Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells.
Abstract The differentiation of embryonic stem cells into various lineages is highly dependent on the chromatin state of the genome and patterns of gene expression. To identify lineage-specific enhancers driving the differentiation of progenitors into pancreatic cells, we used a previously described computational framework called Total Functional Score of Enhancer Elements (TFSEE), which integrates multiple genomic assays that probe both transcriptional and epigenomic states. First, we evaluated and compared TFSEE as an enhancer-calling algorithm with enhancers called using GRO-seq-defined enhancer transcripts (me...
Source: Bioinformatics and Biology Insights - July 15, 2020 Category: Bioinformatics Authors: Malladi VS, Nagari A, Franco HL, Kraus WL Tags: Bioinform Biol Insights Source Type: research

Identifying Herbal Adverse Events From Spontaneous Reporting Systems Using Taxonomic Name Resolution Approach.
This study aimed to extract, standardize, and summarize supplement-relevant reports from two SRSs: (1) Food and Drug Administration Adverse Event Reporting System (FAERS) and (2) Canada Vigilance Adverse Reaction (CVAR) database. A thesaurus of plant names was developed and integrated with a mapping and normalization approach that accommodated misspellings and variants. The reports gathered from FAERS between the years 2004 and 2016 show 185,915 herbal and 7,235,330 non-herbal accounting for 2.51%. The data from CVAR found 36,940 reports of herbal and 503,580 non-herbal reports between the years 1965 and 2017 for a total o...
Source: Bioinformatics and Biology Insights - July 1, 2020 Category: Bioinformatics Authors: Sharma V, Gelin LFF, Sarkar IN Tags: Bioinform Biol Insights Source Type: research

Comparative Analysis of Sample Extraction and Library Construction for Shotgun Metagenomics.
In this study, quality comparisons for shotgun metagenomics sequencing were performed between 2 DNA extraction methods for fresh and freeze-thaw samples, 2 library preparation protocols, and various sample inputs. The results indicate that Mag-Bind® Universal Metagenomics Kit (OM) outperformed DNeasy PowerSoil Kit (QP) with a higher DNA quantity. Controlling on library preparation protocol, OM detected on-average more genes than QP. For library construction comparison by controlling on the same DNA sample, KAPA Hyper Prep Kit (KH) outperformed the TruePrep DNA Library Prep Kit V2 (TP) with the higher number of detected...
Source: Bioinformatics and Biology Insights - June 18, 2020 Category: Bioinformatics Authors: Peng Z, Zhu X, Wang Z, Yan X, Wang G, Tang M, Jiang A, Kristiansen K Tags: Bioinform Biol Insights Source Type: research

Integrative Analysis of the Genes Induced by the Intestine Microbiota of Infant Born to Term and Breastfed.
Abstract Nowadays, the integration of biological data is a major challenge for bioinformatics. Many studies have examined gene expression in the epithelial tissue in the intestines of infants born to term and breastfed, generating a large amount of data. The integration of these data is important to understand the biological processes involved during bacterial colonization of the newborns intestine, particularly through breast milk. This work aims to exploit the bioinformatics approaches, to provide a new representation and interpretation of the interactions between differentially expressed genes in the host intes...
Source: Bioinformatics and Biology Insights - May 21, 2020 Category: Bioinformatics Authors: Nouadi B, Sbaoui Y, El Messal M, Bennis F, Chegdani F Tags: Bioinform Biol Insights Source Type: research

An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.
Abstract The rapid development of high-performance technologies has greatly promoted studies of molecular oncology producing large amounts of data. Even if these data are publicly available, they need to be processed and studied to extract information useful to better understand mechanisms of pathogenesis of complex diseases, such as tumors. In this article, we illustrated a procedure for mining biologically meaningful biomarkers from microarray datasets of different tumor histotypes. The proposed methodology allows to automatically identify a subset of potentially informative genes from microarray data matrices, ...
Source: Bioinformatics and Biology Insights - May 21, 2020 Category: Bioinformatics Authors: Esposito F, Boccarelli A, Del Buono N Tags: Bioinform Biol Insights Source Type: research

