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CAKMAK LAB

Publications

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2022

Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models
Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models
Ali Cakmak, Huzeyfe Ayaz, Soykan Arıkan, Ali R. Ibrahimzada, Şeyda Demirkol, Dilara Sönmez, Mehmet T. Hakan, Saime T. Sürmen, Cem Horozoğlu, Mehmet B. Doğan, Özlem Küçükhüseyin, Canan Cacına, Bayram Kıran, Ümit Zeybek, Mehmet Baysan, İlhan Yaylım
Medical & Biological Engineering & Computing
Creating hybrid and top-frequency histograms
Creating hybrid and top-frequency histograms
Sunil P. Chakkappen, Mohamed Zait, Allison W. Lee, Ali Cakmak
US Patent

2021

Benchmarking Apache Spark and Hadoop MapReduce on Big Data Classification
Benchmarking Apache Spark and Hadoop MapReduce on Big Data Classification
Taha Tekdogan, Ali Cakmak
2021 5th International Conference on Cloud and Big Data Computing (ICCBDC)
Personalized Metabolic Analysis of Diseases
Personalized Metabolic Analysis of Diseases
Ali Cakmak, M. Hasan Celik
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Using positional sequence patterns to estimate the selectivity of SQL LIKE queries
Using positional sequence patterns to estimate the selectivity of SQL LIKE queries
Mehmet Aytimur, Ali Cakmak
Expert Systems with Applications

2020

Scalable classification of organisms into a taxonomy using hierarchical supervised learners
Scalable classification of organisms into a taxonomy using hierarchical supervised learners
Gihad N. Sohsah, Ali Reza Ibrahimzada, Huzeyfe Ayaz, Ali Cakmak
Journal of Bioinformatics and Computational Biology
Exploring the power of supervised learning methods for company name disambiguation in microblog posts
Exploring the power of supervised learning methods for company name disambiguation in microblog posts
Esma Nafiye POLAT, Ali ÇAKMAK, Rabia Nuray TURAN
TURKISH JOURNAL OF ELECTRICAL ENGINEERING & COMPUTER SCIENCES

2019

A system and method for sportsman training
A system and method for sportsman training
Emrullah Delibas, Ali Uzun, Mehmet Fatih Inan, Onur Guzey, Ali Cakmak
US Patent
Interactive exploratory soccer data analytics
Interactive exploratory soccer data analytics
Emrullah Delibas, Ali Uzun, Mehmet Fatih Inan, Onur Guzey, Ali Cakmak
INFOR: Information Systems and Operational Research

2018

Estimating the selectivity of LIKE queries using pattern-based histograms
Estimating the selectivity of LIKE queries using pattern-based histograms
Mehmet AYTİMUR, Ali ÇAKMAK
TURKISH JOURNAL OF ELECTRICAL ENGINEERING & COMPUTER SCIENCES
COMPUTATIONAL MODELING OF PASS EFFECTIVENESS IN SOCCER
COMPUTATIONAL MODELING OF PASS EFFECTIVENESS IN SOCCER
ALI CAKMAK, ALI UZUN, EMRULLAH DELIBAS
Advances in Complex Systems

2017

Predicting Student Success in Courses via Collaborative Filtering
Predicting Student Success in Courses via Collaborative Filtering
Ali Cakmak
International Journal of Intelligent Systems and Applications in Engineering

2016

Creating and using data that indicates misestimates of actual costs
Creating and using data that indicates misestimates of actual costs
Sunil P. Chakkappen, Mohamed Zait, Allison W. Lee, Ali Cakmak
US Patent

2014

High Impact Academic Paper Prediction Using Temporal and Topological Features
High Impact Academic Paper Prediction Using Temporal and Topological Features
Feruz Davletov, Ali Selman Aydin, Ali Cakmak
Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management
Training the Data Scientists of the Future
Training the Data Scientists of the Future
Ahmet Bulut, Tarik Arici, Onur Guzey, Baris Arslan, Ali Cakmak
BIG DATA AND ANALYTICS EDUCATION CONFERENCE
An online system for metabolic network analysis
An online system for metabolic network analysis
A. E. Cicek, X. Qi, A. Cakmak, S. R. Johnson, X. Han, S. Alshalwi, Z. M. Ozsoyoglu, G. Ozsoyoglu
Database

2013

PathCase-MAW
PathCase-MAW
A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Ozsoyoglu
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Oracle Database SQL Tuning Guide, 12c Release 1 (12.1) E15858-15
Oracle Database SQL Tuning Guide, 12c Release 1 (12.1) E15858-15
Pete Belknap, Ali Cakmak, Sunil Chakkappen, Immanuel Chan, Deba Chatterjee, Dinesh Das, Leonidas Galanis, Bruce Golbus, Shantanu Joshi, Tom Kyte, Allison Lee, Sue Lee, David McDermid, Colin McGregor, Hong Su, Murali Thiyagarajah, Mark Townsend, Randy Urbano, Bharath Venkatakrishnan, Hailing Yu
Case Western Reserve University

2012

PathCase-SB
PathCase-SB
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. Özsoyoǧlu, Z. M. Özsoyoǧlu
ACM SIGBioinformatics Record
PathCase-SB: integrating data sources and providing tools for systems biology research
PathCase-SB: integrating data sources and providing tools for systems biology research
Sarp A Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A Ercument Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K Dash, Nicola Lai, Gultekin Ozsoyoglu, Zehra Meral Ozsoyoglu
BMC Systems Biology
A NEW METABOLOMICS ANALYSIS TECHNIQUE: STEADY-STATE METABOLIC NETWORK DYNAMICS ANALYSIS
A NEW METABOLOMICS ANALYSIS TECHNIQUE: STEADY-STATE METABOLIC NETWORK DYNAMICS ANALYSIS
ALI CAKMAK, XINJIAN QI, A. ERCUMENT CICEK, ILYA BEDERMAN, LEIGH HENDERSON, MITCHELL DRUMM, GULTEKIN OZSOYOGLU
Journal of Bioinformatics and Computational Biology

