Ali Cakmak

Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell Drumm, Gultekin Özsoyoglu: A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinformatics and Computational Biology 10(1) (2012)

Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu: Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB 2011: 387-392

Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson: Querying metabolism under Different Physiological Constraints. J. Bioinformatics and Computational Biology 8(2): 247-293 (2010)

Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu: Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. BCB 2010: 137-146

En Cheng, Ali Cakmak, Z. Meral Özsoyoglu: Efficient query evaluation for DAG-shaped hierarchies. BCB 2010: 454-456

Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Advanced querying interface for biochemical network databases. SAC 2010: 1526-1533

Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: Corrigendum for Elliott, B. et al., 'PathCase pathways database system', Bioinformatics 2008, 24(21) 2526-2533. Bioinformatics 25(20): 2773 (2009)

Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Özsoyoglu: Context-based literature digital collection search. VLDB J. 18(1): 277-301 (2009)

Ali Cakmak, Mustafa Kirac, Gultekin Özsoyoglu: PopulusLog: People information database. ISCIS 2009: 165-170

Ali Cakmak, Arun Dsouza, Richard W. Hanson, Gultekin Özsoyoglu, Z. Meral Özsoyoglu: A web-based data source for metabolomics. ISCIS 2009: 454-459

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)

Ali Cakmak, Gultekin Özsoyoglu: Discovering gene annotations in biomedical text databases. BMC Bioinformatics 9 (2008)

Ali Cakmak, Gultekin Özsoyoglu: Taxonomy-superimposed graph mining. EDBT 2008: 217-228

Ali Cakmak, Gultekin Özsoyoglu: Mining biological networks for unknown pathways. Bioinformatics 23(20): 2775-2783 (2007)

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

Ali Cakmak, Gultekin Özsoyoglu: Annotating Genes Using Textual Patterns. Pacific Symposium on Biocomputing 2007: 221-232

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

Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu: Task-Oriented Integrated Use of Biological Web Data Sources. SSDBM 2006: 81-90

Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu: On Data and Visualization Models for Signaling Pathways. SSDBM 2006: 133-142

Sulieman Bani-Ahmad, Ali Cakmak, Gultekin Özsoyoglu, Abdullah Al-Hamdani: Evaluating Publication Similarity Measures. IEEE Data Eng. Bull. 28(4): 21-28 (2005)

Sulieman Bani-Ahmad, Ali Cakmak, Abdullah Al-Hamdani, Gultekin Özsoyoglu: Evaluating Score and Publication Similarity Functions in Digital Libraries. ICADL 2005: 483-485