Mining Metabolic Networks and Biomedical Literature (2009)
With the advent of high-throughput experimental and genome sequencing technologies, the amounts of produced biological data and the related literature have increased dramatically. A significant...
HITS- and PageRank-based importance score computations for ACM anthology papers (2008)
With the rapid growth in the amount of data available to the public, in recent years, applications that search for the resources containing a given topic or a phrase, are becoming more and more...
Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-ahmad, Gultekin Ozsoyoglu, G. Ozsoyoglu, ...
Abstract We identify two issues with searching literature digital collections within digital libraries: (a) there are no effective paper-scoring and ranking mechanisms. Without a scoring and ranking...
Sulieman Bani-ahmad, Ali Cakmak, Gultekin Ozsoyoglu, Abdullah Al-hamdani, Xiaoyan Yu, O Das-neves, ...
The Bulletin of the Technical Committee on Data Engineering is published quarterly and is distributed to all TC members. Its scope includes the design, implementation, modelling, theory and...
Data and text mining Mining Biological Networks for Unknown Pathways (2008)
Ali Cakmak, Gultekin Ozsoyoglu, Prof John Quackenbush
Motivation: Biological pathways provide significant insights on the interaction mechanisms of molecules. Presently, many essential pathways still remain unknown or incomplete for newly sequenced...
Evaluating Publication Similarity Measures (2008)
Sulieman Bani-ahmad, Ali Cakmak, Gultekin Ozsoyoglu, Abdullah Al-hamdani
Publication searching based on keywords provided by users is traditional in digital libraries. While useful in many circumstances, the success of locating related publications via keyword-based...
ANNOTATING GENES USING TEXTUAL PATTERNS (2008)
Ali Cakmak, Gultekin Ozsoyoglu
Annotating genes with Gene Ontology (GO) terms is crucial for biologists to characterize the traits of genes in a standardized way. However, manual curation of textual data, the most reliable form of...
On Data and Visualization Models for Signaling Pathways (2008)
Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Ozsoyoglu
Signaling pathways are chains of interacting proteins, through which the cell converts a (usually) extracellular signal into a biological response. The number of known signaling pathways in the...
Discovering gene annotations in biomedical text databases (2008)
Cakmak, Ali, Ozsoyoglu, Gultekin
Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about...
Discovering gene annotations in biomedical text databases. (2008)
Cakmak, Ali, Ozsoyoglu, Gultekin
BACKGROUND: Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a...
PathCase: pathways database system (2008)
Elliott, Brendan, Kirac, Mustafa, Cakmak, Ali, Yavas, Gokhan, Mayes, Stephen, Cheng, En, ...
Motivation: As the blueprints of cellular actions, biological pathways characterize the roles of genomic entities in various cellular mechanisms, and as such, their availability, manipulation and...
Mining biological networks for unknown pathways (2007)
Cakmak, Ali, Ozsoyoglu, Gultekin
Motivation: Biological pathways provide significant insights on the interaction mechanisms of molecules. Presently, many essential pathways still remain unknown or incomplete for newly sequenced...