2011

PathCase-SB architecture and database design
PathCase-SB architecture and database design
Ali Cakmak, Xinjian Qi, Sarp A Coskun, Mitali Das, En Cheng, A Ercument Cicek, Nicola Lai, Gultekin Ozsoyoglu, Z Meral Ozsoyoglu
BMC Systems Biology
Computational interpretation of metabolomics measurements
Computational interpretation of metabolomics measurements
Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoǧlu
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine

2010

Efficient query evaluation for DAG-shaped hierarchies
Efficient query evaluation for DAG-shaped hierarchies
En Cheng, Ali Cakmak, Z. Meral Ozsoyoglu
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Analyzing metabolite measurements for automated prediction of underlying biological mechanisms
Analyzing metabolite measurements for automated prediction of underlying biological mechanisms
Ali Cakmak, Arun Dsouza, Richard W. Hanson, Meral Ozsoyoglu
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
QUERYING METABOLISM UNDER DIFFERENT PHYSIOLOGICAL CONSTRAINTS
QUERYING METABOLISM UNDER DIFFERENT PHYSIOLOGICAL CONSTRAINTS
ALI CAKMAK, GULTEKIN OZSOYOGLU, RICHARD W. HANSON
Journal of Bioinformatics and Computational Biology
Advanced querying interface for biochemical network databases
Advanced querying interface for biochemical network databases
Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu
Proceedings of the 2010 ACM Symposium on Applied Computing

2009

Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing
Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing
Ali Cakmak, Gultekin Ozsoyoglu, Richard W Hanson
8th International Conference on Computational Systems Bioinformatics (CSB)
A web-based data source for metabolomics
A web-based data source for metabolomics
Ali Cakmak, Arun Dsouza, Richard Hanson, Gultekin Ozsoyoglu, Meral Ozsoyoglu
2009 24th International Symposium on Computer and Information Sciences
PopulusLog: People information database
PopulusLog: People information database
Ali Cakmak, Mustafa Kirac, Gultekin Ozsoyoglu
2009 24th International Symposium on Computer and Information Sciences
Corrigendum for Elliott,B. et al., 'PathCase pathways database system', Bioinformatics, Nov. 2008, 24(21), pp. 2526-2533
Corrigendum for Elliott,B. et al., 'PathCase pathways database system', Bioinformatics, Nov. 2008, 24(21), pp. 2526-2533
B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. M. Ozsoyoglu
Bioinformatics
Mining Metabolic Networks and Biomedical Literature
Mining Metabolic Networks and Biomedical Literature
Ali Cakmak
Case Western Reserve University

2008

PathCase: pathways database system
PathCase: pathways database system
Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, Zehra Meral Ozsoyoglu
Bioinformatics
Context-based literature digital collection search
Context-based literature digital collection search
Nattakarn Ratprasartporn, Jonathan Po, Ali Cakmak, Sulieman Bani-Ahmad, Gultekin Ozsoyoglu
The VLDB Journal
Taxonomy-superimposed graph mining
Taxonomy-superimposed graph mining
Ali Cakmak, Gultekin Ozsoyoglu
Proceedings of the 11th international conference on Extending database technology: Advances in database technology
Discovering gene annotations in biomedical text databases
Discovering gene annotations in biomedical text databases
Ali Cakmak, Gultekin Ozsoyoglu
BMC Bioinformatics

2007

Mining biological networks for unknown pathways
Mining biological networks for unknown pathways
Ali Cakmak, Gultekin Ozsoyoglu
Bioinformatics
Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways
Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways
Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Zehra M. Ozsoyoglu, Gultekin Ozsoyoglu
19th International Conference on Scientific and Statistical Database Management (SSDBM 2007)
Evaluating Different Ranking Functions for Context-Based Literature Search
Evaluating Different Ranking Functions for Context-Based Literature Search
Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin Ozsoyoglu
2007 IEEE 23rd International Conference on Data Engineering Workshop

2006

ANNOTATING GENES USING TEXTUAL PATTERNS
ANNOTATING GENES USING TEXTUAL PATTERNS
ALI CAKMAK, GULTEKIN OZSOYOGLU
Biocomputing 2007
On Data and Visualization Models for Signaling Pathways
On Data and Visualization Models for Signaling Pathways
N. Ratprasartporn, A. Cakmak, G. Ozsoyoglu
18th International Conference on Scientific and Statistical Database Management (SSDBM'06)
Task-Oriented Integrated Use of Biological Web Data Sources
Task-Oriented Integrated Use of Biological Web Data Sources
M. Kirac, A. Cakmak, G. Ozsoyoglu
18th International Conference on Scientific and Statistical Database Management (SSDBM'06)

2005

Evaluating Score and Publication Similarity Functions in Digital Libraries
Evaluating Score and Publication Similarity Functions in Digital Libraries
S. Bani-Ahmad, A. Cakmak, A. Al-Hamdani, Gultekin Ozsoyoglu
Digital Libraries: Implementing Strategies and Sharing Experiences

2003

HITS- AND PAGERANK-BASED IMPORTANCE SCORE COMPUTATIONS FOR ACM ANTHOLOGY PAPERS
HITS- AND PAGERANK-BASED IMPORTANCE SCORE COMPUTATIONS FOR ACM ANTHOLOGY PAPERS
Ali Cakmak
Tech. Report, CWRU