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

Current Developments in Machine Learning Techniques in Biological Data Mining.
Abstract This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Machine learning methods in particular, a subfield of computer science, have evolved as an indi...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Dumancas GG, Adrianto I, Bello G, Dozmorov M Tags: Bioinform Biol Insights Source Type: research

Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships.
Abstract The detection of orthologs is a key approach in genomics, useful to understand gene evolution and phylogenetic relationships and essential for gene function prediction. However, a reliable annotation of the encoded protein regions is still a limiting aspect in genomics, mainly due to the lack of confirmatory experimental evidence at proteome level. Nevertheless, the current ortholog collections are generally based on protein sequence comparisons, in addition to the availability of large transcriptome sequence collections. We developed Transcriptologs, a method for the prediction of orthologs based on simi...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Ambrosino L, Chiusano ML Tags: Bioinform Biol Insights Source Type: research

Plasma MicroRNA Levels Following Resection of Metastatic Melanoma.
Abstract Melanoma remains the leading cause of skin cancer-related deaths. Surgical resection and adjuvant therapies can result in disease-free intervals for stage III and stage IV disease; however, recurrence is common. Understanding microRNA (miR) dynamics following surgical resection of melanomas is critical to accurately interpret miR changes suggestive of melanoma recurrence. Plasma of 6 patients with stage III (n = 2) and stage IV (n = 4) melanoma was evaluated using the NanoString platform to determine pre- and postsurgical miR expression profiles, enabling analysis of more than 800 miRs simultaneously in 1...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Latchana N, Abrams ZB, Howard JH, Regan K, Jacob N, Fadda P, Terando A, Markowitz J, Agnese D, Payne P, Carson WE Tags: Bioinform Biol Insights Source Type: research

PISMA: A Visual Representation of Motif Distribution in DNA Sequences.
era S, Galván SC Abstract BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either ...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Alcántara-Silva R, Alvarado-Hermida M, Díaz-Contreras G, Sánchez-Barrios M, Carrera S, Galván SC Tags: Bioinform Biol Insights Source Type: research

An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of Cymbopogon winterianus.
This study reports the isolation, characterization, and tissue-specific expression analysis of HMGR from citronella. The modelled HMGR is a class I type of HMGR enzyme with 3-domain architecture. The active site comprises a cofactor (nicotinamide adenine dinucleotide phosphate) and the substrate-binding motifs. The real-time and quantitative reverse transcription-polymerase chain reaction results revealed equal expression level in both leaf sheath and root tissue. The results from our study shall be a valuable resource for future molecular intervention to alter the metabolic flux towards improvement of key active ingredien...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Devi K, Patar L, Modi MK, Sen P Tags: Bioinform Biol Insights Source Type: research

In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.
In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeat...
Source: Bioinformatics and Biology Insights - May 6, 2017 Category: Bioinformatics Authors: Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Júnior MTS Tags: Bioinform Biol Insights Source Type: research

Integrating Epigenomics into the Understanding of Biomedical Insight.
Abstract Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and ...
Source: Bioinformatics and Biology Insights - December 17, 2016 Category: Bioinformatics Authors: Han Y, He X Tags: Bioinform Biol Insights Source Type: research

Clustering Algorithms: Their Application to Gene Expression Data.
Abstract Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techni...
Source: Bioinformatics and Biology Insights - December 12, 2016 Category: Bioinformatics Authors: Oyelade J, Isewon I, Oladipupo F, Aromolaran O, Uwoghiren E, Ameh F, Achas M, Adebiyi E Tags: Bioinform Biol Insights Source Type: research

Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.
Abstract Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today's supercomputer often consists of clusters of SMP...
Source: Bioinformatics and Biology Insights - December 12, 2016 Category: Bioinformatics Authors: Shrimankar DD, Sathe SR Tags: Bioinform Biol Insights Source Type: research

Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks.
Abstract As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pi...
Source: Bioinformatics and Biology Insights - November 6, 2016 Category: Bioinformatics Authors: Laczik M, Hendrickx J, Veillard AC, Tammoh M, Marzi S, Poncelet D Tags: Bioinform Biol Insights Source Type: research

Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins.
Abstract It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca(2+) uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson-Boltzmann equation. Several different bioinformatics tools and available web servers were...
Source: Bioinformatics and Biology Insights - November 6, 2016 Category: Bioinformatics Authors: Grasso EJ, Sottile AE, Coronel CE Tags: Bioinform Biol Insights Source Type: research

