263 results match your criteria Bioinformatics and biology insights[Journal]


Discovering Selected Antibodies From Deep-Sequenced Phage-Display Antibody Library Using ATTILA.

Bioinform Biol Insights 2020 30;14:1177932220915240. Epub 2020 Apr 30.

Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil.

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. Read More

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http://dx.doi.org/10.1177/1177932220915240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218273PMC

An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.

Bioinform Biol Insights 2020 8;14:1177932220906827. Epub 2020 May 8.

Department of Mathematics, University of Bari Aldo Moro, Bari, Italy.

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. Read More

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http://dx.doi.org/10.1177/1177932220906827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218276PMC

Integrative Analysis of the Genes Induced by the Intestine Microbiota of Infant Born to Term and Breastfed.

Bioinform Biol Insights 2020 29;14:1177932220906168. Epub 2020 Apr 29.

Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco.

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. Read More

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http://dx.doi.org/10.1177/1177932220906168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218278PMC

Gene-Based Clustering Algorithms: Comparison Between Denclue, Fuzzy-C, and BIRCH.

Bioinform Biol Insights 2020 1;14:1177932220909851. Epub 2020 Apr 1.

Department of Biomedical Informatics, University of Nebraska Omaha, Omaha, NE, USA.

The current study seeks to compare 3 clustering algorithms that can be used in gene-based bioinformatics research to understand disease networks, protein-protein interaction networks, and gene expression data. Denclue, Fuzzy-C, and Balanced Iterative and Clustering using Hierarchies (BIRCH) were the 3 gene-based clustering algorithms selected. These algorithms were explored in relation to the subfield of bioinformatics that analyzes omics data, which include but are not limited to genomics, proteomics, metagenomics, transcriptomics, and metabolomics data. Read More

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http://dx.doi.org/10.1177/1177932220909851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133071PMC

Comparative Analysis of the Biosimilar and Innovative G-CSF Modulated Pathways on Umbilical Cord Blood-Derived Mononuclear Cells.

Bioinform Biol Insights 2020 20;14:1177932220913307. Epub 2020 Mar 20.

CINIBA-CIC-PBA, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina.

Biosimilars of granulocyte colony-stimulating factor (G-CSF) have been routinely introduced into clinical practice. However, not functional genomics characterization has been performed yet in comparison with the innovator G-CSF. This study aimed to evaluate the transcriptomic changes in an in vitro model of umbilical cord blood cells (UBC) exposed to G-CSF for the identification of their modulated pathways. Read More

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http://dx.doi.org/10.1177/1177932220913307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088127PMC

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them.

Authors:
Sailen Barik

Bioinform Biol Insights 2020 4;14:1177932220906434. Epub 2020 Mar 4.

Mobile, AL, USA.

The tricopeptide (amino acid number in the 30s) repeats constitute some of the most common amino acid repeats in proteins of diverse organisms. The most important representatives of this class are the 34-residue and 35-residue repeats, eponymously known as tetratricopeptide repeat (TPR) and pentatricopeptide repeat (PPR), respectively. The unit motif of both consists of a pair of alpha helices. Read More

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http://dx.doi.org/10.1177/1177932220906434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059232PMC

Multi-omics Data Integration, Interpretation, and Its Application.

Bioinform Biol Insights 2020 31;14:1177932219899051. Epub 2020 Jan 31.

LABS, Persistent Systems, Pune, India.

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 disease subtyping, biomarker prediction, and deriving insights into the data. Read More

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http://dx.doi.org/10.1177/1177932219899051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003173PMC
January 2020

PostSV: A Post-Processing Approach for Filtering Structural Variations.

Bioinform Biol Insights 2020 20;14:1177932219892957. Epub 2020 Jan 20.

Computer Science Department, King Saud University, Riyadh, Saudi Arabia.

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. Read More

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http://dx.doi.org/10.1177/1177932219892957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974750PMC
January 2020

Interaction of Selected Terpenoids From With Catalytic Domain of Matrix Metalloproteinase-1: An In Silico Assessment of Their Anti-wrinkling Potential.

Bioinform Biol Insights 2019 24;13:1177932219896538. Epub 2019 Dec 24.