Discovering Selected Antibodies From Deep-Sequenced Phage-Display Antibody Library Using ATTILA.
Brigido MM Abstract Phage display is a powerful technique to select high-affinity antibodies for different purposes, including biopharmaceuticals. Next-generation sequencing (NGS) presented itself as a robust solution, making it possible to assess billions of sequences of the variable domains from selected sublibraries. Handling this process, a central difficulty is to find the selected clones. Here, we present the AutomaTed Tool For Immunoglobulin Analysis (ATTILA), a new tool to analyze and find the enriched variable domains throughout a biopanning experiment. The ATTILA is a workflow that combines publicly ava...
Source: Bioinformatics and Biology Insights - May 21, 2020 Category: Bioinformatics Authors: Maranhão AQ, Silva HM, da Silva WMC, França RKA, De Leo TC, Dias-Baruffi M, Burtet RT, Brigido MM Tags: Bioinform Biol Insights Source Type: research

Comparative Analysis of the Biosimilar and Innovative G-CSF Modulated Pathways on Umbilical Cord Blood-Derived Mononuclear Cells.
In conclusion, our study suggests that G-CSF impacts UBC-derived cells through the modulation of several signaling pathways associated with cell survival, migration, and proliferation. The concordance observed between biosimilar and innovator G-CSF emphasizes their similarity in regards to their specificity and biological responses. PMID: 32231428 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - April 2, 2020 Category: Bioinformatics Authors: Avila-Portillo LM, Aristizabal F, Perdomo S, Riveros A, Ospino B, Avila JP, Butti M, Abba MC Tags: Bioinform Biol Insights Source Type: research

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them.
In this study, a comprehensive bioinformatic analysis of the PPR units and the linkers that connect them was conducted. The results suggested the existence of PPR repeats of various formats, as well as smaller, PPR-unrelated repeats. Besides their length, these repeats differed in amino acid arrangements and location of key amino acids. These findings provide a broader and unified perspective of the pentatricopeptide family while raising provocative questions about the assembly and evolution of these domains. PMID: 32180683 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - March 19, 2020 Category: Bioinformatics Authors: Barik S Tags: Bioinform Biol Insights Source Type: research

Multi-omics Data Integration, Interpretation, and Its Application.
Abstract To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data to highlight the interrelationships of the involved biomolecules and their functions. With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and interpretation. In this review, we collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as ...
Source: Bioinformatics and Biology Insights - February 22, 2020 Category: Bioinformatics Authors: Subramanian I, Verma S, Kumar S, Jere A, Anamika K Tags: Bioinform Biol Insights Source Type: research

PostSV: A Post-Processing Approach for Filtering Structural Variations.
Abstract Genomic structural variations are significant causes of genome diversity and complex diseases. With advances in sequencing technologies, many algorithms have been designed to identify structural differences using next-generation sequencing (NGS) data. Due to repetitions in the human genome and the short reads produced by NGS, the discovery of structural variants (SVs) by state-of-the-art SV callers is not always accurate. To improve performance, multiple SV callers are often used to detect variants. However, most SV callers suffer from high false-positive rates, which diminishes the overall performance, e...
Source: Bioinformatics and Biology Insights - February 7, 2020 Category: Bioinformatics Authors: Alzaid E, Allali AE Tags: Bioinform Biol Insights Source Type: research

In Silico Screening and Analysis of Broad-Spectrum Molecular Targets and Lead Compounds for Diarrhea Therapy.
In conclusion, bacteria DnaE gene or its protein is a highly promising molecular target for the next generation of antibacterial drugs of the class of N-coeleneterazine. PMID: 31695343 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - November 9, 2019 Category: Bioinformatics Authors: Ugboko HU, Nwinyi OC, Oranusi SU, Fatoki TH, Akinduti PA, Enibukun JM Tags: Bioinform Biol Insights Source Type: research

Pathway Analysis of Global Metabolomic Profiles Identified Enrichment of Caffeine, Energy, and Arginine Metabolism in Smokers but Not Moist Snuff Consumers.
In this study, we investigated the effects of tobacco consumption on additional metabolic pathways using pathway-based analysis tools. To this end, metabolic pathway enrichment analysis and topology analysis were performed through pair-wise comparisons of global metabolomic profiles of SMK, MSC, and NTC. The analyses identified>8 significantly perturbed metabolic pathways in SMK compared with NTC and MSC in all 3 matrices. Among these differentially enriched pathways, perturbations of caffeine metabolism, energy metabolism, and arginine metabolism were mostly observed. In comparison, fewer enriched metabolic pathways we...
Source: Bioinformatics and Biology Insights - November 2, 2019 Category: Bioinformatics Authors: Liu G, Lee DP, Schmidt E, Prasad GL Tags: Bioinform Biol Insights Source Type: research

