Yayın tarihi için Mühendislik Fakültesi / Faculty of Engineering listeleme

Toplam kayıt 289, 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 integrated permanent magnet Micro-turbo- generator supported on microball bearings 

      Beyaz, Mustafa İlker; Hanrahan, Brendan M.; Feldman, Jeremy H.; Ghodssi, Reza (Journal of Microelectromechanical Systems, 2013)
      This paper presents the design, fabrication, and testing of an integrated microturbogenerator utilizing permanent magnets and microball bearings. The key components of this generator are the following: 1) a silicon ...

    • Monitoring of actuation conditions in a micro- turbo-generator 

      Beyaz, Mustafa İlker; Hanrahan, Brendan M.; Feldman, Jeremy H.; Ghodssi, Reza (IEEE Sensors Journal, 2013)
      This paper presents the theory and implementation of an integrated sensing technique for the real-time measurement of applied actuation conditions in a micro-turbo-generator. The device is composed of a microturbine rotor ...

    • 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 ...

    • An adhesion-dominated rolling Friction regime unique to micro-scale ball bearings 

      Hanrahan, Brendan M.; Misra, Saswat; Beyaz, Mustafa İlker; Feldman, Jeremy H.; Waits, Christopher M.; Ghodssi, Reza (Tribology Letters, 2014)
      We demonstrate that micro-scale rolling bearings exhibit friction and wear properties markedly different from their macro-scale counterparts. A microfabricated testing platform uses variable rolling element diameters or ...

    • On the eigenvalues and eigenvectors of a lorentzian rotation matrix by using split quaternions 

      Özdemir, Mustafa; Erdoğdu, Melek; Şimşek, Hakan (Advances in Applied Clifford Algebras, 2014)
      In this paper, we examine eigenvalue problem of a rotation matrix in Minkowski 3 space by using split quaternions. We express the eigenvalues and the eigenvectors of a rotation matrix in term of the coefficients of the ...

    • An investigation on the electromagnetic design optimization of rotary micromachines with double-layer permanent magnets 

      Özkaya, Kamil Yunus; Beyaz, Mustafa İlker (Sensors and Actuators A: Physical, 2015)
      Electromagnetic design optimization of axial-flux rotary micromachines utilizing double-layer permanent magnets is presented and applied to a micro-scale generator/spirometer currently under development. Double-layer magnet ...

    • 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 ...

    • Similar and self-similar curves in minkowski n-space 

      Şimşek, Hakan; Özdemir, Mustafa (Bulletin of Korean Mathematical Society, 2015)
      In this paper, we investigate the similarity transformations in the Minkowski n-space. We study the geometric invariants of nonnull curves under the similarity transformations. Besides, we extend the fundamental theorem ...

    • 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 ...

    • 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 ...

    • Generating hyperbolical rotation matrix for a given hyperboloid 

      Şimşek, Hakan; Özdemir, Mustafa (Linear Algebra and Its Applications, 2016)
      Hyperbolic rotation is hyperbolically the motion of a smooth object on general hyperboloids given by −a1x2+a2y2+a3z2=±λ, λ ∈R+. In this paper, we investigate the hyperbolical rotation matrices in order to get the motion ...

    • 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 ...

    • The development and performance characterization of turbine prototypes for a MEMS spirometer 

      Göreke, Utku; Habibiabad, Sahar; Azgın, Kıvanç; Serinağaoğlu Doğrusöz, Yeşim; Beyaz, Mustafa İlker (IEEE Sensors Journal, 2016)
      The design, optimization, and performance characterization of turbine prototypes for the development of a Microelectromechanical Systems spirometer is reported. Four different turbines were designed based on large-scale ...

    • 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 ...

    • On conformal curves in 2-dimensional de sitter space 

      Şimşek, Hakan; Özdemir, Mustafa (Advances in Applied Clifford Algebras, 2016)
      In this paper, we examine the pseudo-spherical curves, which are equivalent to each other under the conformal maps preserving a fixed point in the de Sitter 2-space, by using the Clifford algebra Cl 2,1. Also, we find the ...

    • Bäcklund’s theorem for n dimensional lorentzian submanifold in the minkowski space 𝔼21𝑛−1 

      Şimşek, Hakan; Özdemir, Mustafa (Results in Mathematics, 2016)
      In this paper, Bäcklund’s Theorem is introduced on the Lorentzian n-submanifold of the Minkowski space 𝔼2𝑛−11 by using the method of moving frames. Also, we prove the Integrability Theorem for the Lorentzian n-submanifold ...

    • 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 ...

    • 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 ...

    • Rotations on a lightcone in minkowski 3-Space 

      Şimşek, Hakan; Özdemir, Mustafa (Advances in Applied Clifford Algebras, Springer, 2017)
      In this paper the generalization of the rotations on any lightcone in Minkowski 3-space ℝ1,2𝑔 is given. The rotation motion on the lightcone is examined by means of a bilinear form and Lorentzian notions. We use the ...