Agriculture Plant Biotechnology Lab (ARL-316), University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector-16 C, Dwarka, New Delhi-110078, India.

Matrix metalloproteinase-1 (MMP-1) is a predominant collagenase enzyme that cleaves collagen fibers, contributing to skin wrinkling. Matrix metalloproteinase-1 inhibitors of herbal origin may provide an earnest probability to offer a novel curative approach against MMP-1-mediated collagenolysis, prompted by ultraviolet (UV)-induced overexpression of MMP-1. In this in silico study, we have explored the MMP-1 inhibitory potential of selected terpenoids from extracts. Read More

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http://dx.doi.org/10.1177/1177932219896538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6931142PMC
December 2019

In Silico Screening and Analysis of Broad-Spectrum Molecular Targets and Lead Compounds for Diarrhea Therapy.

Bioinform Biol Insights 2019 24;13:1177932219884297. Epub 2019 Oct 24.

Molecular Biology and Environmental Microbiology Research Unit, Department of Microbiology, The Federal University of Technology, Akure, Nigeria.

Diarrhoeal disease kills about 1.5 million human beings per year across the continents. The enterotoxigenic (ETEC) pathotype has been noted as a major cause of diarrheal disease in human and livestock. Read More

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http://dx.doi.org/10.1177/1177932219884297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6820192PMC
October 2019

Pathway Analysis of Global Metabolomic Profiles Identified Enrichment of Caffeine, Energy, and Arginine Metabolism in Smokers but Not Moist Snuff Consumers.

Bioinform Biol Insights 2019 17;13:1177932219882961. Epub 2019 Oct 17.

RAI Services Company, Winston-Salem, NC, USA.

Existing US epidemiological data demonstrate that consumption of smokeless tobacco, particularly moist snuff, is less harmful than cigarette smoking. However, the molecular and biochemical changes due to moist snuff consumption relative to smoking remain incompletely understood. We previously reported that smokers (SMK) exhibit elevated oxidative stress and inflammation relative to moist snuff consumers (MSC) and non-tobacco consumers (NTC), based on metabolomic profiling data of saliva, plasma, and urine from MSC, SMK, and NTC. Read More

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http://dx.doi.org/10.1177/1177932219882961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798164PMC
October 2019

CoMM: A Collaborative Mixed Model That Integrates GWAS and eQTL Data Sets to Investigate the Genetic Architecture of Complex Traits.

Bioinform Biol Insights 2019 13;13:1177932219881435. Epub 2019 Oct 13.

Centre for Quantitative Medicine, Programme in Health Services and System Research, Duke-NUS Medical School, Singapore.

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. Read More

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http://dx.doi.org/10.1177/1177932219881435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792274PMC
October 2019

Protein Tetratricopeptide Repeat and the Companion Non-tetratricopeptide Repeat Helices: Bioinformatic Analysis of Interhelical Interactions.

Authors:
Sailen Barik

Bioinform Biol Insights 2019 24;13:1177932219863363. Epub 2019 Sep 24.

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. Read More

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http://dx.doi.org/10.1177/1177932219863363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759711PMC
September 2019

Corrigendum to Tackling the Challenges of FASTQ Referential Compression.

Authors:

Bioinform Biol Insights 2019;13:1177932219876803. Epub 2019 Sep 17.

[This corrects the article DOI: 10.1177/1177932218821373.]. Read More

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http://dx.doi.org/10.1177/1177932219876803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6749778PMC
September 2019

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.

Bioinform Biol Insights 2019 6;13:1177932219873884. Epub 2019 Sep 6.

Department of Legal Medicine, School of Medicine, Toho University, Tokyo, Japan.

The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Read More

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http://dx.doi.org/10.1177/1177932219873884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6732850PMC
September 2019

On the Upper Bounds of the Real-Valued Predictions.

Bioinform Biol Insights 2019 23;13:1177932219871263. Epub 2019 Aug 23.

Department of Medical Sciences, University of Turin, Turin, Italy.

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). Read More

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http://dx.doi.org/10.1177/1177932219871263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6710671PMC

Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS.

Bioinform Biol Insights 2019 16;13:1177932219868223. Epub 2019 Aug 16.

Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

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. Read More

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http://dx.doi.org/10.1177/1177932219868223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6698994PMC

Enjoy the Silence: Nearly Half of Human tRNA Genes Are Silent.

Bioinform Biol Insights 2019 8;13:1177932219868454. Epub 2019 Aug 8.

Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain.

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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932219868454
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http://dx.doi.org/10.1177/1177932219868454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688141PMC
August 2019
1 Read

Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[]imidazol-1-yl)methyl)benzimidamide Scaffolds on Adenylosuccinate Lyase Receptor.

Bioinform Biol Insights 2019 31;13:1177932219865533. Epub 2019 Jul 31.

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.

adenylosuccinate lyase (ADSL) is an important enzyme in purine metabolism. Although several benzimidazole derivatives have been commercially developed into drugs, the template design as inhibitor against ADSL has not been fully explored. This study aims to model the 3-dimensional (3D) structure of ADSL, design and predict in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) of 8 substituted benzo[]imidazol-1-yl)methyl)benzimidamide compounds as well as predict the potential interaction modes and binding affinities of the designed ligands with the modelled ADSL. Read More

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http://dx.doi.org/10.1177/1177932219865533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6669854PMC
July 2019
1 Read

Characterization and Expression Analysis of Heme Oxygenase Genes from .

Bioinform Biol Insights 2019 12;13:1177932219860813. Epub 2019 Jul 12.

SensorLab, Department of Chemistry, University of the Western Cape, Bellville, South Africa.

Heme oxygenases (HOs) have a major role in phytochrome chromophore biosynthesis, and chromophores in turn have anti-oxidant properties. Plant heme oxygenases are divided into the HO1 sub-family comprising HO1, HO3, and HO4, and the HO2 sub-family, which consists of 1 member, HO2. This study identified and characterized 4 heme oxygenase members from . Read More

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http://dx.doi.org/10.1177/1177932219860813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628516PMC
July 2019
1 Read

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data.

Bioinform Biol Insights 2019 8;13:1177932219860817. Epub 2019 Jul 8.

Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

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. Read More

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http://dx.doi.org/10.1177/1177932219860817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614939PMC

Moving Just Enough Deep Sequencing Data to Get the Job Done.

Bioinform Biol Insights 2019 14;13:1177932219856359. Epub 2019 Jun 14.

Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.

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-Seq workflow. Read More

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http://dx.doi.org/10.1177/1177932219856359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6572328PMC
June 2019
1 Read

Time-Frequency Approach Applied to Finding Interaction Regions in Pathogenic Proteins.

Bioinform Biol Insights 2019 4;13:1177932219850172. Epub 2019 Jun 4.

Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia.

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. Read More

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http://dx.doi.org/10.1177/1177932219850172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6552352PMC
June 2019
8 Reads

Cancer Genetic Network Inference Using Gaussian Graphical Models.

Bioinform Biol Insights 2019 8;13:1177932219839402. Epub 2019 Apr 8.

Integrated Bioscience Program, The University of Akron, Akron, OH, USA.

The Cancer Genome Atlas (TCGA) provides a rich resource that can be used to understand how genes interact in cancer cells and has collected RNA-Seq gene expression data for many types of human cancer. However, mining the data to uncover the hidden gene-interaction patterns remains a challenge. Gaussian graphical model (GGM) is often used to learn genetic networks because it defines an undirected graphical structure, revealing the conditional dependences of genes. Read More

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http://dx.doi.org/10.1177/1177932219839402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456846PMC
April 2019
3 Reads

High-Throughput Analysis of Clinical Flow Cytometry Data by Automated Gating.

Bioinform Biol Insights 2019 3;13:1177932219838851. Epub 2019 Apr 3.

Clinical Flow Cytometry, Translational Medicine, Bristol-Myers Squibb, Pennington, NJ, USA.

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. Read More

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http://dx.doi.org/10.1177/1177932219838851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448119PMC
April 2019
1 Read

Tackling the Challenges of FASTQ Referential Compression.

Bioinform Biol Insights 2019 14;13:1177932218821373. Epub 2019 Feb 14.

