Yazar "0000-0003-2461-4579 [Kazan, Hilal]" için Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering listeleme

Toplam kayıt 25, 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 ...

    • 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 ...

    • 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 ...

    • The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool 

      Kolaj, Adelaida; Zahr, Siraj K.; Wang, Beatrix S.; Krawec, Taylor; Kazan, Hilal; Yang, Guang; Kaplan, David R.; Miller, Freda D. (Elsevier, 2023)
      Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that ...

    • 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 ...

    • 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 ...