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Understanding the nature of many diseases, including cancer, requires locating somatically acquired rearrangements corresponding to large-scale chromosomal aberrations. Computational methods to detect inter-chromosomal rearrangements based on next-generation sequencing platforms face the big challenge of accurately predicting the location of sites spanned by a typically small number of reads, while...
MicroRNA is a type of short non-coding RNAs, which post-transcriptionally regulate gene expressions. It has been well-documented that human microRNAs contribute in the disease development, such as cancers and obesity. While most microRNA functional studies heavily rely on the regulatory interactions between microRNAs and their target messenger RNAs, the accumulating evidence has shown that the altered...
DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a...
Gastric cancer (GC) is one of the lethal cancer types as well as one of the heterogeneous cancer types. To elucidate GC molecular mechanisms, mutational co-occurrence analyses have been suggested. However, an association between mutational co-occurrences and known GC signaling contexts has yet to be identified. In this study, the known GC signaling contexts including cancer hallmarks (DNA repair,...
In the era of information explosion, biological data is being produced at an alarming rate. With the amount of data currently available, computational methods have become an integral part of sequence alignment. In protain homology analysis and sequence alignments, the demand for the distinguish of specific gene mutation types has been increased rapidly in recent years. In this paper, we presents an...
Recent literature has found Microhomology-mediated break-induced replication (MMBIR) to be a common mechanism producing complex mutations. Complex mutations underlie the genomic instability that results in various cancers. MMBIRFinder is a tool that has successfully detected the MMBIR mutations in budding yeast DNA by comparing sampled DNA reads to a whole reference genome. A major challenge for the...
LKB1(Liver Kinase B1) gene is a tumor suppressor gene, which regulates the pathophysiological function of many cells, but the mechanism of LKB1 gene is still unclear. The double transgenic mice with positive homozygous and negative homozygous were screened by PCR amplification technique and gel electrophoresis technique. The expression level of LKB1 gene in smooth muscle cells was detected by Westernblot...
The paper is devoted to the history and prospects of gene therapy, a new area of biotechnology that holds great promise for the treatment genetic disorders, cancer and dangerous infections such as HIV and hepatitis B. A brief history of gene therapy is described. The paper discusses the main lines of research in this area as well as the mechanisms, approaches, and techniques employed by gene therapy,...
Pancreatic cancer is the fourth most common cause of cancer-related deaths across the globe and it is one of the most difficult cancer types to recognize early. Early diagnosis of pancreatic cancer is crucial to increase survival for patients. In this study, it was tried to be estimated that persons were pancreatic cancer or healthy using microarray gene expression profile. In accordance with this...
Cancer is defined as a genetic and epigenetic disease involving the chemical and structural alteration of DNA. Because optical techniques measure overlapped and synthetic signals of materials, regardless of “ordering” features (such as the nucleotide order of a DNA sequence), it is difficult to sequence a genome to detect cancerous genetic changes using optical techniques. For this reason, previous...
Genetic mutations are the first warning to the onset of lung cancer. The ability to early predict these mutations could open the door for a targeted treatment options for lung cancer patients. Three top candidate genes previously reported to have the highest frequency of lung cancer mutations. Each gene is encoded as a symbolic sequence of four letters. A novel method for gene representation is introduced...
Cancer is the second cause of death in developed countries after cardiovascular diseases. Our work serves in a better understanding of pRb-E2F process, a significant pathway of the cell cycle control and a frequent target of mutational events in the most human cancers. Using a mathematical model, the simulated phenomena that characterize the real system, preserves the logical structure, allowing to...
DNA methylation (DNAm) is an epigenetic mechanism used by cells to control gene expression, and identification of DNAm biomarkers can assist in early diagnosis of cancer. Identification of these biomarkers can be done using CpG (Cytosine-phosphate guanine) sites, or particular regions in DNA. Previous machine learning methods known as MS-SPCA and EVORA have been used to link DNAm biomarkers to specific...
Since the first whole-genome sequencing, the biomedical research community has made significant steps towards a more precise, predictive and personalized medicine. Genomic data is nowadays widely considered privacy-sensitive and consequently protected by strict regulations and released only after careful consideration. Various additional types of biomedical data, however, are not shielded by any dedicated...
Cancer is a heterogeneous disease characterized by a high degree of variation between affected individuals. An emergent task in precision oncology is to determine patient subtypes based on their molecular profiles in order to provide more accurate treatments. To this end, integrative approaches have been addressed recently to combine multi-omics datasets. In this paper, we propose an unsupervised...
Dynamic programming in bioinformatics is a memory based data structure for saving computational time with one-time storage of each problem solution. Algorithm and Scoring parameters are used to evaluate Brainstem Glioma patients DNA Sequence and comparing each other. 1. Local comparison a. Ignoring disparate sequences outside similar sequences b. locally arrange similar sequence. 2. Global comparison...
Knowledge discovery in multiple sequences is very important for a variety of applications such as gene sequence identification, stock prediction, Internet data optimization and so forth. This paper proposes a new method for segmenting multiple sequences to highlight the important periods (or sub-sequences). We have conducted diverse experiments on cancer relevant gene sequences. The results have shown...
A big data on Healthcare applications which is require big data management as well as intensive computation. In this paper, focus on Genomics in cancer testing whether the healthcare applications can scale well on commercial big data platforms that implement Map Reduce framework. We selected short read gene data sequence alignment and assembly workloads in genome analysis and Apache Hadoop distributed...
We have reached the era of full genome sequencing using high throughput sequencing technologies pouring out gigabases of reads in a day. To fully benefit from such a profusion of data high performance tools and systems are needed to extract the information lying within the sequences. This paper provides an overview of the evolution of high-throughput sequencing and the tools, infrastructure and data...
To perform segmentation to identify regions of constant copy number is an important key for discovering structural variation in the human genome. It calls for a uniform pipeline to integrate various segmentation methods in a flexible software toolbox for conveniently evaluating outcome. We propose such toolbox and implement an open source Java package called ToolSEG to generate realistic DNA copy...
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