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Bioinformatics and Biology Insights

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https://read.qxmd.com/read/30792576/tackling-the-challenges-of-fastq-referential-compression
#1
Aníbal Guerra, Jaime Lotero, José Édinson Aedo, Sebastián Isaza
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...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30783378/combining-strengths-for-multi-genome-visual-analytics-comparison
#2
Sergio Diaz-Del-Pino, Pablo Rodriguez-Brazzarola, Esteban Perez-Wohlfeil, Oswaldo Trelles
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 post-processing of the massive amount of information derived from such comparisons...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30692846/genome-wide-analysis-of-domain-swap-predicted-products-in-the-genome-of-anti-stress-medicinal-plant-ocimum-tenuiflorum
#3
Atul Kumar Upadhyay, Ramanathan Sowdhamini
Computational approaches to high-throughput data are gaining importance because of explosion of sequences in the post-genomic era. This explosion of sequence data creates a huge gap among the domains of sequence structure and function, since the experimental techniques to determine the structure and function are very expensive, time taking, and laborious in nature. Therefore, there is an urgent need to emphasize on the development of computational approaches in the field of biological systems. Engagement of proteins in quaternary arrangements, such as domain swapping, might be relevant for higher compatibility of such genes at stress conditions...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30670920/anabel-an-online-tool-for-the-real-time-kinetic-analysis-of-binding-events
#4
Stefan D Krämer, Johannes Wöhrle, Christin Rath, Günter Roth
Anabel ( Ana lysis of b inding e vents +  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...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30670919/potential-anti-cancer-flavonoids-isolated-from-caesalpinia-bonduc-young-twigs-and-leaves-molecular-docking-and-in-silico-studies
#5
Franklyn Nonso Iheagwam, Olubanke Olujoke Ogunlana, Oluseyi Ebenezer Ogunlana, Itunuoluwa Isewon, Jelili Oyelade
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...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30670918/heatster-a-database-and-web-server-for-identification-and-classification-of-heat-stress-transcription-factors-in-plants
#6
Jannik Berz, Stefan Simm, Sebastian Schuster, Klaus-Dieter Scharf, Enrico Schleiff, Ingo Ebersberger
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 to classify novel HSFs...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30670917/autoanalyze-in-systems-biology
#7
Christian Saad, Bernhard Bauer, Ulrich R Mansmann, Jian Li
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 perturbations, as demonstrated in a case study...
2019: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30559594/interplay-between-amphetamine-and-activity-level-in-gene-networks-of-the-mouse-striatum
#8
Tassia M Goncalves, Bruce R Southey, Sandra L Rodriguez-Zas
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 control line using RNA-seq...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30546257/genomic-interventions-in-medicine
#9
REVIEW
Oluwadurotimi S Aworunse, Oluwatomiwa Adeniji, Olusola L Oyesola, Itunuoluwa Isewon, Jelili Oyelade, Olawole O Obembe
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...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/30542244/epitope-based-peptide-vaccine-against-fructose-bisphosphate-aldolase-of-madurella-mycetomatis-using-immunoinformatics-approaches
#10
Arwa A Mohammed, Ayman Mh ALnaby, Solima M Sabeel, Fagr M AbdElmarouf, Amina I Dirar, Mostafa M Ali, Mustafa A Khandgawi, Abdelhameed M Yousif, Eman M Abdulgadir, Magdi A Sabahalkhair, Ayman E Abbas, Mohammed A Hassan
Background: Mycetoma is a distinct body tissue destructive and neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections ( actinomycetoma ) such as Streptomyces somaliensis and Nocardiae or true fungi ( eumycetoma ) such as Madurella mycetomatis . To date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29795980/mathematical-model-for-small-size-time-series-data-of-bacterial-secondary-metabolic-pathways
#11
Daisuke Tominaga, Hideo Kawaguchi, Yoshimi Hori, Tomohisa Hasunuma, Chiaki Ogino, Sachiyo Aburatani
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, sufficient information has yet to be published for many cases...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29780242/immune-informatic-analysis-and-design-of-peptide-vaccine-from-multi-epitopes-against-corynebacterium-pseudotuberculosis
#12
Daniela Droppa-Almeida, Elton Franceschi, Francine Ferreira Padilha
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 sequences were obtained, varying from 10 to 16 amino acid residues...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29568220/lipophosphoglycan-3-from-leishmania-infantum-chagasi-binds-heparin-with-micromolar-affinity
#13
Thaís Viana Fialho Martins, Ana Eliza Zeraik, Natália Oliveira Alves, Leandro Licursi de Oliveira, Tiago Antônio de Oliveira Mendes, Ricardo DeMarco, Eduardo de Almeida Marques-da-Silva
Leishmania infantum chagasi is an intracellular protozoan parasite responsible for visceral leishmaniasis, a fatal disease in humans. Heparin-binding proteins (HBPs) are proteins that bind to carbohydrates present in glycoproteins or glycolipids. Evidence suggests that HBPs present on Leishmania surface participate in the adhesion and invasion of parasites to tissues of both invertebrate and vertebrate hosts. 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 (HBP Lc )...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29497285/review-of-statistical-learning-methods-in-integrated-omics-studies-an-integrated-information-science
#14
REVIEW
Irene Sui Lan Zeng, Thomas Lumley
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 framework...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29434468/analysis-of-conserved-computationally-predicted-epitope-regions-for-vp5-and-vp7-across-three-orbiviruses
#15
Bonnie L Russell, Nishal Parbhoo, Samantha Gildenhuys
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...
