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 - January 1, 2020 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 &...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 16, 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 7, 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 6, 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 18, 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 16, 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 17, 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 4, 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 ...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 8, 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 6, 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 17, 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 15, 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 10, 2019 Category: Bioinformatics Source Type: research

Development of an Interactive Web Application “Shiny App for Frequency Analysis on Homo sapiens Genome (SAFA-HsG)”
AbstractThe web application “Shiny App for Frequency Analysis onHomo sapiens Genome (SAFA-HsG) ” was developed using R programming-based bioconductor packages and shiny framework. Through the app, preliminary descriptive data analysis on nucleotide frequency, and CpG island, CpG non-island, and CpG island shores and shelves (downstream and upstream) of human reference genome can be carried out, which will help biologists to work on human epigenomics. Table view of these analyses of all chromosomes can be visualized and downloaded by the end users. Similarly, the respective comparative plots can be used for CpG ...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 1, 2019 Category: Bioinformatics Source Type: research

Quantitative and Visual Characteristics of Primary Central Nervous System Lymphoma on 18 F-FDG-PET
In conclusion, aside from SUVmax andT/N values, other visual characteristics are also available to facilitate the differentiation of PCNSLs from other brain conditions on18F-FDG-PET scans. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - July 1, 2019 Category: Bioinformatics Source Type: research

Accelerated Versus Conventional Corneal Collagen Cross-Linking in the Treatment of Keratoconus: A Meta-analysis and Review of the Literature
AbstractAimOur aim was to examine existing literature, and determine if there are outcome differences between accelerated corneal collagen cross-linking (A-CXL) and conventional corneal collagen cross-linking (C-CXL).MethodsA systematic review of the literature was conducted examining studies which compared A-CXL to C-CXL. Available studies were combined and the weighted mean difference (WMD) was calculated for range of outcome measures including maximal keratometry (Kmax), mean keratometry (Kmean) and minimum keratometry (Kmin), spherical equivalent, best corrected visual acuity (BCVA), and central corneal thickness (CCT)...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 27, 2019 Category: Bioinformatics Source Type: research

Exploring the Influence of Parameters on the p53 Response When Single-Stranded Breaks and Double-Stranded Breaks Coexist
AbstractThe p53 response to DNA damage is closely related to cell fate decisions. P53 preferentially responds to single-stranded breaks (SSBs) exhibiting a graded response when single-stranded breaks (SSBs) and double-stranded breaks (DSBs) coexist. However, how p53 natural preferential response is affected by kinetic parameters remains to be elucidated. Here, based on the hybrid model I, we computationally searched all the parameters and parameter combinations in the parameter space to identify those that could alter the natural preferential response of p53 when SSBs and DSBs coexist. Firstly, when a single parameter is c...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 20, 2019 Category: Bioinformatics Source Type: research

Unearthing Regulatory Axes of Breast Cancer circRNAs Networks to Find Novel Targets and Fathom Pivotal Mechanisms
This study suggested extensive panels of novel therapeutic targets that are in charge of BC progression, hence their impressive role cannot be excluded and needs deeper empirical laboratory designs. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - June 11, 2019 Category: Bioinformatics Source Type: research

Nivolumab-induced Thyroid Dysfunctions in Patients with Previously Treated Non-small Cell Lung Cancer
ConclusionNivolumab-induced thyroid dysfunctions in advanced NSCLC were mostly mild and controlled. Thyroid function needs to be monitored for early prediction and appropriate managements of thyroid dysfunctions. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - June 11, 2019 Category: Bioinformatics Source Type: research

Protection of Primary Dopaminergic Midbrain Neurons Through Impact of Small Molecules Using Virtual Screening of GPR139 Supported by Molecular Dynamic Simulation and Systems Biology
AbstractIntroductionGPCR share a common structural feature, i.e., the presence of seven trans-membrane helices having three intracellular and three extracellular loops. The carboxyl terminal is intracellular whereas amino terminal is extracellular. Various conformational changes are observed in structure of GPCR during the binding with ligand, coupling with G protein and interaction with other proteins. In Rhodopsin class of GPCR the basic structure of GPCR is resolved by X-ray crystallography. Ligand acts as an extracellular stimulus for GPCRs to bring physiological changes in organisms. GPR139 has been found to have effe...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 8, 2019 Category: Bioinformatics Source Type: research

Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types
AbstractHistone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic region...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 4, 2019 Category: Bioinformatics Source Type: research

CISI: A Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences
AbstractMonoclonal antibodies (mAbs) are one of the robust classes of therapeutic proteins. Their stability, specificity, and high solubility allow the successful development and commercialization of antibody-based drugs. Though with these characteristics, mAbs projects are often suspended due to self- or cross-interaction of monoclonal antibodies. This is one of the main reasons which causes the development of mAbs into drugs taking forever and expensive. CISI is short for cross-interaction or self-interaction of mAbs. It can be quantified by several assays. The assays such as poly-specificity reagent and cross-interactio...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 22, 2019 Category: Bioinformatics Source Type: research

Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin
AbstractIn nearly 50% of patients with drug-induced liver injury, the bile flow is impaired known as cholestasis. Intrahepatic cholestasis of pregnancy (ICP) is the most common liver disease that happens in pregnancy. Some of the clinical symptoms include pruritus, dark urine, and abnormal liver function tests. A rise of serum bile acids is the most accurate diagnostic evidence. ICP may lead to premature birth, fetal distress, and even postpartum hemorrhage or stillbirth in some severe cases. Higher bile acid levels (>  40 μmol/L) are associated with higher rates of adverse fetal outcomes. Due to the mult...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 20, 2019 Category: Bioinformatics Source Type: research

PD-L1 Expression and Its Regulation in Lung Adenocarcinoma with ALK Translocation
ConclusionsWe demonstrate that  ALK translocation can upregulate PD-L1 expression by activating ERK, STAT3 and AKT pathways. ALK inhibitor combined with a PD-L1-targeted therapy may be a potential strategy in ALK-translocated lung adenocarcinoma patients. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - May 16, 2019 Category: Bioinformatics Source Type: research

Correlation Between PD-L1 Expression and Clinicopathologic Features in 404 Patients with Lung Adenocarcinoma
AbstractBackgroundPD-1/PD-L1 inhibitors is the important drugs of immunotherapy for malignant tumors. PD-L1 expression is an important biomarker of selecting patients for ICIs therapy. However, the correlation of PD-L1 expression with clinicopathologic features in lung adenocarcinoma remains controversial.MethodsPD-L1 expression was tested using clone SP263 by immunohistochemistry (IHC) on Ventana automated Benchmark in tissue micro-arrays (TMA) in lung adenocarcinoma. The association of PD-L1 expression with clinicopathologic characteristics, including gender, age, histological subtype, smoking history, stage, and genotyp...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 11, 2019 Category: Bioinformatics Source Type: research

Detecting Methylomic Biomarkers of Pediatric Autism in the Peripheral Blood Leukocytes
AbstractAutism was a spectrum of multiple complex diseases that required an interdisciplinary group of experts to make a diagnostic decision. Both genetic and environmental factors play essential roles in causing the onset of Autism. Therefore, this study hypothesized that methylomic biomarkers may facilitate the accurate Autism detection. A comprehensive series of biomarker detection algorithms were utilized to find the best methylomic biomarkers for the Autism detection using the methylomic data of the peripheral blood samples. The best model achieved 99.70% in accuracy with 678 methylomic biomarkers and a tenfold cross ...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 16, 2019 Category: Bioinformatics Source Type: research

Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients
AbstractAcute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients ’ mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathoge...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 10, 2019 Category: Bioinformatics Source Type: research

Distribution of Distances Between Symmetric Words in the Human Genome: Analysis of Regular Peaks
AbstractFinding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2019 Category: Bioinformatics Source Type: research

An Overview of Scoring Functions Used for Protein –Ligand Interactions in Molecular Docking
AbstractCurrently, molecular docking is becoming a key tool in drug discovery and molecular modeling applications. The reliability of molecular docking depends on the accuracy of the adopted scoring function, which can guide and determine the ligand poses when thousands of possible poses of ligand are generated. The scoring function can be used to determine the binding mode and site of a ligand, predict binding affinity and identify the potential drug leads for a given protein target. Despite intensive research over the years, accurate and rapid prediction of protein –ligand interactions is still a challenge in molec...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 15, 2019 Category: Bioinformatics Source Type: research

