Interdisciplinary Sciences, Computational Life Sciences This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

DNA Mismatch Repair Deficiency Detection in Colorectal Cancer by a New Microsatellite Instability Analysis System
ConclusionsThe colorectal cancer can be classified according to MSI status accurately by ProDx ® MSI. More cases with MSI-High feature may be revealed by ProDx® MSI than by previous test systems in colorectal cancer. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - January 24, 2020 Category: Bioinformatics Source Type: research

PPLK + C: A Bioinformatics Tool for Predicting Peptide Ligands of Potassium Channels Based on Primary Structure Information
AbstractPotassium channels play a key role in regulating the flow of ions through the plasma membrane, orchestrating many cellular processes including cell volume regulation, hormone secretion and electrical impulse formation. Ligand peptides of potassium channels are molecules used in basic and applied research and are now considered promising alternatives in the treatment of many diseases, such as cardiovascular diseases and cancer. Currently, there are various bioinformatics tools focused on the prediction of peptides with different activities. However, none of the current tools can predict ligand peptides of potassium ...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 6, 2020 Category: Bioinformatics Source Type: research

Revealing the Mechanism of EGCG, Genistein, Rutin, Quercetin, and Silibinin Against hIAPP Aggregation via Computational Simulations
AbstractTo inhibit hIAPP aggregation and reduce toxicity of its oligomers are one of the potential strategies for the treatment of Type 2 diabetes (T2D). It has been reported that there is an effective inhibitory effect on hIAPP aggregation by five natural flavonoids, including Genistein, Rutin, Quercetin, Epigallocatechin gallate (EGCG), and Silibinin, which are widely found in our daily food. However, the detailed mechanisms to inhibit hIAPP aggregation remain unclear. Here, we explore the mechanisms of the five flavonoids against hIAPP aggregation by molecular docking and molecular dynamics simulations. We show that the...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 31, 2019 Category: Bioinformatics Source Type: research

Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles
AbstractNucleosomal profiling is an effective method to determine the positioning and occupancy of nucleosomes, which is essential to understand their roles in genomic processes. However, the positional randomness across the genome and its relationship with nucleosome occupancy remains poorly understood. Here we present a computational method that segments the profile into nucleosomal domains and quantifies their randomness and relative occupancy level. Applying this method to published data, we find on average  ~ 3-fold differences in the degree of positional randomness between regions typically considered “well-ord...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 15, 2019 Category: Bioinformatics Source Type: research

CytoMegaloVirus Infection Database: A Public Omics Database for Systematic and Comparable Information of CMV
AbstractCytoMegaloVirus (CMV) is known to cause infection in humans and may remain dormant throughout the life span of an individual. CMV infection has been reported to be fatal in patients with weak immunity. It is transmitted through blood, saliva, urine, semen and breast milk. Although medications are available to treat the infected patients, there is no cure for CMV. This concern prompted us to construct a comprehensive database having exhaustive information regarding CMV, its infections and therapies to be available on a single platform. Thus, we propose a newly designed database that includes all the information from...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 6, 2019 Category: Bioinformatics Source Type: research

Plant miRNA –lncRNA Interaction Prediction with the Ensemble of CNN and IndRNN
AbstractNon-coding RNA (ncRNA) plays an important role in regulating biological activities of animals and plants, and the representative ones are microRNA (miRNA) and long non-coding RNA (lncRNA). Recent research has found that predicting the interaction between miRNA and lncRNA is the primary task for elucidating their functional mechanisms. Due to the small scale of data, a large amount of noise, and the limitations of human factors, the prediction accuracy and reliability of traditional feature-based classification methods are often affected. Besides, the structure of plant ncRNA is complex. This paper proposes an ensem...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 5, 2019 Category: Bioinformatics Source Type: research

AGONOTES: A Robot Annotator for Argonaute Proteins
AbstractThe argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and an...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 17, 2019 Category: Bioinformatics Source Type: research

