, Onur Guzey, Ali Cakmak. Exploratory Soccer Data Analytics. PCT/TR Patent App. 2016/050507 & 2016/12725.
  • 5. Ali akmak, Serpil Kaya: Parallel Surfaces of General Cylinder. Journal of Logic, Mathematics and Linguistics in Applied Sciences 1(1): (2016).
  • 6. Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu: An online system for metabolic network analysis. Database 2014: (2014). [3 Citations]
  • 7. Feruz Davletov, Ali Selman Aydin, Ali Cakmak: High Impact Academic Paper Prediction Using Temporal and Topological Features. CIKM 2014: 491-498. [7 Citations]
  • 8. A.Bulut, T. Arıcı, O. Guzey, B. Arslan and A. Cakmak. "Training the Data Scientists of the Future", Big Data and Analytics Education Conference (EDCON), 2014.
  • 9. A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu: PathCase-MAW: An Online Metabolic Network Analysis Workbench. BCB 2013: 219.
  • 10. Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Systems Biology 6:67 (2012). [7 Citations]
  • 11. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu: A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinformatics and Computational Biology 10(1): (2012). [7 Citations]
  • 12. 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.
  • 13. Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercument Cicek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB architecture and database design. BMC Systems Biology 5:188 (2011). [11 Citations]
  • 14. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu: Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB 2011: 387-392. [3 Citations]
  • 15. Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson: Querying metabolism under Different Physiological Constraints. J. Bioinformatics and Computational Biology 8(2):247-293 (2010). [6 Citations]
  • 16. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu: Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. BCB 2010: 137-146. [8 Citations]
  • 17. En Cheng, Ali Cakmak, Z. Meral Özsoyoglu: Efficient query evaluation for DAG-shaped hierarchies. BCB 2010: 454-456. [4 Citations]
  • 18. Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Advanced querying interface for biochemical network databases. SAC 2010: 1526-1533. [7 Citations]
  • 19. Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Özsoyoglu: Context-based literature digital collection search. VLDB J. 18(1):277-301 (2009). [21 Citations]
  • 20. Ali Cakmak, Mustafa Kirac, Gultekin Özsoyoglu: PopulusLog: People information database. ISCIS 2009: 165-170.
  • 21. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: A web-based data source for metabolomics. ISCIS 2009: 454-459. [3 Citations]
  • 22. 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): 2009. [2 Citations]
  • 23. Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase: pathways database system. Bioinformatics 24(21):2526-2533 (2008). [51 Citations]
  • 24. Ali Cakmak, Gultekin Özsoyoglu: Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9: (2008). [10 Citations]
  • 25. Ali Cakmak, Gultekin Özsoyoglu: Taxonomy-superimposed graph mining. EDBT 2008: 217-228. [19 Citations]
  • 26. Ali Cakmak, Gultekin Özsoyoglu: Mining biological networks for unknown pathways. Bioinformatics 23(20):2775-2783 (2007). [34 Citations]
  • 27. Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Z. Meral Özsoyoglu, Gultekin Özsoyoglu: Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. SSDBM 2007: 33. [9 Citations]
  • 28. Ali Cakmak, Gultekin Özsoyoglu: Annotating Genes Using Textual Patterns. Pacific Symposium on Biocomputing 2007: 221-232. [13 Citations]
  • 29. Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Özsoyoglu: Evaluating Different Ranking Functions for Context-Based Literature Search. ICDE Workshops 2007: 261-268. [5 Citations]
  • 30. Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu: On Data and Visualization Models for Signaling Pathways. SSDBM 2006: 133-142. [4 Citations]
  • 31. Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu: Task-Oriented Integrated Use of Biological Web Data Sources. SSDBM 2006: 81-90.
  • 32. Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Özsoyoglu, Abdullah Al-Hamdani: Evaluating Publication Similarity Measures. IEEE Data Eng. Bull. 28(4):21-28 (2005). [17 Citations]
  • 33. Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Özsoyoglu: Evaluating Score and Publication Similarity Functions in Digital Libraries. ICADL 2005: 483-485. [8 Citations]

2017 (1)

  • 1. Ali Cakmak: Predicting Student Success in Courses via Collaborative Filtering. International Journal of Intelligent Systems and Applications in Engineering 5(1):10-17 (2017).