Neighboring genes are closely related to whole genome duplications after their separation
ConclusionsThese results provide new insight into the understanding of evolutionary roles of locations and the relationship of neighboring gene pairs with whole genome duplications. Furthermore, understanding the proposed mechanism for intrachromosomal colocalization of separated genes benefits our knowledge of chromosomal interactions in the nucleus. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 14, 2019 Category: Bioinformatics Source Type: research

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics
AbstractMany scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent to that input. Because subgraph isomorphism is NP-complete, methods to solve it have to use heuristics. This work evaluates subgraph isomorphism methods to assess their computational behavior on a wide range of synthetic and real graphs. Surprisingly, our experiments show that, among the leading algorithms, certain heuristics based only on pattern graphs are the most efficient. (Source: Interdisciplinary Scie...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 21, 2019 Category: Bioinformatics Source Type: research

Identifying a Gene Knockout Strategy Using a Hybrid of Simple Constrained Artificial Bee Colony Algorithm and Flux Balance Analysis to Enhance the Production of Succinate and Lactate in Escherichia Coli
The objective function of the hybrid algorithm is optimized using a  swarm intelligence optimization algorithm and a Simple Constrained Artificial Bee Colony (SCABC) algorithm. The results maximize the production of lactate and succinate by resembling the gene knockout inE. coli. The  Flux Balance Analysis (FBA) is integrated in a hybrid algorithm to evaluate the growth rate ofE. coli as well as the  productions of lactate and succinate. This results in the identification of a gene knockout list that contributes to maximizing the production of lactate and succinate inE. col...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 13, 2019 Category: Bioinformatics Source Type: research

Seasonality and Trend Forecasting of Tuberculosis Incidence in Chongqing, China
In conclusion, the occurrence of TB in Chongqing is controlled, which may be attributed to socioeconomic developments and improved TB prevention and control services. Applying the X12-ARIMA model is an effective method to forecast and analyze the trend and seasonality of TB. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - February 8, 2019 Category: Bioinformatics Source Type: research

AC: A Compression Tool for Amino Acid Sequences
AbstractAdvancement of protein sequencing technologies has led to the production of a huge volume of data that needs to be stored and transmitted. This challenge can be tackled by compression. In this paper, we propose AC, a state-of-the-art method for lossless compression of amino acid sequences. The proposed method works based on the cooperation between finite-context models and substitutional tolerant Markov models. Compared to several general-purpose and specific-purpose protein compressors, AC provides the best bit-rates. This method can also compress the sequences nine times faster than its competitor, paq8l. In addi...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 5, 2019 Category: Bioinformatics Source Type: research

Co-expression Network Analysis Revealing the Potential Regulatory Roles of lncRNAs in Alzheimer ’s Disease
AbstractAlzheimer ’s disease (AD) is one of the most common types of dementia among the elderly. Previous studies had revealed that the dysregulation of lncRNAs played important roles in human diseases, including AD. However, there is still a lack of comprehensive analysis of differently expressed long non-coding R NAs (lncRNAs) in different distinct regions related to AD. In present study, we identified a total of 678, 593, 941, 1445, 1179, 466 differently expressed lncRNAs that were found in entorhinal cortex (EC), middle temporal gyrus(MTG), hippocampus (HIP), superior frontal gyrus (SFG), posterior cingula te (PC...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 4, 2019 Category: Bioinformatics Source Type: research

BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S -Locus
AbstractNowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene families, or to get evidence for adaptive amino acid evolution, among others. Nevertheless, sequence data are very often spread over several databases, many useful genomes and transcriptomes are non-annotated, the available annotation is not for the desired coding sequence iso...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 2, 2019 Category: Bioinformatics Source Type: research

EvoPPI 1.0: a Web Platform for Within- and Between-Species Multiple Interactome Comparisons and Application to Nine PolyQ Proteins Determining Neurodegenerative Diseases
AbstractProtein –protein interaction (PPI) data is essential to elucidate the complex molecular relationships in living systems, and thus understand the biological functions at cellular and systems levels. The complete map of PPIs that can occur in a living organism is called the interactome. For animals, PPI dat a is stored in multiple databases (e.g., BioGRID, CCSB, DroID, FlyBase, HIPPIE, HitPredict, HomoMINT, INstruct, Interactome3D, mentha, MINT, and PINA2) with different formats. This makes PPI comparisons difficult to perform, especially between species, since orthologous proteins may have different n ames. Mo...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 1, 2019 Category: Bioinformatics Source Type: research