CoMM: A Collaborative Mixed Model That Integrates GWAS and eQTL Data Sets to Investigate the Genetic Architecture of Complex Traits.
Abstract Genome-wide association study (GWAS) analyses have identified thousands of associations between genetic variants and complex traits. However, it is still a challenge to uncover the mechanisms underlying the association. With the growing availability of transcriptome data sets, it has become possible to perform statistical analyses targeted at identifying influential genes whose expression levels correlate with the phenotype. Methods such as PrediXcan and transcriptome-wide association study (TWAS) use the transcriptome data set to fit a predictive model for gene expression, with genetic variants as covari...
Source: Bioinformatics and Biology Insights - October 31, 2019 Category: Bioinformatics Authors: Yeung KF, Yang Y, Yang C, Liu J Tags: Bioinform Biol Insights Source Type: research

Protein Tetratricopeptide Repeat and the Companion Non-tetratricopeptide Repeat Helices: Bioinformatic Analysis of Interhelical Interactions.
Abstract The tetratricopeptide repeat (TPR) of proteins consists of a 34-amino acid, alpha-helical motif that comprises a pattern of small and large hydrophobic residues, leading to a recognizable signature sequence. Structural and functional studies have documented that tandem TPRs form a superhelix that interacts with client molecules through strategically placed amino acids. Interestingly, most of the known TPRs are flanked by alpha-helices that lack the TPR signature but often appear as a continuation of the TPR superhelix. The exact role and specificity of these TPR-accompanying non-TPR helices have remained ...
Source: Bioinformatics and Biology Insights - October 4, 2019 Category: Bioinformatics Authors: Barik S Tags: Bioinform Biol Insights Source Type: research

Corrigendum to Tackling the Challenges of FASTQ Referential Compression.
Authors: Abstract [This corrects the article DOI: 10.1177/1177932218821373.]. PMID: 31555045 [PubMed - in process] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - September 28, 2019 Category: Bioinformatics Tags: Bioinform Biol Insights Source Type: research

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.
In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp. PMID: 31523131 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - September 18, 2019 Category: Bioinformatics Authors: Ishiya K, Mizuno F, Wang L, Ueda S Tags: Bioinform Biol Insights Source Type: research

On the Upper Bounds of the Real-Valued Predictions.
Abstract Predictions are fundamental in science as they allow to test and falsify theories. Predictions are ubiquitous in bioinformatics and also help when no first principles are available. Predictions can be distinguished between classifications (when we associate a label to a given input) or regression (when a real value is assigned). Different scores are used to assess the performance of regression predictors; the most widely adopted include the mean square error, the Pearson correlation (ρ), and the coefficient of determination (or R 2 ). The common conception related to the last 2 indices is that the th...
Source: Bioinformatics and Biology Insights - September 7, 2019 Category: Bioinformatics Authors: Benevenuta S, Fariselli P Tags: Bioinform Biol Insights Source Type: research

Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS.
Abstract The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS (https://masstools.ipbs.fr/m...
Source: Bioinformatics and Biology Insights - August 29, 2019 Category: Bioinformatics Authors: Lesne J, Bousquet MP, Marcoux J, Locard-Paulet M Tags: Bioinform Biol Insights Source Type: research

Enjoy the Silence: Nearly Half of Human tRNA Genes Are Silent.
Abstract Transfer RNAs (tRNAs) are key components of the translation machinery. They read codons on messenger RNAs (mRNAs) and deliver the appropriate amino acid to the ribosome for protein synthesis. The human genome encodes more than 500 tRNA genes but their individual contribution to the cellular tRNA pool is unclear. In recent years, novel methods were developed to improve the quantification of tRNA gene expression, most of which rely on next-generation sequencing such as small RNA-Seq applied to tRNAs (tRNA-Seq). In a previous study, we presented a bioinformatics strategy to analyse tRNA-Seq datasets that we ...
Source: Bioinformatics and Biology Insights - August 28, 2019 Category: Bioinformatics Authors: Torres AG Tags: Bioinform Biol Insights Source Type: research

Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor.
This study aims to model the 3-dimensional (3D) structure of PfADSL, design and predict in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) of 8 substituted benzo[d]imidazol-1-yl)methyl)benzimidamide compounds as well as predict the potential interaction modes and binding affinities of the designed ligands with the modelled PfADSL. PfADSL 3D structure was modelled using SWISS-MODEL, whereas the compounds were designed using ChemDraw Professional. ADMET predictions were done using OSIRIS Property Explorer and Swiss ADME, whereas molecular docking was done with AutoDock Tools. All designed compound...
Source: Bioinformatics and Biology Insights - August 9, 2019 Category: Bioinformatics Authors: Oduselu GO, Ajani OO, Ajamma YU, Brors B, Adebiyi E Tags: Bioinform Biol Insights Source Type: research

Characterization and Expression Analysis of Heme Oxygenase Genes from Sorghum bicolor.
This study identified and characterized 4 heme oxygenase members from Sorghum bicolor. Multiple sequence alignments showed that the heme oxygenase signature motif (QAFICHFYNI/V) is conserved across all SbHO proteins and that they share above 90% sequence identity with other cereals. Quantitative real-time polymerase chain reaction revealed that SbHO genes were expressed in leaves, stems, and roots, but most importantly their transcript level was induced by osmotic stress, indicating that they might play a role in stress responses. These findings will strengthen our understanding of the role of heme oxygenases in plant stre...
Source: Bioinformatics and Biology Insights - July 21, 2019 Category: Bioinformatics Authors: Mulaudzi-Masuku T, Ikebudu V, Muthevhuli M, Faro A, Gehring CA, Iwuoha E Tags: Bioinform Biol Insights Source Type: research

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data.
Abstract Empirical Bayes is a choice framework for differential expression (DE) analysis for multi-group RNA-seq count data. Its characteristic ability to compute posterior probabilities for predefined expression patterns allows users to assign the pattern with the highest value to the gene under consideration. However, current Bayesian methods such as baySeq and EBSeq can be improved, especially with respect to normalization. Two R packages (baySeq and EBSeq) with their default normalization settings and with other normalization methods (MRN and TCC) were compared using three-group simulation data and real count ...
Source: Bioinformatics and Biology Insights - July 19, 2019 Category: Bioinformatics Authors: Osabe T, Shimizu K, Kadota K Tags: Bioinform Biol Insights Source Type: research

Moving Just Enough Deep Sequencing Data to Get the Job Done.
Abstract Motivation: As the size of high-throughput DNA sequence datasets continues to grow, the cost of transferring and storing the datasets may prevent their processing in all but the largest data centers or commercial cloud providers. To lower this cost, it should be possible to process only a subset of the original data while still preserving the biological information of interest. Results: Using 4 high-throughput DNA sequence datasets of differing sequencing depth from 2 species as use cases, we demonstrate the effect of processing partial datasets on the number of detected RNA transcripts using an RNA-...
Source: Bioinformatics and Biology Insights - June 28, 2019 Category: Bioinformatics Authors: Mills N, Bensman EM, Poehlman WL, Ligon WB, Feltus FA Tags: Bioinform Biol Insights Source Type: research

Time-Frequency Approach Applied to Finding Interaction Regions in Pathogenic Proteins.
Abstract Protein-protein interactions govern all molecular processes for living organisms, even those involved in pathogen infection. Pathogens such as virus, bacteria, and parasites contain proteins that help the pathogen to attach, penetrate, and settle inside the target cell. Thus, it is necessary to know the regions in pathogenic proteins that interact with host cell receptors. Currently, powerful pathogen databases are available and many pathogenic proteins have been recognized, but many pathogenic proteins have not been characterized. This work developed a program in MATLAB environment based on the time-freq...
Source: Bioinformatics and Biology Insights - June 19, 2019 Category: Bioinformatics Authors: Arenas AF, Arango-Plaza N, Arenas JC, Salcedo GE Tags: Bioinform Biol Insights Source Type: research

