Browsing Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering by Title
Now showing items 1-20 of 35
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Chemogenomics and orthology‐based design of antibiotic combination therapies
(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
(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)
(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 ... -
Domination and efficient domination in cubic and quartic Cayley graphs on abelian groups
(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 ... -
DriveWays: a method for identifying possibly overlapping driver pathways in cancer
(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 ... -
Effect of vitamin d levels on lipid, glucose, vitamin b12 and c-reactive protein in acute ischemic stroke
(Annals of Medical Research, 2020)Aim: Stroke ranks second among the causes of death world wideand related disability and death rates are high. Recent studies have shown that vitamin D deficiency is higher in patients with ischemic stroke compared to other ... -
Efficient domination in Cayley graphs of generalized dihedral groups
(Discussiones Mathematicae Graph Theory, 2020)An independent subset D of the vertex set V of the graph is an effcient dominating set for this graph if each vertex v in V \ D has precisely one neighbour in D. In this article, we classify the connected cubic Cayley ... -
Global alignment of PPI networks
(Springer, 2021)Given multiple PPI networks from different species, the global PPI network alignment problem is that of providing a global mapping between the nodes of the networks or subnetworks within them. Functional orthology detection, ... -
Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes
(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 ... -
A hybrid movie recommender system and rating prediction model
(International Journal of Information Technology and Applied Sciences, 2021-07-01)In the current era, a rapid increase in data volume produces redundant information on the internet. This predicts the appropriate items for users a great challenge in information systems. As a result, recommender systems ... -
Identification and prioritization of personalized cancer drivers
(German Conference on Bioinformatics, 2022) -
Inferring RBP-mediated regulation in lung squamous cell carcinoma
(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
(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
(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
(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
(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
(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
(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
(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 ... -
A new multi-party private set intersection protocol based on OPRFs
(Muğla Journal of Science and Technology, 2022-06-28)In many crucial real-world applications, parties must jointly perform some secure multi-party computation (MPC) while keeping their inputs hidden from other parties. Private Set Intersection (PSI), the specific area of ...
