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The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool
(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 ... -
SCITUNA: a network alignment approach for integrating multiple single-cell RNA-Seq datasets
(15th International Symposium on Health Informatics and Bioinformatics, 2022)The throughput and cost of single-cell RNA sequencing (scRNA-seq) are in continuous improvement, and so is the demand for larger-scale scRNA-seq data, which could require integrating multiple datasets from different ... -
Identification and prioritization of personalized cancer drivers
(German Conference on Bioinformatics, 2022) -
Sex-biased expression of neuroimmune guidance cues in cardiovascular diseases
(15th International Symposium on Health Informatics and Bioinformatics, 2022)Atherosclerotic vascular disease continues to be a leader of morbidity and mortality. Although sex hormones are known to play a role in this lipid- and inflammatory-driven disease, the underlying mechanisms are largely ... -
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 ... -
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers
(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 ... -
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 ... -
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 ... -
Ranking cancer drivers via betweenness-based outlier detection and random walks
(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 ... -
Sparse data embedding and prediction by tropical matrix factorization
(BMC Bioinformatics, 2021)Background Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose ... -
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, ... -
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 ... -
Prediction of VLDL cholesterol value with machine learning techniques
(Springer, 2021)Cholesterol is an oil-like substance that is found in the membranes of animal cells and also carried in blood plasma, which has some vital functions in the human body, especially in the endocrine and digestive systems. ... -
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 ... -
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 ... -
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 ... -
A novel fuzzy random forest model for meteorological drought classification and prediction in ungauged catchments
(Pure and Applied Geophysics, 2020)This paper presents a new tree-based model, namely Fuzzy Random Forest (FRF), for one month ahead Standardized Precipitation Evapotranspiration Index (SPEI) classification and prediction with a noteworthy application in ... -
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 ... -
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 ... -
Structure of conflict graphs in constraint alignment problems and algorithms
(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 ...
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