Cancer Genetic Network Inference Using Gaussian Graphical Models.
In this study, we focus on inferring gene interactions in 15 specific types of human cancer using RNA-Seq expression data and GGM with graphical lasso. We take advantage of the corresponding Kyoto Encyclopedia of Genes and Genomes pathway maps to define the subsets of related genes. RNA-Seq expression levels of the subsets of genes in solid cancerous tumor and normal tissues were extracted from TCGA. The gene expression data sets were cleaned and formatted, and the genetic network corresponding to each cancer type was then inferred using GGM with graphical lasso. The inferred networks reveal stable conditional dependences ...
Source: Bioinformatics and Biology Insights - April 23, 2019 Category: Bioinformatics Authors: Zhao H, Duan ZH Tags: Bioinform Biol Insights Source Type: research

High-Throughput Analysis of Clinical Flow Cytometry Data by Automated Gating.
Abstract Advancements in flow cytometers with capability to measure 15 or more parameters have enabled us to characterize cell populations at unprecedented levels of detail. Beyond discovery research, there is now a growing demand to dive deeper into evaluating the immune response in clinical trials for immune modulating compounds. However, for high-volume, complex flow cytometry data generated in clinical trials, conventional manual gating remains the standard of practice. Traditional manual gating is resource intense and becomes a bottleneck and an impractical method to complete high volumes of flow cytometry da...
Source: Bioinformatics and Biology Insights - April 17, 2019 Category: Bioinformatics Authors: Lee H, Sun Y, Patti-Diaz L, Hedrick M, Ehrhardt AG Tags: Bioinform Biol Insights Source Type: research

Tackling the Challenges of FASTQ Referential Compression.
aza S Abstract The exponential growth of genomic data has recently motivated the development of compression algorithms to tackle the storage capacity limitations in bioinformatics centers. Referential compressors could theoretically achieve a much higher compression than their non-referential counterparts; however, the latest tools have not been able to harness such potential yet. To reach such goal, an efficient encoding model to represent the differences between the input and the reference is needed. In this article, we introduce a novel approach for referential compression of FASTQ files. The core of our compre...
Source: Bioinformatics and Biology Insights - February 24, 2019 Category: Bioinformatics Authors: Guerra A, Lotero J, Aedo JÉ, Isaza S Tags: Bioinform Biol Insights Source Type: research

Combining Strengths for Multi-genome Visual Analytics Comparison.
Abstract The eclosion of data acquisition technologies has shifted the bottleneck in molecular biology research from data acquisition to data analysis. Such is the case in Comparative Genomics, where sequence analysis has transitioned from genes to genomes of several orders of magnitude larger. This fact has revealed the need to adapt software to work with huge experiments efficiently and to incorporate new data-analysis strategies to manage results from such studies. In previous works, we presented GECKO, a software to compare large sequences; now we address the representation, browsing, data exploration, and pos...
Source: Bioinformatics and Biology Insights - February 21, 2019 Category: Bioinformatics Authors: Diaz-Del-Pino S, Rodriguez-Brazzarola P, Perez-Wohlfeil E, Trelles O Tags: Bioinform Biol Insights Source Type: research

Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum.
In this study, the capacity to engage in domain swapping was predicted from mere sequence information in the whole genome of holy Basil (Ocimum tenuiflorum), which is well known to be an anti-stress agent. Approximately, one-fourth of the proteins of O tenuiflorum are predicted to undergo three-dimensional (3D)-domain swapping. Furthermore, function annotation was carried out on all the predicted domain-swap sequences from the O tenuiflorum and Arabidopsis thaliana for their distribution in different Pfam protein families and gene ontology (GO) terms. These domain-swapped protein sequences are associated with many Pfam pro...
Source: Bioinformatics and Biology Insights - January 31, 2019 Category: Bioinformatics Authors: Upadhyay AK, Sowdhamini R Tags: Bioinform Biol Insights Source Type: research

AutoAnalyze in Systems Biology.
Abstract AutoAnalyze is a highly customizable framework for the visualization and analysis of large-scale model graphs. Originally developed for use in the automotive domain, it also supports efficient computation within molecular networks represented by reaction equations. A static analysis approach is used for efficient treatment-condition-specific simulation. The chosen method relies on the computation of a global network data-flow resulting from the evaluation of individual genetic data. The approach facilitates complex analyses of biological components from a molecular network under specific therapeutic pertu...
Source: Bioinformatics and Biology Insights - January 25, 2019 Category: Bioinformatics Authors: Saad C, Bauer B, Mansmann UR, Li J Tags: Bioinform Biol Insights Source Type: research

HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants.
Abstract Heat stress transcription factors (HSFs) regulate transcriptional response to a large number of environmental influences, such as temperature fluctuations and chemical compound applications. Plant HSFs represent a large and diverse gene family. The HSF members vary substantially both in gene expression patterns and molecular functions. HEATSTER is a web resource for mining, annotating, and analyzing members of the different classes of HSFs in plants. A web-interface allows the identification and class assignment of HSFs, intuitive searches in the database and visualization of conserved motifs, and domains...
Source: Bioinformatics and Biology Insights - January 25, 2019 Category: Bioinformatics Authors: Berz J, Simm S, Schuster S, Scharf KD, Schleiff E, Ebersberger I Tags: Bioinform Biol Insights Source Type: research

Potential Anti-Cancer Flavonoids Isolated From Caesalpinia bonduc Young Twigs and Leaves: Molecular Docking and In Silico Studies.
Abstract Tyrosine kinase (TK), vascular endothelial growth factor (VEGF), and matrix metalloproteinases (MMP) are important cancer therapeutic target proteins. Based on reported anti-cancer and cytotoxic activities of Caesalpinia bonduc, this study isolated phytochemicals from young twigs and leaves of C bonduc and identified the interaction between them and cancer target proteins (TK, VEGF, and MMP) in silico. AutoDock Vina, iGEMDOCK, and analysis of pharmacokinetic and pharmacodynamic properties of the isolated bioactives as therapeutic molecules were performed. Seven phytochemicals (7-hydroxy-4'-methoxy-3,11-de...
Source: Bioinformatics and Biology Insights - January 25, 2019 Category: Bioinformatics Authors: Iheagwam FN, Ogunlana OO, Ogunlana OE, Isewon I, Oyelade J Tags: Bioinform Biol Insights Source Type: research

Anabel: An Online Tool for the Real-Time Kinetic Analysis of Binding Events.
Roth G Abstract Anabel (Analysis of binding events + l) is an open source online software tool (www.skscience.org/anabel) for the convenient analysis of molecular binding interactions. Currently, exported datasets from Biacore (surface plasmon resonance [SPR]), FortéBio (biolayer interference [BLI]), and Biametrics (single color reflectometry [SCORE]) can be uploaded and evaluated in Anabel using 2 different evaluation methods. Moreover, a universal data template format is provided to upload any other binding dataset to Anabel. This enables an easier comparison of different analysis methods f...
Source: Bioinformatics and Biology Insights - January 25, 2019 Category: Bioinformatics Authors: Krämer SD, Wöhrle J, Rath C, Roth G Tags: Bioinform Biol Insights Source Type: research

Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum.
Abstract The psychostimulant amphetamine can be prescribed to ameliorate the symptoms of narcolepsy, attention-deficit hyperactivity disorder and to facilitate weight loss. This stimulant can also have negative effects including toxicity and addiction risk. The impact of amphetamine on gene networks is partially understood and this study addresses this gap in consideration of the physical activity. The striata of mice exposed to either amphetamine or saline treatment were compared in a mouse line selected for home cage physical overactivity, a phenotype that can be mitigated with amphetamine, and in a contemporary...
Source: Bioinformatics and Biology Insights - December 20, 2018 Category: Bioinformatics Authors: Goncalves TM, Southey BR, Rodriguez-Zas SL Tags: Bioinform Biol Insights Source Type: research

Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches.
This study recommends an in vivo assessment for the most promising peptides especially FFKEHGVPL. PMID: 30542244 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - December 15, 2018 Category: Bioinformatics Authors: Mohammed AA, ALnaby AM, Sabeel SM, AbdElmarouf FM, Dirar AI, Ali MM, Khandgawi MA, Yousif AM, Abdulgadir EM, Sabahalkhair MA, Abbas AE, Hassan MA Tags: Bioinform Biol Insights Source Type: research

Genomic Interventions in Medicine.
Abstract Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics ...
Source: Bioinformatics and Biology Insights - December 15, 2018 Category: Bioinformatics Authors: Aworunse OS, Adeniji O, Oyesola OL, Isewon I, Oyelade J, Obembe OO Tags: Bioinform Biol Insights Source Type: research