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha.
In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman's rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the ...
Source: Bioinformatics and Biology Insights - October 2, 2016 Category: Bioinformatics Authors: Karumathil S, Dirisala VR, Srinadh U, Nikhil V, Kumar NS, Nair RR Tags: Bioinform Biol Insights Source Type: research

Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach.
Abstract The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and...
Source: Bioinformatics and Biology Insights - September 8, 2016 Category: Bioinformatics Authors: Borkotoky S, Meena CK, Murali A Tags: Bioinform Biol Insights Source Type: research

In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.
Abstract Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidati...
Source: Bioinformatics and Biology Insights - August 27, 2016 Category: Bioinformatics Authors: John A, Umashankar V, Samdani A, Sangeetha M, Krishnakumar S, Deepa PR Tags: Bioinform Biol Insights Source Type: research

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.
We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID: 27499617 [PubMed] (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - August 10, 2016 Category: Bioinformatics Authors: Poehlman WL, Rynge M, Branton C, Balamurugan D, Feltus FA Tags: Bioinform Biol Insights Source Type: research

Computational Identification of Novel Genes: Current and Future Perspectives.
Abstract While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and specia...
Source: Bioinformatics and Biology Insights - August 7, 2016 Category: Bioinformatics Authors: Klasberg S, Bitard-Feildel T, Mallet L Tags: Bioinform Biol Insights Source Type: research

Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2).
The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). A full coding sequence of the Sox2 gene from the brain of C. dromedarius was amplified by reverse transcription PCRjmc and then sequenced using the 3730XL series platform Sequencer (Applied Biosystem) for the first time. The cDNA sequence displayed an open reading frame of 822 nucleotides, encoding a protein of 273 amino acids. The molecular weight and the isoelectric point of the translated protein were calculated as 29.825 kDa and 10.11, respectively, using bioinformatics analysis. The pr...
Source: Bioinformatics and Biology Insights - August 4, 2016 Category: Bioinformatics Authors: Alawad A, Alharbi S, Alhazzaa O, Alagrafi F, Alkhrayef M, Alhamdan Z, Alenazi A, Al-Johi H, Alanazi IO, Hammad M Tags: Bioinform Biol Insights Source Type: research

Molecular Shape Analysis-Guided Virtual Screening Platform for Adenosine Kinase Inhibitors.
Abstract We propose a new application of molecular shape descriptors in hierarchical selection during virtual screening (VS). Here, a structure-based pharmacophore and docking-guided VS protocol have been evolved to identify inhibitors against adenosine kinase (AK). The knowledge gained on the shape requirements has been extrapolated in classifying active and inactive molecules against this target. This classification enabled us to pick the appropriate ligand conformation in the binding site. We have suggested a set of hierarchical filters for VS, from a simple molecular shape analysis (MSA) descriptor-based recur...
Source: Bioinformatics and Biology Insights - August 3, 2016 Category: Bioinformatics Authors: Bhutoria S, Das B, Ghoshal N Tags: Bioinform Biol Insights Source Type: research

PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
Abstract Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. These details include the results of the quantification and analysis of all the interactions in the complex. The ava...
Source: Bioinformatics and Biology Insights - August 3, 2016 Category: Bioinformatics Authors: Mathew OK, Sowdhamini R Tags: Bioinform Biol Insights Source Type: research

S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition.
This report describes a stochastic simulation model, S2M, which can be used to generate hypothetical outcomes based on known mechanisms of genetic diversity. S2M begins with predefined genotypes based on the Sabin-1 and Mahoney wild-type sequences, constructs a set of independent cell-based populations, and performs in-cell replication and cell-to-cell infection cycles while quantifying genetic changes that track the transition from Sabin-1 toward Mahoney. Realism is incorporated into the model by assigning defaults for variables that constrain mechanisms of genetic variability based roughly on metrics reported in the lite...
Source: Bioinformatics and Biology Insights - July 9, 2016 Category: Bioinformatics Authors: Ecale Zhou CL Tags: Bioinform Biol Insights Source Type: research

PDBparam: Online Resource for Computing Structural Parameters of Proteins.
Abstract Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified int...
Source: Bioinformatics and Biology Insights - June 24, 2016 Category: Bioinformatics Authors: Nagarajan R, Archana A, Thangakani AM, Jemimah S, Velmurugan D, Gromiha MM Tags: Bioinform Biol Insights Source Type: research