Recent Submissions

  • Domination and efficient domination in cubic and quartic Cayley graphs on abelian groups 

    Çalışkan, Cafer; Miklavic, Stefko; Özkan, Sibel (Discrete Applied Mathematics, 2019)
    In this paper, we characterise cubic and quartic Cayley graphs on abelian groups that admit an efficient dominating set, and then we give domination numbers, even when they do not have an efficient dominating set, when it ...
  • 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 is ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...