2016 (4)

  • 2. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating hybrid and top-frequency histograms - US Patent App 15/295,539 2016.
  • 3. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating and using data that indicates misestimates of actual costs - US Patent 9471631 2016. [1 Citation]
  • 4. Emrullah Delibas, Ali Uzun, M. Fatih Inan, Onur Guzey, Ali Cakmak. Exploratory Soccer Data Analytics. PCT/TR Patent App. 2016/050507 & 2016/12725.
  • 5. Ali akmak, Serpil Kaya: Parallel Surfaces of General Cylinder. Journal of Logic, Mathematics and Linguistics in Applied Sciences 1(1): (2016).

2014 (3)

  • 6. Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu: An online system for metabolic network analysis. Database 2014: (2014). [3 Citations]
  • 7. Feruz Davletov, Ali Selman Aydin, Ali Cakmak: High Impact Academic Paper Prediction Using Temporal and Topological Features. CIKM 2014: 491-498. [7 Citations]
  • 8. A.Bulut, T. Arıcı, O. Guzey, B. Arslan and A. Cakmak. "Training the Data Scientists of the Future", Big Data and Analytics Education Conference (EDCON), 2014.

2013 (1)

  • 9. A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu: PathCase-MAW: An Online Metabolic Network Analysis Workbench. BCB 2013: 219.

2012 (3)

  • 10. Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Systems Biology 6:67 (2012). [7 Citations]
  • 11. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu: A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinformatics and Computational Biology 10(1): (2012). [7 Citations]
  • 12. 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.

2011 (2)

  • 13. Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercument Cicek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB architecture and database design. BMC Systems Biology 5:188 (2011). [11 Citations]
  • 14. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu: Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB 2011: 387-392. [3 Citations]

2010 (4)

  • 15. Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson: Querying metabolism under Different Physiological Constraints. J. Bioinformatics and Computational Biology 8(2):247-293 (2010). [6 Citations]
  • 16. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu: Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. BCB 2010: 137-146. [8 Citations]
  • 17. En Cheng, Ali Cakmak, Z. Meral Özsoyoglu: Efficient query evaluation for DAG-shaped hierarchies. BCB 2010: 454-456. [4 Citations]
  • 18. Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Advanced querying interface for biochemical network databases. SAC 2010: 1526-1533. [7 Citations]

2009 (4)

  • 19. Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Özsoyoglu: Context-based literature digital collection search. VLDB J. 18(1):277-301 (2009). [21 Citations]
  • 20. Ali Cakmak, Mustafa Kirac, Gultekin Özsoyoglu: PopulusLog: People information database. ISCIS 2009: 165-170.
  • 21. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: A web-based data source for metabolomics. ISCIS 2009: 454-459. [3 Citations]
  • 22. 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): 2009. [2 Citations]

2008 (3)

  • 23. Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase: pathways database system. Bioinformatics 24(21):2526-2533 (2008). [51 Citations]
  • 24. Ali Cakmak, Gultekin Özsoyoglu: Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9: (2008). [10 Citations]
  • 25. Ali Cakmak, Gultekin Özsoyoglu: Taxonomy-superimposed graph mining. EDBT 2008: 217-228. [19 Citations]

2007 (4)

  • 26. Ali Cakmak, Gultekin Özsoyoglu: Mining biological networks for unknown pathways. Bioinformatics 23(20):2775-2783 (2007). [34 Citations]
  • 27. Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Z. Meral Özsoyoglu, Gultekin Özsoyoglu: Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. SSDBM 2007: 33. [9 Citations]
  • 28. Ali Cakmak, Gultekin Özsoyoglu: Annotating Genes Using Textual Patterns. Pacific Symposium on Biocomputing 2007: 221-232. [13 Citations]
  • 29. Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Özsoyoglu: Evaluating Different Ranking Functions for Context-Based Literature Search. ICDE Workshops 2007: 261-268. [5 Citations]

2006 (2)

  • 30. Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu: On Data and Visualization Models for Signaling Pathways. SSDBM 2006: 133-142. [4 Citations]
  • 31. Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu: Task-Oriented Integrated Use of Biological Web Data Sources. SSDBM 2006: 81-90.

2005 (2)

  • 32. Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Özsoyoglu, Abdullah Al-Hamdani: Evaluating Publication Similarity Measures. IEEE Data Eng. Bull. 28(4):21-28 (2005). [17 Citations]
  • 33. Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Özsoyoglu: Evaluating Score and Publication Similarity Functions in Digital Libraries. ICADL 2005: 483-485. [8 Citations]

Patents (3)

  • 1. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating hybrid and top-frequency histograms - US Patent App 15/295,539 2016.
  • 2. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating and using data that indicates misestimates of actual costs - US Patent 9471631 2016. [1 Citation]
  • 3. Emrullah Delibas, Ali Uzun, M. Fatih Inan, Onur Guzey, Ali Cakmak. Exploratory Soccer Data Analytics. PCT/TR Patent App. 2016/050507 & 2016/12725.

