Yayın tarihi için PubMed İndeksli Yayınlar Koleksiyonu listeleme

Toplam kayıt 46, listelenen: 1-20

    • 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 ...

    • An analytic decision support tool for resident allocation 

      Talay, Işılay; Holmes, Casey J.; Kuo, Paul C.; Jennings, Otis B. (Journal of Surgical Education, 2013)
      Moving residents through an academic residency program is complicated by a number of factors. Across all residency programs the percentage of residents that leave for any reason is between 3.4% and 3.8%.1 There are a number ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 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 ...

    • 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 ...

    • 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 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) ...

    • Multigene genetic programming for sediment transport modeling in sewers for conditions of non-deposition with a bed deposit 

      Safari, Mir Jafar Sadegh; Danandeh Mehr, Ali (Elsevier, 2018)
      It is known that construction of large sewers based on consideration of flow with non-deposition without a bed deposit is not economical. Sewer design based on consideration of flow with non-deposition with a bed deposit ...

    • 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 ...

    • A non-resonant kinetic energy harvester for bioimplantable applications 

      Beyaz, Mustafa İlker; Baelhadj, Hacene; Habibiabad, Sahar; Adhikari, Shyam; Davoodi, Hossein; Badilita, Vlad (Micromachines, 2018)
      A linear non-resonant kinetic energy harvester for implantable devices is presented. The design contains a metal platform with permanent magnets, two stators with three-dimensional helical coils for increased power generation, ...

    • 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 ...

    • 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 ...

    • 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 ...

    • Independent effects on cellular and humoral immune responses underlie genotype-by- genotype interactions between Drosophila and parasitoids 

      Leitão, Alexandre B.; Bian, Xueni; Day, Jonathan P.; Pitton, Simone; Demir, Eşref; Jiggins, Francis M. (PLoS Pathogens, 2019)
      It is common to find abundant genetic variation in host resistance and parasite infectivity within populations, with the outcome of infection frequently depending on genotype-specific interactions. Underlying these effects ...

    • Pythagorean fuzzy VIKOR-based approach for safety risk assessment in mine industry 

      Gül, Muhammet; Ak, Muhammet Fatih; Güneri, Ali Fuat (Journal of Safety Research, 2019)
      Introduction: Underground mining is considered one of the most hazardous industries and is often associated with serious work-related fatalities; this paper addresses job-related hazards and associated risks. Method: A ...

    • Datasets on mathematical modeling of multi-product multi-stage production to analyze the relationship between production yield, demand, and costs 

      Talay, Işılay; Özdemir-Akyıldırım, Öznur (Data in Brief, 2019)
      The data presented in this article are related to the research article “Optimal procurement and production planning for multi-product multi-stage production under yield uncertainty” (Talay and Özdemir-Akyıldırım, in press) ...