Facultad de Ciencias y Tecnología (FaCyT), Universidad de Carabobo (UC), Valencia, Venezuela.

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. Read More

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http://dx.doi.org/10.1177/1177932218821373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376532PMC
February 2019
1 Read

Combining Strengths for Multi-genome Visual Analytics Comparison.

Bioinform Biol Insights 2019 1;13:1177932218825127. Epub 2019 Feb 1.

Department of Computer Architecture, University of Málaga and Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain.

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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932218825127
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http://dx.doi.org/10.1177/1177932218825127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365554PMC
February 2019
6 Reads

Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: .

Bioinform Biol Insights 2019 9;13:1177932218821362. Epub 2019 Jan 9.

National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.

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. Read More

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http://dx.doi.org/10.1177/1177932218821362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335655PMC
January 2019
2 Reads

Anabel: An Online Tool for the Real-Time Kinetic Analysis of Binding Events.

Bioinform Biol Insights 2019 9;13:1177932218821383. Epub 2019 Jan 9.

Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.

Anabel (lysis of inding vents + ) is an open source online software tool (www.skscience.org/anabel) for the convenient analysis of molecular binding interactions. Read More

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http://dx.doi.org/10.1177/1177932218821383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328958PMC
January 2019

Potential Anti-Cancer Flavonoids Isolated From Young Twigs and Leaves: Molecular Docking and In Silico Studies.

Bioinform Biol Insights 2019 7;13:1177932218821371. Epub 2019 Jan 7.

Bioinformatics Research Unit, Covenant University, Ota, Nigeria.

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 , this study isolated phytochemicals from young twigs and leaves of 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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932218821371
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http://dx.doi.org/10.1177/1177932218821371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327336PMC
January 2019
6 Reads

HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants.

Bioinform Biol Insights 2019 7;13:1177932218821365. Epub 2019 Jan 7.

Department of Biosciences, Inst. of Cell Biology and Neuroscience, Applied Bioinformatics Group, Goethe University, Frankfurt am Main, Germany.

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. Read More

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http://dx.doi.org/10.1177/1177932218821365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327235PMC
January 2019
2 Reads

AutoAnalyze in Systems Biology.

Bioinform Biol Insights 2019 9;13:1177932218818458. Epub 2019 Jan 9.

Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany.

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. Read More

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http://dx.doi.org/10.1177/1177932218818458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328952PMC
January 2019
3 Reads

Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum.

Bioinform Biol Insights 2018 11;12:1177932218815152. Epub 2018 Dec 11.

Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932218815152
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http://dx.doi.org/10.1177/1177932218815152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291885PMC
December 2018
42 Reads

Genomic Interventions in Medicine.

Bioinform Biol Insights 2018 3;12:1177932218816100. Epub 2018 Dec 3.

Department of Biological Sciences, Covenant University, Ota, Nigeria.

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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932218816100
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http://dx.doi.org/10.1177/1177932218816100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6287307PMC
December 2018
36 Reads

Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Using Immunoinformatics Approaches.

Bioinform Biol Insights 2018 12;12:1177932218809703. Epub 2018 Nov 12.

Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.

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 () such as and Nocardiae or true fungi () such as . Read More

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http://dx.doi.org/10.1177/1177932218809703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6236636PMC
November 2018
23 Reads

Mathematical Model for Small Size Time Series Data of Bacterial Secondary Metabolic Pathways.

Bioinform Biol Insights 2018 16;12:1177932218775076. Epub 2018 May 16.

Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Waseda University, Tokyo, Japan.

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. Read More

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http://dx.doi.org/10.1177/1177932218775076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958428PMC
May 2018
20 Reads

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against .

Bioinform Biol Insights 2018 14;12:1177932218755337. Epub 2018 May 14.

Institute of Technology and Research, Universidade Tiradentes, Aracaju, Brazil.

Caseous lymphadenitis (CLA) is a disease caused by 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. Read More

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http://dx.doi.org/10.1177/1177932218755337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954444PMC
May 2018
9 Reads

Lipophosphoglycan 3 From Binds Heparin With Micromolar Affinity.

Bioinform Biol Insights 2018 13;12:1177932218763363. Epub 2018 Mar 13.

Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil.