Journal Papers (13)

  • 4. Ali Cakmak: Predicting Student Success in Courses via Collaborative Filtering. International Journal of Intelligent Systems and Applications in Engineering 5(1):10-17 (2017).
  • 5. Ali akmak, Serpil Kaya: Parallel Surfaces of General Cylinder. Journal of Logic, Mathematics and Linguistics in Applied Sciences 1(1): (2016).
  • 6. Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu: An online system for metabolic network analysis. Database 2014: (2014). [3 Citations]
  • 7. Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Systems Biology 6:67 (2012). [7 Citations]
  • 8. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu: A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinformatics and Computational Biology 10(1): (2012). [7 Citations]
  • 9. 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.
  • 10. Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercument Cicek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB architecture and database design. BMC Systems Biology 5:188 (2011). [11 Citations]
  • 11. Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson: Querying metabolism under Different Physiological Constraints. J. Bioinformatics and Computational Biology 8(2):247-293 (2010). [6 Citations]
  • 12. Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Özsoyoglu: Context-based literature digital collection search. VLDB J. 18(1):277-301 (2009). [21 Citations]
  • 13. Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase: pathways database system. Bioinformatics 24(21):2526-2533 (2008). [51 Citations]
  • 14. Ali Cakmak, Gultekin Özsoyoglu: Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9: (2008). [10 Citations]
  • 15. Ali Cakmak, Gultekin Özsoyoglu: Mining biological networks for unknown pathways. Bioinformatics 23(20):2775-2783 (2007). [34 Citations]
  • 16. Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Özsoyoglu, Abdullah Al-Hamdani: Evaluating Publication Similarity Measures. IEEE Data Eng. Bull. 28(4):21-28 (2005). [17 Citations]

Conference / Workshop Papers (17)

