ABU yazarı "Erten, Cesim" için Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering listeleme
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DriveWays: a method for identifying possibly overlapping driver pathways in cancer
Baali, Ilyes; Erten, Cesim; Kazan, Hilal (Nature Research, 2020)The majority of the previous methods for identifying cancer driver modules output nonoverlapping modules. This assumption is biologically inaccurate as genes can participate in multiple molecular pathways. This is particularly ... -
Global alignment of PPI networks
Erten, Cesim (Springer, 2021)Given multiple PPI networks from different species, the global PPI network alignment problem is that of providing a global mapping between the nodes of the networks or subnetworks within them. Functional orthology detection, ... -
Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes
Erten, Cesim; Dopazo, Joaquin (BMC Systems Biology, 2017)Background: Identification of driver genes related to certain types of cancer is an important research topic. Several systems biology approaches have been suggested, in particular for the identification of breast cancer ... -
Identification and prioritization of personalized cancer drivers
Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Taleb, Ahmed Amine (German Conference on Bioinformatics, 2022) -
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
Ahmed, Rafsan; Baali, Ilyes; Erten, Cesim; Hoxha, Evis; Kazan, Hilal (Bioinformatics, 2019)Motivation: Genomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem ... -
A network-centric framework for the evaluation of mutual exclusivity tests on cancer drivers
Ahmed, Rafsan; Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Yalcin, Cansu (Frontiers in Genetics, 2021)One of the key concepts employed in cancer driver gene identification is that of mutual exclusivity (ME); a driver mutation is less likely to occur in case of an earlier mutation that has common functionality in the same ... -
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers
Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Taleb Bahmed, Ahmed Amine (Bioinformatics, 2022)Motivation: A major challenge in cancer genomics is to distinguish the driver mutations that are causally linked to cancer from passenger mutations that do not contribute to cancer development. The majority of existing ... -
Ranking cancer drivers via betweenness-based outlier detection and random walks
Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal (BMC Bioinformatics, 2021)Background Recent cancer genomic studies have generated detailed molecular data on a large number of cancer patients. A key remaining problem in cancer genomics is the identification of driver genes. Results We propose ... -
SCITUNA: a network alignment approach for integrating multiple single-cell RNA-Seq datasets
Doğan, Onur; Erten, Burak Onur; Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Krichen, Mohamed; Marouf, Yacine (15th International Symposium on Health Informatics and Bioinformatics, 2022)The throughput and cost of single-cell RNA sequencing (scRNA-seq) are in continuous improvement, and so is the demand for larger-scale scRNA-seq data, which could require integrating multiple datasets from different ... -
Structure of conflict graphs in constraint alignment problems and algorithms
Alkan, Ferhat; Bıyıkoğlu, Türker; Demange, Marc; Erten, Cesim (Discrete Mathematics Theoretical Computer Science, 2019)We consider the constrained graph alignment problem which has applications in biological network analysis. Given two input graphs G1 = (V1, E1), G2 = (V2, E2), two vertices u1, v1 of G1 paired respectively to two vertices ...