Evaluating Score and Publication Similarity Functions in Digital Libraries. - Sulieman Bani-Ahmad; Ali Cakmak 001; Abdullah Al-Hamdani; Gultekin Özsoyoglu (ICADL, 2005)

Evaluating Publication Similarity Measures. - Sulieman Bani-Ahmad; Ali Cakmak 001; Gultekin Özsoyoglu; Abdullah Al-Hamdani (IEEE Data Eng. Bull., 2005)

Task-Oriented Integrated Use of Biological Web Data Sources. - Mustafa Kirac; Ali Cakmak 001; Gultekin Özsoyoglu (SSDBM, 2006)

On Data and Visualization Models for Signaling Pathways. - Nattakarn Ratprasartporn; Ali Cakmak 001; Gultekin Özsoyoglu (SSDBM, 2006)

Evaluating Different Ranking Functions for Context-Based Literature Search. - Nattakarn Ratprasartporn; Sulieman Bani-Ahmad; Ali Cakmak 001; Jonathan Po; Gultekin Özsoyoglu (ICDE Workshops, 2007)

Annotating Genes Using Textual Patterns. - Ali Cakmak 001; Gultekin Özsoyoglu (Pacific Symposium on Biocomputing, 2007)

Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. - Ali Cakmak 001; Mustafa Kirac; Marc R. Reynolds; Z. Meral Özsoyoglu; Gultekin Özsoyoglu (SSDBM, 2007)

Mining biological networks for unknown pathways. - Ali Cakmak 001; Gultekin Özsoyoglu (Bioinform., 2007)

Taxonomy-superimposed graph mining. - Ali Cakmak 001; Gultekin Özsoyoglu (EDBT, 2008)

PathCase: pathways database system. - Brendan Elliott; Mustafa Kirac; Ali Cakmak 001; Gökhan Yavas; Stephen Mayes; En Cheng; Yuan Wang; Chirag Gupta; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (Bioinform., 2008)

Discovering gene annotations in biomedical text databases. - Ali Cakmak 001; Gultekin Özsoyoglu (BMC Bioinform., 2008)

A web-based data source for metabolomics. - Ali Cakmak 001; Arun Dsouza; Richard W. Hanson; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (ISCIS, 2009)

PopulusLog: People information database. - Ali Cakmak 001; Mustafa Kirac; Gultekin Özsoyoglu (ISCIS, 2009)

Corrigendum for Elliott, B. et al., 'PathCase pathways database system', Bioinformatics 2008, 24(21) 2526-2533. - Brendan Elliott; Mustafa Kirac; Ali Cakmak 001; Gökhan Yavas; Stephen Mayes; En Cheng; Yuan Wang; Chirag Gupta; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (Bioinform., 2009)

Context-based literature digital collection search. - Nattakarn Ratprasartporn; Jonathan Po; Ali Cakmak 001; Sulieman Bani-Ahmad; Gultekin Özsoyoglu (VLDB J., 2009)

Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. - Ali Cakmak 001; Arun Dsouza; Richard W. Hanson; Z. Meral Özsoyoglu (BCB, 2010)

Efficient query evaluation for DAG-shaped hierarchies. - En Cheng; Ali Cakmak 001; Z. Meral Özsoyoglu (BCB, 2010)

Advanced querying interface for biochemical network databases. - Brendan Elliott; Stephen Mayes; Ali Cakmak 001; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (SAC, 2010)

Querying metabolism under Different Physiological Constraints. - Ali Cakmak 001; Gultekin Özsoyoglu; Richard W. Hanson (J. Bioinform. Comput. Biol., 2010)

Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. - Ali Cakmak 001; Xinjian Qi; A. Ercüment Çiçek; Gultekin Özsoyoglu (BCB, 2011)

PathCase-SB architecture and database design. - Ali Cakmak 001; Xinjian Qi; Sarp A. Coskun; Mitali Das; En Cheng; A. Ercüment Çiçek; Nicola Lai; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (BMC Syst. Biol., 2011)

PathCase-SB: integrating data sources and providing tools for systems biology research. - Sarp A. Coskun; Xinjian Qi; Ali Cakmak 001; En Cheng; A. Ercüment Çiçek; Lei Yang; Rishiraj Jadeja; Ranjan K. Dash; Nicola Lai; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (BMC Syst. Biol., 2012)

A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. - Ali Cakmak 001; Xinjian Qi; A. Ercüment Çiçek; Ilya Bederman; Leigh Henderson; Mitchell L. Drumm; Gultekin Özsoyoglu (J. Bioinform. Comput. Biol., 2012)

PathCase-MAW: An Online Metabolic Network Analysis Workbench. - A. Ercüment Çiçek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Gultekin Özsoyoglu (BCB, 2013)

High Impact Academic Paper Prediction Using Temporal and Topological Features. - Feruz Davletov; Ali Selman Aydin; Ali Cakmak 001 (CIKM, 2014)

An online system for metabolic network analysis. - Abdullah Ercument Cicek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Zehra Meral Özsoyoglu; Gultekin Özsoyoglu (Database J. Biol. Databases Curation, 2014)

Computational Modeling of Pass Effectiveness in Soccer. - Ali Cakmak 001; Ali Uzun; Emrullah Delibas (Adv. Complex Syst., 2018)

Estimating the selectivity of LIKE queries using pattern-based histograms. - Mehmet Aytimur; Ali Cakmak 001 (Turkish J. Electr. Eng. Comput. Sci., 2018)

Interactive exploratory soccer data analytics. - Emrullah Delibas; Ali Uzun; Mehmet Fatih Inan; Onur Guzey; Ali Cakmak 001 (INFOR Inf. Syst. Oper. Res., 2019)

Exploring the power of supervised learning methods for company name disambiguation in microblog posts. - Esma Nafiye Polat; Ali Cakmak 001; Rabia Nuray-Turan (Turkish J. Electr. Eng. Comput. Sci., 2020)

Scalable classification of organisms into a taxonomy using hierarchical supervised learners. - Gihad N. Sohsah; Ali Reza Ibrahimzada; Huzeyfe Ayaz; Ali Cakmak 001 (J. Bioinform. Comput. Biol., 2020)

Benchmarking Apache Spark and Hadoop MapReduce on Big Data Classification. - Taha Tekdogan; Ali Cakmak 001 (ICCBDC, 2021)

Using positional sequence patterns to estimate the selectivity of SQL LIKE queries. - Mehmet Aytimur; Ali Cakmak 001 (Expert Syst. Appl., 2021)

Personalized Metabolic Analysis of Diseases. - Ali Cakmak 001; M. Hasan Celik (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models. - Ali Cakmak 001; Huzeyfe Ayaz; Soykan Arikan; Ali Reza Ibrahimzada; Seyda Demirkol; Dilara Sönmez; Mehmet T. Hakan; Saime T. Sürmen; Cem Horozoglu; Mehmet B. Dogan; Özlem Küçükhüseyin; Canan Cacina; et al. (Medical Biol. Eng. Comput., 2023)