  • 17. Feruz Davletov, Ali Selman Aydin, Ali Cakmak: High Impact Academic Paper Prediction Using Temporal and Topological Features. CIKM 2014: 491-498. [7 Citations]
  • 18. A.Bulut, T. Arıcı, O. Guzey, B. Arslan and A. Cakmak. "Training the Data Scientists of the Future", Big Data and Analytics Education Conference (EDCON), 2014.
  • 19. A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu: PathCase-MAW: An Online Metabolic Network Analysis Workbench. BCB 2013: 219.
  • 20. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu: Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB 2011: 387-392. [3 Citations]
  • 21. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu: Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. BCB 2010: 137-146. [8 Citations]
  • 22. En Cheng, Ali Cakmak, Z. Meral Özsoyoglu: Efficient query evaluation for DAG-shaped hierarchies. BCB 2010: 454-456. [4 Citations]
  • 23. Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Advanced querying interface for biochemical network databases. SAC 2010: 1526-1533. [7 Citations]
  • 24. Ali Cakmak, Mustafa Kirac, Gultekin Özsoyoglu: PopulusLog: People information database. ISCIS 2009: 165-170.
  • 25. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: A web-based data source for metabolomics. ISCIS 2009: 454-459. [3 Citations]
  • 26. 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): 2009. [2 Citations]
  • 27. Ali Cakmak, Gultekin Özsoyoglu: Taxonomy-superimposed graph mining. EDBT 2008: 217-228. [19 Citations]
  • 28. Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Z. Meral Özsoyoglu, Gultekin Özsoyoglu: Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. SSDBM 2007: 33. [9 Citations]
  • 29. Ali Cakmak, Gultekin Özsoyoglu: Annotating Genes Using Textual Patterns. Pacific Symposium on Biocomputing 2007: 221-232. [13 Citations]
  • 30. Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Özsoyoglu: Evaluating Different Ranking Functions for Context-Based Literature Search. ICDE Workshops 2007: 261-268. [5 Citations]
  • 31. Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu: On Data and Visualization Models for Signaling Pathways. SSDBM 2006: 133-142. [4 Citations]
  • 32. Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu: Task-Oriented Integrated Use of Biological Web Data Sources. SSDBM 2006: 81-90.
  • 33. Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Özsoyoglu: Evaluating Score and Publication Similarity Functions in Digital Libraries. ICADL 2005: 483-485. [8 Citations]
  • 1. Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase: pathways database system. Bioinformatics 24(21):2526-2533 (2008). [51 Citations]
  • 2. Ali Cakmak, Gultekin Özsoyoglu: Mining biological networks for unknown pathways. Bioinformatics 23(20):2775-2783 (2007). [34 Citations]
  • 3. Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Özsoyoglu: Context-based literature digital collection search. VLDB J. 18(1):277-301 (2009). [21 Citations]
  • 4. Ali Cakmak, Gultekin Özsoyoglu: Taxonomy-superimposed graph mining. EDBT 2008: 217-228. [19 Citations]
  • 5. Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Özsoyoglu, Abdullah Al-Hamdani: Evaluating Publication Similarity Measures. IEEE Data Eng. Bull. 28(4):21-28 (2005). [17 Citations]
  • 6. Ali Cakmak, Gultekin Özsoyoglu: Annotating Genes Using Textual Patterns. Pacific Symposium on Biocomputing 2007: 221-232. [13 Citations]
  • 7. Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercument Cicek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB architecture and database design. BMC Systems Biology 5:188 (2011). [11 Citations]
  • 8. Ali Cakmak, Gultekin Özsoyoglu: Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9: (2008). [10 Citations]
  • 9. Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Z. Meral Özsoyoglu, Gultekin Özsoyoglu: Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. SSDBM 2007: 33. [9 Citations]
  • 10. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu: Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. BCB 2010: 137-146. [8 Citations]
  • 11. Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Özsoyoglu: Evaluating Score and Publication Similarity Functions in Digital Libraries. ICADL 2005: 483-485. [8 Citations]
  • 12. Feruz Davletov, Ali Selman Aydin, Ali Cakmak: High Impact Academic Paper Prediction Using Temporal and Topological Features. CIKM 2014: 491-498. [7 Citations]
  • 13. Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Systems Biology 6:67 (2012). [7 Citations]
  • 14. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu: A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinformatics and Computational Biology 10(1): (2012). [7 Citations]
  • 15. Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Advanced querying interface for biochemical network databases. SAC 2010: 1526-1533. [7 Citations]
  • 16. Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson: Querying metabolism under Different Physiological Constraints. J. Bioinformatics and Computational Biology 8(2):247-293 (2010). [6 Citations]
  • 17. Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Özsoyoglu: Evaluating Different Ranking Functions for Context-Based Literature Search. ICDE Workshops 2007: 261-268. [5 Citations]
  • 18. En Cheng, Ali Cakmak, Z. Meral Özsoyoglu: Efficient query evaluation for DAG-shaped hierarchies. BCB 2010: 454-456. [4 Citations]
  • 19. Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu: On Data and Visualization Models for Signaling Pathways. SSDBM 2006: 133-142. [4 Citations]
  • 20. Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu: An online system for metabolic network analysis. Database 2014: (2014). [3 Citations]
  • 21. Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu: Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB 2011: 387-392. [3 Citations]
  • 22. Ali Cakmak, Arun Dsouza, Richard W. Hanson, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: A web-based data source for metabolomics. ISCIS 2009: 454-459. [3 Citations]
  • 23. 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): 2009. [2 Citations]
  • 24. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating and using data that indicates misestimates of actual costs - US Patent 9471631 2016. [1 Citation]
  • 25. A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu: PathCase-MAW: An Online Metabolic Network Analysis Workbench. BCB 2013: 219.
  • 26. Ali Cakmak, Mustafa Kirac, Gultekin Özsoyoglu: PopulusLog: People information database. ISCIS 2009: 165-170.
  • 27. Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu: Task-Oriented Integrated Use of Biological Web Data Sources. SSDBM 2006: 81-90.
  • 28. A.Bulut, T. Arıcı, O. Guzey, B. Arslan and A. Cakmak. "Training the Data Scientists of the Future", Big Data and Analytics Education Conference (EDCON), 2014.
  • 29. 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.
  • 30. Sunil P Chakkappen, Mohamed Zait, Allison W Lee, Ali Cakmak: Creating hybrid and top-frequency histograms - US Patent App 15/295,539 2016.
  • 31. Ali Cakmak: Predicting Student Success in Courses via Collaborative Filtering. International Journal of Intelligent Systems and Applications in Engineering 5(1):10-17 (2017).
  • 32. Emrullah Delibas, Ali Uzun, M. Fatih Inan, Onur Guzey, Ali Cakmak. Exploratory Soccer Data Analytics. PCT/TR Patent App. 2016/050507 & 2016/12725.
  • 33. Ali akmak, Serpil Kaya: Parallel Surfaces of General Cylinder. Journal of Logic, Mathematics and Linguistics in Applied Sciences 1(1): (2016).
İstanbul Şehir University
Altunizade Mah. Oymacı Sok. No: 15
34660 Istanbul, Turkey
Email: cs@sehir.edu.tr
Phone: +90 216 559 9000