Toplam kayıt 34, listelenen: 25-34

    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Sex-biased expression of neuroimmune guidance cues in cardiovascular diseases 

      Marouf, Yacine; Doğan, Onur S.; Benavente, Ernest Diez; Pasterkamp, Gerard; den Ruijter, Hester M.; van Gils, Janine; Rayner, Katey; Kazan, Hilal (15th International Symposium on Health Informatics and Bioinformatics, 2022)
      Atherosclerotic vascular disease continues to be a leader of morbidity and mortality. Although sex hormones are known to play a role in this lipid- and inflammatory-driven disease, the underlying mechanisms are largely ...
    • Sparse data embedding and prediction by tropical matrix factorization 

      Omanović, Amra; Kazan, Hilal; Oblak, Polona; Curk, Tomaž (BMC Bioinformatics, 2021)
      Background Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose ...
    • 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 ...
    • 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 ...
    • 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) ...