Toplam kayıt 30, listelenen: 1-20

    • 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 ...
    • Community assessment of the predictability of cancer protein and phosphoprotein levels from genomics and transcriptomics 

      Kazan, Hilal; many other, authors (Cell Systems, 2020)
      Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments ...
    • 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 ...
    • A computational approach for prioritization of patient-specific cancer drivers 

      Taleb Bahmed, Ahmed Amine (Antalya Bilim Üniversitesi Lisansüstü Eğitim Enstitüsü, 2020)
      major challenge in cancer genomics is to distinguish the driver mutations that are causally linked to cancer from passenger mutations that are neutral and do not contribute to cancer development. The identification of these ...
    • DriveWays: a method for identifying possibly overlapping driver pathways in cancer 

      Baali, Ilyes; Erten, Cesim; Kazan, Hilal (Nature Research, 2020)
      The majority of the previous methods for identifying cancer driver modules output nonoverlapping modules. This assumption is biologically inaccurate as genes can participate in multiple molecular pathways. This is particularly ...
    • A graph theoretical approach for aligning cell lines and tumors 

      Akay, Muhammet Edip (Antalya Bilim Üniversitesi Lisansüstü Eğitim Enstitüsü, 2022)
      Cell line have now been shown in lots of research to be the most important primary tool for preclinical cancer research, but their representative quality in patient tumor samples remains unclear. The comparison of RNA-seq ...
    • Identification and prioritization of personalized cancer drivers 

      Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Taleb, Ahmed Amine (German Conference on Bioinformatics, 2022)
    • 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 ...
    • 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 ...
    • 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 ...
    • miR-223 exerts translational control of proatherogenic genes in macrophages 

      Nguyen, My-Anh; Hoang, Huy-Dung; Rasheed, Adil; Duchez, Anne-Claire; Wyatt, Hailey; Cottee, Mary Lynn; Graber, Tyson E.; Susser, Leah; Robichaud, Sabrina; Berber, İbrahim; Geoffrion, Michele; Ouimet, Mireille; Kazan, Hilal; Maegdefessel, Lars; Mulvihill, Erin E.; Alain, Tommy; Rayner, Katey J. (AHA Journals, 2022)
      Background: A significant burden of atherosclerotic disease is driven by inflammation. Recently, microRNAs (miRNAs) have emerged as important factors driving and protecting from atherosclerosis. miR-223 regulates cholesterol ...
    • 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 ...
    • 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 ...
    • A network-centric framework for the evaluation of mutual exclusivity tests on cancer drivers 

      Ahmed, Rafsan; Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Yalcin, Cansu (Frontiers in Genetics, 2021)
      One of the key concepts employed in cancer driver gene identification is that of mutual exclusivity (ME); a driver mutation is less likely to occur in case of an earlier mutation that has common functionality in the same ...
    • PersonaDrive: a method for the identification and prioritization of personalized cancer drivers 

      Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Taleb Bahmed, Ahmed Amine (Bioinformatics, 2022)
      Motivation: A major challenge in cancer genomics is to distinguish the driver mutations that are causally linked to cancer from passenger mutations that do not contribute to cancer development. The majority of existing ...
    • 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 ...
    • Predicting the impact of cancer somatic mutations on protein-protein interactions 

      Berber, İbrahim (Antalya Bilim Üniversitesi Lisansüstü Eğitim Enstitüsü, 2022)
      Cancer is a complex disease with one of the highest mortality rates. An existence challenge in cancer research is to identify the cancer driver mutation that causes cancer progression. Many biological processes are ...
    • 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 ...