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Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies showed that genomic alterations represent the most common mechanism for molecular alterations that cause the development and progression of PC. Great efforts have been done to identify common protein-coding genetic variations; however, the impact of non-coding variations including regulatory genetic variants is not still well understood. To gain an understanding of the functional impact of genetic variants, particularly, regulatory variants in PC, we developed an integrative pipeline (AGV) that used whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 of them significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants may affect 131 coding and non-coding genes. Interestingly, our study showed the 131 protein-coding genes are involved in disease-related pathways including Reactome and MSigDB in which for most of them targeted treatment options are currently available. Together, our results provide a comprehensive map of genomic variants in PC and revealed their potential contribution to prostate cancer progression and development.

Here we developed KARAJ, a fast and flexible Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of genomic and transcriptomic sequence data types. The input to KARAJ is a list of PMCIDs or publication URLs or various types of accession numbers to automate four tasks as follows; firstly, it provides a summary list of accessible datasets generated by or used in these scientific articles, enabling users to select appropriate datasets; secondly, KARAJ calculates the size of files that users want to download and confirms the availability of adequate space on the local disk; thirdly, it generates a metadata table containing sample information and the experimental design of the corresponding study; and lastly, it enables users to download supplementary data tables attached to publications. Further, KARAJ provides a parallel downloading framework powered by Aspera connect which reduces the downloading time significantly.

Copy Number Variation (CNV) refers to a type of structural genomic alteration in which a segment of chromosome is duplicated or deleted. To date, many CNVs have been identified as causative genetic elements for several diseases and phenotypes. However, performing a CNV-based genome-wide association study is challenging due to inconsistency in length and occurrence of CNVs across different individuals under investigation. One of the most efficient strategies to address this issue is building CNV regions (genomic regions in which CNVs are overlapping - CNVRs). However, this approach is susceptible to a high false positive rate due to overlapping and co-occurring of confounding CNVRs with true positive CNVRs. Here, we develop PeakCNV that differentiates false-positive CNVRs from true positives by calculating a new metric, independence ranking score, (IR-score) via a feature ranking approach. We compared the performance of PeakCNV with other current existing tools by carrying out two case studies one using the CNV genotype data for individuals with prostate cancer (194 cases and 2,392 healthy individuals) and the second one for individuals with neurodevelopmental disorders (19,642 cases and 6,451 healthy individuals). Crucially, our benchmarking analyses on prostate cancer cohort indicated that PeakCNV identifies a fewer risk candidate CNVRs with shorter lengths compared to other tools. Importantly, these CNVRs cover a greater proportion of case over healthy individuals compared to other tools. The accuracy of PeakCNV in identifying relevant candidate CNVRs was reproducible in the case study on neurodevelopmental disorders. Using data from the FANTOM5 expression atlas and the Clinical Genomic Database, we show that the candidate CNVRs identified by PeakCNV for neurodevelopmental disorders overlap with a greater number of genes with the brain-enriched expression, and a greater number of genes that are associated with neurological conditions compared to candidate CNVRs identified by other tools. Taken together, PeakCNV outperformed current existing CNV association study tools by identifying more biologically meaningful CNVRs relevant to the phenotype of interest. PeakCNV is publicly available for the analysis of CNV-associated diseases and is accessible from https://rdrr.io/github/mahdieh1/PeakCNV.

With increasing number of documents in digital format, automatic text categorization has become a crucial task in pattern recognition problems. To ease the classification task, feature selection methods have been introduced to reduce the dimensionality of the feature space, and thus improve the classification performance. In this paper a novel filter method for feature selection, called Multivariate Relative Discrimination Criterion (MRDC), is proposed for text classification. The proposed method focuses on the reduction of redundant features using minimal-redundancy and maximal-relevancy concepts. To this end, the proposed method takes into account document frequencies for each term, while estimating their usefulness. The proposed method not only selects the features with maximum relevancy, but also the redundancy between them is takes into account using a correlation metric. MRDC does not employ any learning algorithm to evaluate the usefulness of the selected features, and thus it can be categorized as a filter method. In order to assess the effectiveness of the proposed method, several experiments are performed on three real-world datasets. The obtained results are compared to the state-of-the-art filter methods. The reported results show that in most cases MRDC results in better classification performance than others.

With exponentially increasing the number of digital documents, text classification has become a major task in data science applications. Selecting discriminative features highly relevant to class labels while having low levels of redundancy is essential to improve the performance of text classification methods. In this paper, we propose a novel multi-objective algorithm for text feature selection, called Multi-Objective Relative Discriminative Criterion (MORDC), which balances minimal redundant features against those maximally relevant to the target class. The proposed method employs a multi-objective evolutionary framework to search through the solution space. The first objective function measures the relevance of the text features to the target class, whereas the second one evaluates the correlation between the features. None of these objectives use learning to evaluate the goodness of the selected features; thus, the proposed method can be classified as a multivariate filter method. In order to assess the effectiveness of the proposed method, several experiments are performed on three real-world datasets. Comparisons with state-of-the-art feature selection methods show that in most cases MORDC results in better classification performance.

Feature selection is one of the important research areas in pattern recognition. The aim of feature selection is to select those of informative features to improve the classifier's performance. In this paper, we propose a novel multi-objective algorithm based on mutual information for feature selection, called multi-objective mutual information (MOMI). The proposed method identifies a set of features with minimal redundancy and maximum relevancy with the target class. Several experiments are performed to evaluate the performance of MOMI compared to that of well-known and state-of-the-art feature selection methods over five benchmark datasets. The results show that in most cases MOMI achieves better classification performance than others.