相关论文: Using profiles based on hydropathy properties to d…
Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological…
The primary step in search of the gene prediction is an identification of the coding region from genomic DNA sequence. Gene structure in the case of a eukaryotic organism is composed of promoter, intron, start codon, exons, stop codon, etc.…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
A eukaryotic gene consists of multiple exons (protein coding regions) and introns (non-coding regions), and a splice junction refers to the boundary between a pair of exon and intron. Precise identification of spice junctions on a gene is…
Background: Exonic splice enhancers are sequences embedded within exons which promote and regulate the splicing of the transcript in which they are located. A class of exonic splice enhancers are the SR proteins, which are thought to…
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
Identifying gene splicing is a core and significant task confronted in modern collaboration between artificial intelligence and bioinformatics. Past decades have witnessed great efforts on this concern, such as the bio-plausible splicing…
We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
It has been recently argued that the depletion attraction may play an important role in different aspects of the cellular organization, ranging from the organization of transcriptional activity in transcription factories to the formation of…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is…
Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between…
Bioinformatics incorporates information regarding biological data storage, accessing mechanisms and presentation of characteristics within this data. Most of the problems in bioinformatics and be addressed efficiently by computer…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Motivation: Despite being often perceived as the main contributors to cell fate and physiology, genes alone cannot predict cellular phenotype. During the process of gene expression, 95% of human genes can code for multiple proteins due to…
Mapping genotypes to phenotypes (G2P) is a fundamental goal in biology. So called PhyloG2P methods are a relatively new set of tools that leverage replicated evolution in phylogenetically independent lineages to identify genomic regions…