Mathematical Model for Small Size Time Series Data of Bacterial Secondary Metabolic Pathways.
Abstract Measuring the concentrations of metabolites and estimating the reaction rates of each reaction step consisting of metabolic pathways are significant for an improvement in microorganisms used in maximizing the production of materials. Although the reaction pathway must be identified for such an improvement, doing so is not easy. Numerous reaction steps have been reported; however, the actual reaction steps activated vary or change according to the conditions. Furthermore, to build mathematical models for a dynamical analysis, the reaction mechanisms and parameter values must be known; however, to date, suf...
Source: Bioinformatics and Biology Insights - May 30, 2018 Category: Bioinformatics Authors: Tominaga D, Kawaguchi H, Hori Y, Hasunuma T, Ogino C, Aburatani S Tags: Bioinform Biol Insights Source Type: research

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis.
Abstract Caseous lymphadenitis (CLA) is a disease caused by Corynebacterium pseudotuberculosis bacteria that affects sheep and goats. The absence of a serologic diagnose is a factor that contributes for the disease dissemination, and due to the formation of granuloma, the treatment is very expensive. Therefore, prophylaxis is the approach with best cost-benefit relation; however, it still lacks an effective vaccine. In this sense, this work seeks to apply bioinformatic tools to design an effective vaccine against CLA, using CP40 protein as standard for the design of immunodominant epitopes, from which a total of 6...
Source: Bioinformatics and Biology Insights - May 23, 2018 Category: Bioinformatics Authors: Droppa-Almeida D, Franceschi E, Padilha FF Tags: Bioinform Biol Insights Source Type: research

Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity.
In this study, we identified the product with an HSP90 (heat shock protein 90) domain encoded by lipophosphoglycan (LPG3) gene as a L infantum chagasi HBP (HBPLc). Structural analysis using the LPG3 recombinant protein suggests that it is organized as a tetramer. Binding analysis confirms that it is capable of binding heparin with micromolar affinity. Inhibition of adenosine triphosphatase activity in the presence of heparin, molecular modeling, and in silico docking analysis suggests that heparin-binding site superimposes with the adenosine triphosphate-binding site. Together, these results show new properties of LPG3 and...
Source: Bioinformatics and Biology Insights - March 27, 2018 Category: Bioinformatics Authors: Martins TVF, Zeraik AE, Alves NO, de Oliveira LL, de Oliveira Mendes TA, DeMarco R, de Almeida Marques-da-Silva E Tags: Bioinform Biol Insights Source Type: research

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).
Abstract Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framewor...
Source: Bioinformatics and Biology Insights - March 3, 2018 Category: Bioinformatics Authors: Zeng ISL, Lumley T Tags: Bioinform Biol Insights Source Type: research

Analysis of Conserved, Computationally Predicted Epitope Regions for VP5 and VP7 Across three Orbiviruses.
Abstract Orbiviruses are double-stranded RNA viruses that have profound economic and veterinary significance, 3 of the most important being African horse sickness virus (AHSV), bluetongue virus (BTV), and epizootic hemorrhagic disease virus (EHDV). Currently, vaccination and vector control are used as preventative measures; however, there are several problems with the current vaccines. Comparing viral amino acid sequences, we obtained an AHSV-BTV-EHDV consensus sequence for VP5 (viral protein 5) and for VP7 (viral protein 7) and generated homology models for these proteins. The structures and sequences were analyz...
Source: Bioinformatics and Biology Insights - February 14, 2018 Category: Bioinformatics Authors: Russell BL, Parbhoo N, Gildenhuys S Tags: Bioinform Biol Insights Source Type: research

Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes.
Conclusions: Although 4 of 7 finally outputted genes have been previously reported to be clock controlled, heretofore there is no report about the circadian expression of 3 other genes. Considering the importance of oncogenes/TSGs in the initiation and progression of cancer, further studies are suggested for the identification of exact circadian expression patterns of these 3 human oncogenes/TSGs. PMID: 29276378 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - December 27, 2017 Category: Bioinformatics Authors: Salavaty A, Mohammadi N, Shahmoradi M, Naderi Soorki M Tags: Bioinform Biol Insights Source Type: research