Counting Kmers for Biological Sequences at Large Scale
AbstractCounting the abundance of all the distinct kmers in biological sequence data is a fundamental step in bioinformatics. These applications include de novo genome assembly, error correction, etc. With the development of sequencing technology, the sequence data in a single project can reach Petabyte-scale or Terabyte-scale nucleotides. Counting demand for the abundance of these sequencing data is beyond the memory and computing capacity of single computing node, and how to process it efficiently is a challenge on a high-performance computing cluster. As such, we propose SWAPCounter, a highly scalable distributed approa...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 15, 2019 Category: Bioinformatics Source Type: research

A Systems Biology Roadmap to Decode mTOR Control System in Cancer
AbstractMechanistic target of rapamycin (mTOR) is a critical protein in the regulation of cell fate decision making, especially in cancer cells. mTOR acts as a signal integrator and is one of the main elements of interactions among the pivotal cellular processes such as cell death, autophagy, metabolic reprogramming, cell growth, and cell cycle. The temporal control of these processes is essential for the cellular homeostasis and dysregulation of mTOR signaling pathway results in different phenotypes, including aging, oncogenesis, cell survival, cell growth, senescence, quiescence, and cell death. In this paper, we have pr...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 16, 2019 Category: Bioinformatics Source Type: research

A Machine Learning-Based QSAR Model for Benzimidazole Derivatives as Corrosion Inhibitors by Incorporating Comprehensive Feature Selection
ConclusionBased on our model, 6 new benzimidazole molecules were designed and their IE values predicted by this model indicate that two of them have high potential as outstanding corrosion inhibitors. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - September 3, 2019 Category: Bioinformatics Source Type: research

Integrative Analysis of Multi-Genomic Data for Kidney Renal Cell Carcinoma
AbstractAccounting for nine out of ten kidney cancers, kidney renal cell carcinoma (KIRC) is by far the most common type of kidney cancer. In view of limited and ineffective available therapies, understanding the genetic basis of disease becomes important for better diagnosis and treatment. The present studies are based on a single type of  genomic data. These studies do not consider interactions between genomic data types and their underlying biological relationships in the disease. However, the current availability of multiple genomic data and the possibility of combining it have facilitated a better understanding of...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 7, 2019 Category: Bioinformatics Source Type: research

QTL-BSA: A Bulked Segregant Analysis and Visualization Pipeline for QTL-seq
AbstractIn recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic trait values, has gained increasing popularities in research community. However, there is no publicly available user friendly software for the identification and visualization. Hence, we developed a tool named QTL-BSA (QTL-bulked segregant analysis and visualization pipel...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 5, 2019 Category: Bioinformatics Source Type: research

Estimation of Probability Distribution and Its Application in Bayesian Classification and Maximum Likelihood Regression
AbstractNonparametric estimation of cumulative distribution function and probability density function of continuous random variables is a basic and central problem in probability theory and statistics. Although many methods such as kernel density estimation have been presented, it is still quite a challenging problem to be addressed to researchers. In this paper, we proposed a new method of spline regression, in which the spline function could consist of totally different types of functions for each segment with the result of Monte Carlo simulation. Based on the new spline regression, a new method to estimate the distribut...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 16, 2019 Category: Bioinformatics Source Type: research

Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent -Copalyl Diphosphate Synthase
AbstractEnt-copalyl diphosphate synthase controls the biosynthesis of gibberellin plant hormones, which in turn coordinate the expression of numerous enzymes. Some gibberellin-dependent genes encode enzymes coordinating the biosynthesis of tanshinones: diterpene derivatives with broad medical applications. New biotechnological approaches, such as metabolic engineering using naturally occurring or mutated enzymes, have been proposed to meet the growing demand for tanshinones which is currently met by the Chinese medicinal plantSalvia miltiorrhiza Bunge. These mutants may be prepared by directed evolution, saturation mutagen...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 14, 2019 Category: Bioinformatics Source Type: research

Melanoma Detection by Means of Multiple Instance Learning
We present an application to melanoma detection of a multiple instance learning (MIL) approach, whose objective, in the binary case, is to discriminate between positive and negative sets of items. In the MIL terminology these sets are called bags and the items inside the bags are called instances. Under the hypothesis that a bag is positive if at least one of its instances is positive and it is negative if all its instances are negative, the MIL paradigm fits very well with images classification, since an image (bag) is in general classified on the basis of some its subregions (instances). In this work we have applied a MI...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 9, 2019 Category: Bioinformatics Source Type: research