Başlık için Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering listeleme

Toplam kayıt 35, listelenen: 8-27

    • 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 ...

    • A hybrid movie recommender system and rating prediction model 

      Çalışkan, Cafer; Sanwal, Muhammad (International Journal of Information Technology and Applied Sciences, 2021-07-01)
      In the current era, a rapid increase in data volume produces redundant information on the internet. This predicts the appropriate items for users a great challenge in information systems. As a result, recommender systems ...

    • Identification and prioritization of personalized cancer drivers 

      Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Taleb, Ahmed Amine (German Conference on Bioinformatics, 2022)

    • Inferring RBP-mediated regulation in lung squamous cell carcinoma 

      Lafzi, Atefeh; Kazan, Hilal (Plos One, 2016)
      RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation of mRNAs. Dysregulations in RBP-mediated mechanisms have been found to be associated with many steps of cancer initiation and progression. Despite ...

    • JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis 

      Kazan, Hilal; Çolak, Recep; Kim, TaeHyung; Oh, Yoomi; Cruz, Miguel; Valladares Salgado, Adan; Peralta, Jesus; Escobedo, Jorge; Parra, Esteban J.; Kim, Philip M.; Goldenberg, Anna (Bioinformatics, 2015)
      Motivation: Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype–phenotype associations at the resolution of individual markers. However, these associations explain ...

    • 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 ...

    • miR-223 exerts translational control of proatherogenic genes in macrophages 

      Nguyen, My-Anh; Hoang, Huy-Dung; Rasheed, Adil; Duchez, Anne-Claire; Wyatt, Hailey; Cottee, Mary Lynn; Graber, Tyson E.; Susser, Leah; Robichaud, Sabrina; Berber, İbrahim; Geoffrion, Michele; Ouimet, Mireille; Kazan, Hilal; Maegdefessel, Lars; Mulvihill, Erin E.; Alain, Tommy; Rayner, Katey J. (AHA Journals, 2022)
      Background: A significant burden of atherosclerotic disease is driven by inflammation. Recently, microRNAs (miRNAs) have emerged as important factors driving and protecting from atherosclerosis. miR-223 regulates cholesterol ...

    • MITF-MIR211 axis is a novel autophagy amplifier system during cellular stress 

      Öztürk, Deniz Gülfem; Koçak, Muhammed; Akçay, Arzu; Kınoğlu, Kubilay; Kara, Erdoğan; Büyük, Yalçın; Kazan, Hilal; Gözüaçık, Devrim (Autophagy, 2019)
      Macroautophagy (autophagy) is an evolutionarily conserved recycling and stress response mechanism. Active at basal levels in eukaryotes, autophagy is upregulated under stress providing cells with building blocks such as ...

    • Modeling gene regulation in liver hepatocellular carcinoma with random forests 

      Kazan, Hilal (BioMed Research International, 2016)
      Liver hepatocellular carcinoma (HCC) remains a leading cause of cancer-related death. Poor understanding of the mechanisms underlying HCC prevents early detection and leads to high mortality. We developed a random forest ...

    • Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation 

      HafezQorani, Saber; Lafzi, Atefeh; Bruin, Ruben G. de; Zonneveld, Anton Jan van; Veer, Eric P. van der; Aydın Son, Yeşim; Kazan, Hilal (Nucleic Acids Research, 2016)
      Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has ...

    • 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 ...

    • A new multi-party private set intersection protocol based on OPRFs 

      Bay, Aslı; Kayan, Anıl (Muğla Journal of Science and Technology, 2022-06-28)
      In many crucial real-world applications, parties must jointly perform some secure multi-party computation (MPC) while keeping their inputs hidden from other parties. Private Set Intersection (PSI), the specific area of ...

    • A novel fuzzy random forest model for meteorological drought classification and prediction in ungauged catchments 

      Danandeh Mehr, Ali; Tür, Rıfat; Cafer Çalışkan; Taş, Erkin (Pure and Applied Geophysics, 2020)
      This paper presents a new tree-based model, namely Fuzzy Random Forest (FRF), for one month ahead Standardized Precipitation Evapotranspiration Index (SPEI) classification and prediction with a noteworthy application in ...

    • The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool 

      Kolaj, Adelaida; Zahr, Siraj K.; Wang, Beatrix S.; Krawec, Taylor; Kazan, Hilal; Yang, Guang; Kaplan, David R.; Miller, Freda D. (Elsevier, 2023)
      Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that ...

    • 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 ...

    • Predicting clinical outcomes in neuroblastoma with genomic data integration 

      Baali, Ilyes; Acar, D. Alp Emre; Aderinwale, Tunde W.; HafezQorani, Saber; Kazan, Hilal (Biology Direct, 2018)
      Background: Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same risk group can still show variable prognosis. Recently collected ...

    • Prediction of VLDL cholesterol value with machine learning techniques 

      Çalışkan, Cafer; Uysal, İlhan (Springer, 2021)
      Cholesterol is an oil-like substance that is found in the membranes of animal cells and also carried in blood plasma, which has some vital functions in the human body, especially in the endocrine and digestive systems. ...

    • Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression 

      Bruin, Ruben G. de; Shiue, Lily; Prins, Jurrien; Boer, Hetty C. de; Singh, Anjana; Fagg, W. Samuel; Gils, Janine M. vans; Duijs, Jacques M. G. J.; Katzman, Sol; Kraaijeveld, Adriaan O.; Bohringer, Stefan; Leung, Wai Y.; Kielbasa, Szymon M.; Donahue, John P.; Zande, Patrick H. J. van der; Sijbom, Rick; Alem, Carla M. A. van; Bot, Ilze; Kooten, Cees van; Jukema, J. Wouter; Van Esch, Hilde; Rabelink, Ton J.; Kazan, Hilal; Biessen, Erik A. L.; Ares, Manuel; Zonneveld, Anton Jan van; Veer, Eric P. van der (Nature Communications, 2016)
      A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce transcriptional ...

    • 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 ...