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2024

VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison
VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison
Abdullah Asım Emül, Mehmet Arif Ergün, Rumeysa Aslıhan Ertürk, Ömer Çinal, Mehmet Baysan
BMC Bioinformatics
COSAP: Comparative Sequencing Analysis Platform
COSAP: Comparative Sequencing Analysis Platform
Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül, Mehmet Baysan
BMC Bioinformatics
Improving somatic exome sequencing performance by biological replicates
Improving somatic exome sequencing performance by biological replicates
Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun, Mehmet Baysan
BMC Bioinformatcs

2022

Abstract A029: Investigating primary colorectal cancer tumor and liver metastasis clonality through whole exome sequencing of synchronous biopsies
Abstract A029: Investigating primary colorectal cancer tumor and liver metastasis clonality through whole exome sequencing of synchronous biopsies
Duygu Altinok Dindar, Batuhan Kısakol, Sahin Sarihan, Mehmet Arif Ergun, John Cheney, Emel Ergul, Nihal Uren, Ender Dulundu, Emine Bozkurtlar, Nihat Zafer Utkan, Mehmet Baysan
Cancer Research
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
Ranan Aktas, 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
DATA SCIENCE, CANCER AND SEQUENCING ANALYSES
DATA SCIENCE, CANCER AND SEQUENCING ANALYSES
Mehmet Baysan
Sağlık Bilimlerinde İleri Araştırmalar Dergisi / Journal of Advanced Research in Health Sciences

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
Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels
Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels
Batuhan KISAKOL, Şahin SARIHAN, Mehmet Arif ERGÜN, Mehmet BAYSAN
TURKISH JOURNAL OF BIOLOGY
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

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
Homojen Glioblastoma Örneklerinin Yüksek Çözünürlüklü Genetik Teknolojiler ile Analizi
Homojen Glioblastoma Örneklerinin Yüksek Çözünürlüklü Genetik Teknolojiler ile Analizi
Mehmet Baysan
Academic Platform Journal of Engineering and Science
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

Detailed longitudinal sampling of glioma stem cells <i>in situ</i> reveals Chr7 gain and Chr10 loss as repeated events in primary tumor formation and recurrence
Detailed longitudinal sampling of glioma stem cells in situ reveals Chr7 gain and Chr10 loss as repeated events in primary tumor formation and recurrence
Mehmet Baysan, Kevin Woolard, Margaret C. Cam, Wei Zhang, Hua Song, Svetlana Kotliarova, Demosthenes Balamatsias, Amanda Linkous, Susie Ahn, Jennifer Walling, Galina I. Belova, Howard A. Fine
International Journal of Cancer
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

Gene expression profiles of autophagy-related genes in multiple sclerosis
Gene expression profiles of autophagy-related genes in multiple sclerosis
Mehri Igci, Mehmet Baysan, Remzi Yigiter, Mustafa Ulasli, Sirma Geyik, Recep Bayraktar, İbrahim Bozgeyik, Esra Bozgeyik, Ali Bayram, Ecir Ali Cakmak
Gene

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
SC-04 * NON-UNIFORM NOTCH SIGNALING UNDERLIES HETEROGENEITY WITHIN THE GLIOBLASTOMA STEM CELL POPULATION
SC-04 * NON-UNIFORM NOTCH SIGNALING UNDERLIES HETEROGENEITY WITHIN THE GLIOBLASTOMA STEM CELL POPULATION
N. Sumru Bayin, S. Si, A. Modrek, H.-R. Song, D. Zagzag, D. M. Hoang, Y. Z. Wadghiri, I. Dolgalev, M. Baysan, A. Heguy, M. H. Barcellos-Hoff, D. Placantonakis
Neuro-Oncology
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
Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells
Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells
Mehmet Baysan, Kevin Woolard, Serdar Bozdag, Gregory Riddick, Svetlana Kotliarova, Margaret C. Cam, Galina I. Belova, Susie Ahn, Wei Zhang, Hua Song, Jennifer Walling, Holly Stevenson, Paul Meltzer, Howard A. Fine
PLoS ONE
Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes”
Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes”
Serdar Bozdag, Aiguo Li, Mehmet Baysan, Howard A. Fine
Cancer Informatics