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 surface participate in the adhesion and invasion of parasites to tissues of both invertebrate and vertebrate hosts. Read More

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http://dx.doi.org/10.1177/1177932218763363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858678PMC
March 2018
21 Reads

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).

Bioinform Biol Insights 2018 20;12:1177932218759292. Epub 2018 Feb 20.

Department of Statistics, Faculty of Science, The University of Auckland, Auckland, New Zealand.

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. Read More

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http://dx.doi.org/10.1177/1177932218759292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824897PMC
February 2018
15 Reads

Analysis of Conserved, Computationally Predicted Epitope Regions for VP5 and VP7 Across three Orbiviruses.

Bioinform Biol Insights 2018 31;12:1177932218755348. Epub 2018 Jan 31.

Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa.

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. Read More

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http://dx.doi.org/10.1177/1177932218755348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802602PMC
January 2018
14 Reads

In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize.

Bioinform Biol Insights 2017 19;11:1177932217747277. Epub 2017 Dec 19.

Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.

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. Read More

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http://dx.doi.org/10.1177/1177932217747277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753887PMC
December 2017
14 Reads

R Script Approach to Infer Infection Mechanisms From Microarrays and Domain-Domain Protein Interactions.

Bioinform Biol Insights 2017 17;11:1177932217747256. Epub 2017 Dec 17.

Grupo de Estudio en Parasitología Molecular (GEPAMOL), Universidad del Quindío, Armenia, Colombia.

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. Read More

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http://journals.sagepub.com/doi/10.1177/1177932217747256
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http://dx.doi.org/10.1177/1177932217747256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753922PMC
December 2017
16 Reads

Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes.

Bioinform Biol Insights 2017 13;11:1177932217746991. Epub 2017 Dec 13.

Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

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. Read More

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http://dx.doi.org/10.1177/1177932217746991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734456PMC
December 2017
16 Reads

Computational Model of the Effect of a Surface-Binding Site on the R64 α-Amylase to the Substrate Adsorption.

Bioinform Biol Insights 2017 6;11:1177932217738764. Epub 2017 Nov 6.

Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia.

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. Read More

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http://dx.doi.org/10.1177/1177932217738764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676498PMC
November 2017
12 Reads

Finding the Sources of Missing Heritability within Rare Variants Through Simulation.

Bioinform Biol Insights 2017 4;11:1177932217735096. Epub 2017 Oct 4.

BDX Research & Consulting LLC, Fairfax, VA, USA.

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. Read More

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http://dx.doi.org/10.1177/1177932217735096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638154PMC
October 2017
9 Reads

A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines.

Bioinform Biol Insights 2017 27;11:1177932217733422. Epub 2017 Sep 27.

Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.

The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. Read More

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http://dx.doi.org/10.1177/1177932217733422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624349PMC
September 2017
15 Reads

Bioinformatics Study of m.9053G>A Mutation at the Gene in Relation to Type 2 Diabetes Mellitus and Cataract Diseases.

Bioinform Biol Insights 2017 12;11:1177932217728515. Epub 2017 Sep 12.

Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia.

The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Read More

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http://dx.doi.org/10.1177/1177932217728515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598796PMC
September 2017
41 Reads

Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.

Bioinform Biol Insights 2017 13;11:1177932217720405. Epub 2017 Jul 13.

Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.

The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. 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 -nearest neighbor (RNN) search. Read More

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http://dx.doi.org/10.1177/1177932217720405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513527PMC
July 2017
14 Reads

CellTrans: An R Package to Quantify Stochastic Cell State Transitions.

Bioinform Biol Insights 2017 16;11:1177932217712241. Epub 2017 Jun 16.

Fakultät Informatik/Mathematik, Hochschule für Technik und Wirtschaft Dresden, Dresden, Germany.

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. Read More

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http://dx.doi.org/10.1177/1177932217712241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478290PMC
June 2017
10 Reads

A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against .

Bioinform Biol Insights 2017 12;11:1177932217712471. Epub 2017 Jun 12.

Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.

We present an approach for detecting enzymes that are specific of compared with 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 compared with , only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with . Read More

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http://dx.doi.org/10.1177/1177932217712471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470852PMC
June 2017
13 Reads