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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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Kazan, Hilal (13)
HafezQorani, Saber (3)Baali, Ilyes (2)Bruin, Ruben G. de (2)Lafzi, Atefeh (2)Veer, Eric P. van der (2)Yılancıoğlu, Kaan (2)Zonneveld, Anton Jan van (2)Çokol, Murat (2)Acar, D. Alp Emre (1)... View MoreSubjectCancer (2)İfade (2)Kanser (2)Algorithm (1)Algoritma (1)Antimicrobial agents (1)Antimikrobiyal ajanlar (1)Autophagy (1)Bağlayıcı protein (1)Binding protein (1)... View MoreDate Issued2016 (6)2018 (2)2019 (2)2013 (1)2014 (1)2020 (1)Has File(s)Yes (13)

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