2018: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29317803/in-silico-characterization-and-functional-validation-of-cell-wall-modification-genes-imparting-waterlogging-tolerance-in-maize
#16
Kanika Arora, Kusuma Kumari Panda, Shikha Mittal, Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu
Cell wall modification (CWM) promotes the formation of aerenchyma in roots under waterlogging conditions as an adaptive mechanism. Lysigenous aerenchyma formation in roots improves oxygen transfer in plants, which highlights the importance of CWM as a focal point in waterlogging stress tolerance. We investigated the structural and functional compositions of CWM genes and their expression patterns under waterlogging conditions in maize. Cell wall modification genes were identified for 3 known waterlogging-responsive cis -acting regulatory elements, namely, GC motif, anaerobic response elements, and G-box, and 2 unnamed elements...
2017: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29317802/r-script-approach-to-infer-toxoplasma-infection-mechanisms-from-microarrays-and-domain-domain-protein-interactions
#17
Ailan F Arenas, Gladys E Salcedo, Jorge E Gomez-Marin
Pathogen-host protein-protein interaction systems examine the interactions between the protein repertoires of 2 distinct organisms. Some of these pathogen proteins interact with the host protein system and may manipulate it for their own advantages. In this work, we designed an R script by concatenating 2 functions called rowDM and rowCVmed to infer pathogen-host interaction using previously reported microarray data, including host gene enrichment analysis and the crossing of interspecific domain-domain interactions...
2017: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29276378/bioinformatic-analysis-of-circadian-expression-of-oncogenes-and-tumor-suppressor-genes
#18
Abbas Salavaty, Niloufar Mohammadi, Mozhdeh Shahmoradi, Maryam Naderi Soorki
Background: Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. This study aims to investigate the circadian expression of a list of human oncogenes and TSGs...
2017: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29162975/computational-model-of-the-effect-of-a-surface-binding-site-on-the-saccharomycopsis-fibuligera-r64-%C3%AE-amylase-to-the-substrate-adsorption
#19
Muhammad Yusuf, Umi Baroroh, Khomaini Hasan, Saadah Diana Rachman, Safri Ishmayana, Toto Subroto
α-Amylase is one of the important enzymes in the starch-processing industry. However, starch processing requires high temperature, thus resulting in high cost. The high adsorptivity of α-amylase to the substrate allows this enzyme to digest the starch at a lower temperature. α-Amylase from Saccharomycopsis fibuligera R64 (Sfamy R64), a locally sourced enzyme from Indonesia, has a high amylolytic activity but low starch adsorptivity. The objective of this study was to design a computational model of Sfamy R64 with increased starch adsorptivity using bioinformatics method...
2017: Bioinformatics and Biology Insights
https://read.qxmd.com/read/29051702/finding-the-sources-of-missing-heritability-within-rare-variants-through-simulation
#20
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang
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 (<37 weeks) and term births, were significantly correlated with the rare variant aggregations at 1000 single-nucleotide polymorphism loci...
2017: Bioinformatics and Biology Insights
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