P152R Mutation Within MeCP2 Can Cause Loss of DNA-Binding Selectivity
AbstractMeCP2 is a protein highly expressed in the brain that participates in the genetic expression and RNA splicing regulation. MeCP2 binds preferably to methylated DNA and other nuclear corepressors to alter chromatin. MECP2 gene mutations can cause rett syndrome (RTT), a severe neurological disorder that affects around one in ten thousand girls. In this paper, Molecular Dynamics (MD) simulations were performed to scrutinize how the MeCP2 P152R mutation influences the protein binding to DNA. Also, the Umbrella Sampling technique was used to obtain the potential mean forces (PMFs) of both wild-type and mutated MeCP2 Meth...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 23, 2019 Category: Bioinformatics Source Type: research

The disordered charged biased proteins in the human diseasome
AbstractIntrinsically disordered proteins (IDPs) are often involved in diseases and have been shown to be promising targets for drug development. Here, we focus on the human disordered charged biased proteins (HDCBPs). We have investigated the association of the HDCBPs with diseases by integrating various sources that cover public sources of gene –disease associations and intensive literature mining. The results indicate that 95% of HDCBPs are associated with multiple diseases, including mainly various cancers, nervous, endocrine, immune, hematological, and respiratory systems diseases. Our data show that the HDCBP&n...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 11, 2019 Category: Bioinformatics Source Type: research

Predicting Functional Modules of Liver Cancer Based on Differential Network Analysis
In this study, we applied the method of differential network to identify functional modules between control and disease samples, which are different from most of the current approaches that focus on differential expression. In particular, we applied our approach to analyze transcriptome data of liver cancer in The Cancer Genome Atlas (TCGA,https://cancergenome.nih.gov/), and we obtained two modules associated with liver cancer. One is a functional gene module that contains a set of liver cancer-related genes, and another is an lncRNA (long non-coding RNA) module that includes liver cancer-related lncRNAs. The results of su...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 2, 2019 Category: Bioinformatics Source Type: research

CNN-MGP: Convolutional Neural Networks for Metagenomics Gene Prediction
AbstractAccurate gene prediction in metagenomics fragments is a computationally challenging task due to the short-read length, incomplete, and fragmented nature of the data. Most gene-prediction programs are based on extracting a large number of features and then applying statistical approaches or supervised classification approaches to predict genes. In our study, we introduce a convolutional neural network for metagenomics gene prediction (CNN-MGP) program that predicts genes in metagenomics fragments directly from raw DNA sequences, without the need for manual feature extraction and feature selection stages. CNN-MGP is ...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 27, 2018 Category: Bioinformatics Source Type: research

Selected Aspects of Tobacco-Induced Prothrombotic State, Inflammation and Oxidative Stress: Modeled and Analyzed Using Petri Nets
AbstractMany factors, such as endothelial dysfunction, inflammation and hemostatic disturbances, affect formation and progression of atherosclerotic plaque. In our study, we have focused on hemostatic disturbances with particular emphasis on the extrinsic pathways of coagulation. Thrombin is a main enzyme of coagulation and it is engaged in many different subprocesses. It leads to activation of factors of the coagulation cascade, transition of fibrinogen to fibrin monomer, endothelial damage, inflammation, activation of platelets and proliferation. In our study, selected aspects of disorders in prothrombotic states influen...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 24, 2018 Category: Bioinformatics Source Type: research

Model and Application to Support the Coronary Artery Diseases (CAD): Development and Testing
AbstractCardiovascular diseases are among the main causes of morbidity, disability, and mortality. Most of them occur because of an atherosclerotic plaque developing within a coronary artery, which can cause a narrowing of the vessel lumen (coronary stenosis) or even break it. It is, therefore, useful to evaluate the role of the stress state of the endothelial layer of the arterial tissue, both for the maintenance of the blood circulation and for the implications in presence of a pathology that can lead to thromboembolic complications. The aim of the following study was to develop and test an application that is able to ev...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 7, 2018 Category: Bioinformatics Source Type: research

Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences
AbstractUseful insight into the evolution of genes and gene families can be provided by the analysis of all available genome datasets rather than just a few, which are usually those of model species. Handling and transforming such datasets into the desired format for downstream analyses is, however, often a difficult and time-consuming task for researchers without a background in informatics. Therefore, we present two simple and fast protocols for data preparation, using an easy-to-install, open-source, cross-platform software application with user-friendly, rich graphical user interface (SEDA;http://www.sing-group.org/sed...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 3, 2018 Category: Bioinformatics Source Type: research

Functional Annotation and Analysis of Dual Oxidase 1 (DUOX1): a Potential Anti-pyocyanin Immune Component
In this study, we structurally and functionally annotated the DUOX1, predicted its 3d structure, physio-chemical properties, post-translational modifications, and genetic polymorphism analysis with subsequent disease-associated single-nucleotide variations and their impact on DUOX1 functionality by employing in silico approaches. DUOX1 holds greater homology with gorilla and chimpanzee than other primates. The localization signal peptide was present at the beginning of the peptide with cleavage site at 22 aa position. Three distinct functional domains were observed based on homology: An_peroxidase, FRQ1, and oxido-reductas...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 27, 2018 Category: Bioinformatics Source Type: research

Study of Molecular Mechanism of the Interaction Between MEK1/2 and Trametinib with Docking and Molecular Dynamic Simulation
In this study, the focus of investigation was the mechanism of the interaction between trametinib and MEK1/2 via computational simulation. To specify the best interaction site of inhibitor with MEK1/2 based on the interaction energy ranking, first we performed a docking and then we studied the interactions of the  ATP-bound MEK with trametinib, with RAF and the complex of the ATP-bound MEK–trametinib with RAF via molecular dynamic simulations. The results showed that trametinib inactivates the enzyme by bonding to a group of amino acids including Lys97/101, SER218/216, Asp208/212, and Met143/147 in MEK1/ 2....
Source: Interdisciplinary Sciences, Computational Life Sciences - November 21, 2018 Category: Bioinformatics Source Type: research

Ensemble Technique for Prediction of T-cell Mycobacterium tuberculosis Epitopes
AbstractDevelopment of an effective machine-learning model for T-cellMycobacterium tuberculosis (M. tuberculosis) epitopes is beneficial for saving biologist ’s time and effort for identifying epitope in a targeted antigen. Existing NetMHC 2.2, NetMHC 2.3, NetMHC 3.0 and NetMHC 4.0 estimate binding capacity of peptide. This is still a challenge for those servers to predict whether a given peptide isM. tuberculosis epitope or non-epitope. One of the servers, CTLpred, works in this category but it is limited to peptide length of 9-mers. Therefore, in this work direct method of predicting M. tuberculosis epitope or non-...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 7, 2018 Category: Bioinformatics Source Type: research

An In-Silico Investigation of Key Lysine Residues and Their Selection for Clearing off A β and Holo-AβPP Through Ubiquitination
AbstractMalicious progression of neurodegeneration is a consequence of toxic aggregates of proteins or peptides such as amyloid beta (A β) reported in Alzheimer’s disease (AD). These aggregates hinder the electrochemical transmission at neuronal junctions and thus deteriorate neuronal-health by triggering dementia. Electrostatic and hydrophobic interactions among amino-acid residues are the governing principle behind the self-ass embly of aforesaid noxious oligomers or agglomerate. Interestingly, lysine residues are crucial for these interactions and for facilitating the clearance of toxic metabolites through th...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

Computational Study of HCV p7 Channel: Insight into a New Strategy for HCV Inhibitor Design
AbstractHCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydr...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

An In-Silico Investigation of Key Lysine Residues and Their Selection for Clearing off A β and Holo-AβPP Through Ubiquitination
AbstractMalicious progression of neurodegeneration is a consequence of toxic aggregates of proteins or peptides such as amyloid beta (A β) reported in Alzheimer’s disease (AD). These aggregates hinder the electrochemical transmission at neuronal junctions and thus deteriorate neuronal-health by triggering dementia. Electrostatic and hydrophobic interactions among amino-acid residues are the governing principle behind the self-ass embly of aforesaid noxious oligomers or agglomerate. Interestingly, lysine residues are crucial for these interactions and for facilitating the clearance of toxic metabolites through th...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research