2013

Approximation algorithm for the on-line multi-customer two-level supply chain scheduling problem
Approximation algorithm for the on-line multi-customer two-level supply chain scheduling problem
Igor Averbakh, Mehmet Baysan
Operations Research Letters
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
Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels
Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels
Serdar Bozdag, Aiguo Li, Gregory Riddick, Yuri Kotliarov, Mehmet Baysan, Fabio M. Iwamoto, Margaret C. Cam, Svetlana Kotliarova, Howard A. Fine
PLoS ONE
Batching and delivery in semi-online distribution systems
Batching and delivery in semi-online distribution systems
Igor Averbakh, Mehmet Baysan
Discrete Applied Mathematics

2012

Histone Demethylase Jumonji D3 (JMJD3) as a Tumor Suppressor by Regulating p53 Protein Nuclear Stabilization
Histone Demethylase Jumonji D3 (JMJD3) as a Tumor Suppressor by Regulating p53 Protein Nuclear Stabilization
Chibawanye I. Ene, Lincoln Edwards, Gregory Riddick, Mehmet Baysan, Kevin Woolard, Svetlana Kotliarova, Chen Lai, Galina Belova, Maggie Cam, Jennifer Walling, Ming Zhou, Holly Stevenson, Hong Sug Kim, Keith Killian, Timothy Veenstra, Rolanda Bailey, Hua Song, Wei Zhang, Howard A. Fine
PLoS ONE
G-Cimp Status Prediction Of Glioblastoma Samples Using mRNA Expression Data
G-Cimp Status Prediction Of Glioblastoma Samples Using mRNA Expression Data
Mehmet Baysan, Serdar Bozdag, Margaret C. Cam, Svetlana Kotliarova, Susie Ahn, Jennifer Walling, Jonathan K. Killian, Holly Stevenson, Paul Meltzer, Howard A. Fine
PLoS ONE
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
Polynomial time solution to minimum forwarding set problem in wireless networks under disk coverage model
Polynomial time solution to minimum forwarding set problem in wireless networks under disk coverage model
Mehmet Baysan, Kamil Sarac, R. Chandrasekaran
Ad Hoc Networks
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

Semi-online two-level supply chain scheduling problems
Semi-online two-level supply chain scheduling problems
Igor Averbakh, Mehmet Baysan
Journal of Scheduling
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
On a labeling problem in graphs
On a labeling problem in graphs
R. Chandrasekaran, M. Dawande, M. Baysan
Discrete Applied Mathematics

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

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
A Polynomial Time Solution to Minimum Forwarding Set Problem in Wireless Networks under Unit Disk Coverage Model
A Polynomial Time Solution to Minimum Forwarding Set Problem in Wireless Networks under Unit Disk Coverage Model
M. Baysan, K. Sarac, R. Chandrasekaran, S. Bereg
IEEE Transactions on Parallel and Distributed Systems

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
Variable power broadcast using local information in ad hoc networks
Variable power broadcast using local information in ad hoc networks
Avinash Chiganmi, Mehmet Baysan, Kamil Sarac, Ravi Prakash
Ad Hoc Networks
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)
Cluster Based Approaches for End-to-End Complete Feedback Collection in Multicast
Cluster Based Approaches for End-to-End Complete Feedback Collection in Multicast
M. Baysan, K. Sarac
2006 IEEE International Performance Computing and Communications Conference

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

2004

Improving energy savings in power adaptive broadcasting in MANETs
Improving energy savings in power adaptive broadcasting in MANETs
M. Baysan, S. Gowdamachandran, K. Sarac
First International Conference on Broadband Networks