Computational Model of the Effect of a Surface-Binding Site on the Saccharomycopsis fibuligera R64 α-Amylase to the Substrate Adsorption.
The objective of this study was to design a computational model of Sfamy R64 with increased starch adsorptivity using bioinformatics method. The model structure of Sfamy R64 was compared with the positive control, ie, Aspergillus niger α-amylase. The structural comparison showed that Sfamy R64 lacks the surface-binding site (SBS). An SBS was introduced to the structure of Sfamy R64 by S383Y/S386W mutations. The dynamics and binding affinity of the SBS of mutant to the substrate were also improved and comparable with that of the positive control. PMID: 29162975 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - November 23, 2017 Category: Bioinformatics Authors: Yusuf M, Baroroh U, Hasan K, Rachman SD, Ishmayana S, Subroto T Tags: Bioinform Biol Insights Source Type: research

Finding the Sources of Missing Heritability within Rare Variants Through Simulation.
Abstract Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. The "missing heritability" problem can be partly explained by rare variants. We simulated a causality scenario that gestational ages, a quantitative trait that can distinguish preterm (
Source: Bioinformatics and Biology Insights - October 21, 2017 Category: Bioinformatics Authors: Bandyopadhyay B, Chanda V, Wang Y Tags: Bioinform Biol Insights Source Type: research

A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines.
In conclusion, despite their slower growth in liquid LB medium, bacteria from GC-rich genera outcompete the GC-poor bacteria because their specific enzymatic abilities impart a selective advantage in the DTT. PMID: 28989277 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - October 11, 2017 Category: Bioinformatics Authors: Carels N, Gumiel M, da Mota FF, de Carvalho Moreira CJ, Azambuja P Tags: Bioinform Biol Insights Source Type: research

Bioinformatics Study of m.9053G > A Mutation at the ATP6 Gene in Relation to Type 2 Diabetes Mellitus and Cataract Diseases.
This study aims to investigate the mutation effect of m.9053G>A at the ATP6 gene (S167N) to the structure and function of ATPase6 using bioinformatics method. The structure of ATPase6 was constructed using homology modeling method. The crystal structure of bovine's ATP synthase (Protein Data Bank ID 5FIL) was used as a template because of high sequence similarity (77%) and coverage (96%) of the input sequence. The effect of mutation was investigated at the proton translocation channel of ATPase6. It is predicted that the channel was disrupted due to changes in electrostatic potential from serine to asparagine. Furthermo...
Source: Bioinformatics and Biology Insights - September 23, 2017 Category: Bioinformatics Authors: Permana Maksum I, Saputra SR, Indrayati N, Yusuf M, Subroto T Tags: Bioinform Biol Insights Source Type: research

Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.
In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (RkNN) search. The RkNN search was used to identify an impact of a protein on other proteins. Then, associations between proteins and diseases were inferred statistically. The method using the RkNN search yielded a much higher precision than a random selection, standard nearest neighbor search, or when applying the method to a random protein-protein interaction network. A...
Source: Bioinformatics and Biology Insights - August 2, 2017 Category: Bioinformatics Authors: Suratanee A, Plaimas K Tags: Bioinform Biol Insights Source Type: research

CellTrans: An R Package to Quantify Stochastic Cell State Transitions.
e A Abstract Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments. The R package is based on a mathematical model in whic...
Source: Bioinformatics and Biology Insights - July 1, 2017 Category: Bioinformatics Authors: Buder T, Deutsch A, Seifert M, Voss-Böhme A Tags: Bioinform Biol Insights Source Type: research

A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major.
We present an approach for detecting enzymes that are specific of Leishmania major compared with Homo sapiens and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for L major compared with H sapiens, only 40 (23 Enz...
Source: Bioinformatics and Biology Insights - June 25, 2017 Category: Bioinformatics Authors: Catharina L, Lima CR, Franca A, Guimarães ACR, Alves-Ferreira M, Tuffery P, Derreumaux P, Carels N Tags: Bioinform Biol Insights Source Type: research

Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows.
Abstract In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NEL = 1.34 Mcal/kg) or overfed a moder...
Source: Bioinformatics and Biology Insights - June 8, 2017 Category: Bioinformatics Authors: Agrawal A, Khan MJ, Graugnard DE, Vailati-Riboni M, Rodriguez-Zas SL, Osorio JS, Loor JJ Tags: Bioinform Biol Insights Source Type: research