Güncel Gönderiler: Mühendislik Fakültesi / Faculty of Engineering

Toplam kayıt 302, listelenen: 261-280

    • RBPSponge: genome-wide identification of lncRNAs that sponge RBPs 

      HafezQorani, Saber; Houdjedj, Aissa; Arıcı, Mehmet; Said, Abdesselam; Kazan, Hilal (Bioinformatics, 2019)
      Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes of the corresponding RBP of ...

    • A translational repression complex in developing mammalian neural stem cells that regulates neuronal specification 

      Zahr, Siraj K.; Yang, Guang; Kazan, Hilal; Borrett, Michael J.; Voronova, Anastassia; Kaplan, David R.; Miller, Freda D. (Neuron, 2018)
      The mechanisms instructing genesis of neuronal sub-types from mammalian neural precursors are not well understood. To address this issue, we have characterized the transcriptional landscape of radial glial precursors (RPs) ...

    • 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 ...

    • 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 ...

    • A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (structure surfer) 

      Berkowitz, Nathan D.; Silverman, Ian M.; Childress, Daniel M.; Kazan, Hilal; Wang, Li-San; Gregory, Brian D. (BMC Bioinformatics, 2016)
      Background: RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their ...

    • Chemogenomics and orthology‐based design of antibiotic combination therapies 

      Chandrasekaran, Sriram; Çokol-Çakmak, Melike; Şahin, Nil; Yılancıoğlu, Kaan; Kazan, Hilal; Collins, James J.; Çokol, Murat (Molecular Systems Biology, 2016)
      Combination antibiotic therapies are being increasingly used in the clinic to enhance potency and counter drug resistance. However, the large search space of candidate drugs and dosage regimes makes the identification ...

    • 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 ...

    • 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 ...

    • 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 ...

    • Target-independent prediction of drug synergies using only drug lipophilicity 

      Kazan, Hilal; Yılancıoğlu, Kaan; Weinstein, Zohar B.; Meydan, Cem; Akhmetov, Azat; Toprak, Işıl; Durmaz, Arda; Iossifov, Ivan; Roth, Frederick P.; Çokol, Murat (Journal of Chemical Information and Modeling, 2014)
      Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency ...

    • Climate change impacts on meteorological drought using SPI and SPEI: case study of Ankara, Turkey 

      Danandeh Mehr, Ali; Sorman, Ali Ünal; Kahya, Ercan; Hesami Afshar, Mahdi (Hydrological Sciences Journal, 2019)
      Using regionally downscaled and adjusted outputs of three global climate models (GCMs), meteorological drought analysis was accomplished across Ankara, the capital city of Turkey. To this end, standardized precipitation ...

    • Cr: Colquiriite Lasers: Current Status and Challenges for Further Progress 

      Demirbaş, Ümit (Progress in Quantum Electronics, 2019)
      Cr: Colquiriite laser materials (Cr:LiCAF, Cr:LiSAF, Cr:LiSGaF) own broad absorption bands in the visible region that allow direct-diode pumping by well-developed low-cost red diodes. Moreover, they possess broad emission ...

    • RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins 

      Kazan, Hilal; Morris, Quaid (Nucleic acids research, 2013)
      RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif ...

    • Havalimanlarında kalkış öncesi, acil durumlarda, yardım alınabilecek en uygun lokasyonun Weber problemine uyarlanarak belirlenmesi 

      Demir, Emre (Türk Coğrafya Dergisi, 2018)
      Türkiye’de son yıllarda sivil havacılık hızlı bir şekilde gelişmiştir ve bu ivme artarak devam etmektedir. Tüm dünyada ve ülkemizde hızla büyüyen sivil havacılık sektörü ve işletmeciliği hemen hemen herkesin kullanımına ...

    • Facility location determined by an iterative technique 

      Demir, Emre; Koçkal, Niyazi Uğur (1st Mediterranean International Conference of Pure and Applied Mathematics and Related Areas 2018 (MICOPAM 2018), 2018)
      For many decades, mathematical models and methodologies have been essential in order to provide the understanding of countless engineering processes and technologies. Using mathematical models in many academic research, ...

    • Assigning convenient paths by an approach of dynamic programming 

      Demir, Emre (1st Mediterranean International Conference of Pure and Applied Mathematics and Related Areas 2018 (MICOPAM 2018), 2018)
      For many decades, mathematical models and methodologies have been essential in order to provide the understanding of countless engineering processes and technologies. Using mathematical models in many academic research, ...

    • Approach for siting a support facility for transporting supplies in emergency cases in the Republic of Bulgaria 

      Demir, Emre (MATEC Web of Conferences, 2018)
      In this paper, the author determines the most suitable transportation location for intervention in a large scale disaster in the Republic of Bulgaria, by means of the Weber Problem and the Weiszfeld method. The objective ...

    • Iterative methodology on locating a cement plant 

      Demir, Emre; Kockal, Niyazi Ugur (Journal of Inequalities and Applications, 2019)
      In this study, a cement plant location was determined by considering essential parameters such as the locations of resources and their importance in the manufacturing process. A crucial mathematical problem, named Weber ...

    • Streamflow and sediment load prediction using linear genetic programming 

      Danandeh Mehr, Ali; Şorman, Ali Ünal (Uludağ University Journal of The Faculty of Engineering, 2018)
      Daily flow and suspended sediment discharge are two major hydrological variables that affect rivers’ morphology and ecosystem, particularly during flood events. Artificial neural networks (ANNs) have been successfully used ...