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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/29213995/lrsim-a-linked-reads-simulator-generating-insights-for-better-genome-partitioning
#1
Ruibang Luo, Fritz J Sedlazeck, Charlotte A Darby, Stephen M Kelly, Michael C Schatz
Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclude from the phasing and assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing genomes of different sizes and complexities...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29187960/meta-analysis-of-liver-and-heart-transcriptomic-data-for-functional-annotation-transfer-in-mammalian-orthologs
#2
Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume Devailly
Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from over 1500 experiments with varied treatments. We used a hyper-graph clustering method to identify clusters of orthologous genes co-expressed in both mouse and rat...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29158876/challenges-in-the-setup-of-large-scale-next-generation-sequencing-analysis-workflows
#3
REVIEW
Pranav Kulkarni, Peter Frommolt
While Next-Generation Sequencing (NGS) can now be considered an established analysis technology for research applications across the life sciences, the analysis workflows still require substantial bioinformatics expertise. Typical challenges include the appropriate selection of analytical software tools, the speedup of the overall procedure using HPC parallelization and acceleration technology, the development of automation strategies, data storage solutions and finally the development of methods for full exploitation of the analysis results across multiple experimental conditions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29158875/a-gene-module-based-eqtl-analysis-prioritizing-disease-genes-and-pathways-in-kidney-cancer
#4
Mary Qu Yang, Dan Li, William Yang, Yifan Zhang, Jun Liu, Weida Tong
Clear cell renal cell carcinoma (ccRCC) is the most common and most aggressive form of renal cell cancer (RCC). The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29085573/assessing-species-diversity-using-metavirome-data-methods-and-challenges
#5
REVIEW
Damayanthi Herath, Duleepa Jayasundara, David Ackland, Isaam Saeed, Sen-Lin Tang, Saman Halgamuge
Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29034064/personalized-therapy-against-preeclampsia-by-replenishing-placental-protein-13-pp13-targeted-to-patients-with-impaired-pp13-molecule-or-function
#6
REVIEW
Hamutal Meiri, George Osol, Irene Cetin, Sveinbjörn Gizurarson, Berthold Huppertz
Hypertensive disorders affect about one third of all people aged 20 and above, and are treated with anti-hypertensive drugs. Preeclampsia (PE) is one form of such disorders that only develops during pregnancy. It affects ten million pregnant women globally and additionally causes fetal loss and major newborn disabilities. The syndrome's origin is multifactorial, and anti-hypertensive drugs are ineffective in treating it. Biomarkers are helpful for predict its development. Generic drugs, such as low dose aspirin, were proven effective in preventing preterm PE...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28924459/genetic-code-optimization-for-cotranslational-protein-folding-codon-directional-asymmetry-correlates-with-antiparallel-betasheets-trna-synthetase-classes
#7
Hervé Seligmann, Ganesh Warthi
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28883909/computing-platforms-for-big-biological-data-analytics-perspectives-and-challenges
#8
REVIEW
Zekun Yin, Haidong Lan, Guangming Tan, Mian Lu, Athanasios V Vasilakos, Weiguo Liu
The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28855977/multi-level-and-hybrid-modelling-approaches-for-systems-biology
#9
REVIEW
R Bardini, G Politano, A Benso, S Di Carlo
During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28819548/a-random-forest-classifier-for-detecting-rare-variants-in-ngs-data-from-viral-populations
#10
Raunaq Malhotra, Manjari Jha, Mary Poss, Raj Acharya
We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS) data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28794828/scalability-and-validation-of-big-data-bioinformatics-software
#11
REVIEW
Andrian Yang, Michael Troup, Joshua W K Ho
This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28748045/sigtree-a-microbial-community-analysis-tool-to-identify-and-visualize-significantly-responsive-branches-in-a-phylogenetic-tree
#12
REVIEW
John R Stevens, Todd R Jones, Michael Lefevre, Balasubramanian Ganesan, Bart C Weimer
Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28660014/apolipoprotein-e-a-multifunctional-protein-with-implications-in-various-pathologies-as-a-result-of-its-structural-features
#13
REVIEW
Irina Florina Tudorache, Violeta Georgeta Trusca, Anca Violeta Gafencu
Apolipoprotein E (apoE), a 34 kDa glycoprotein, mediates hepatic and extrahepatic uptake of plasma lipoproteins and cholesterol efflux from lipid-laden macrophages. In humans, three structural different apoE isoforms occur, with subsequent functional changes and pathological consequences. Here, we review data supporting the involvement of apoE structural domains and isoforms in normal and altered lipid metabolism, cardiovascular and neurodegenerative diseases, as well as stress-related pathological states...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28652896/resurrecting-the-dead-molecules
#14
REVIEW
Jan Zaucha, Jonathan G Heddle
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28652895/exploring-components-of-the-co2-concentrating-mechanism-in-alkaliphilic-cyanobacteria-through-genome-based-analysis
#15
Amornpan Klanchui, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
In cyanobacteria, the CO2-concentrating mechanism (CCM) is a vital biological process that provides effective photosynthetic CO2 fixation by elevating the CO2 level near the active site of Rubisco. This process enables the adaptation of cyanobacteria to various habitats, particularly in CO2-limited environments. Although CCM of freshwater and marine cyanobacteria are well studied, there is limited information on the CCM of cyanobacteria living under alkaline environments. Here, we aimed to explore the molecular components of CCM in 12 alkaliphilic cyanobacteria through genome-based analysis...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28487762/modern-technologies-of-solution-nuclear-magnetic-resonance-spectroscopy-for-three-dimensional-structure-determination-of-proteins-open-avenues-for-life-scientists
#16
REVIEW
Toshihiko Sugiki, Naohiro Kobayashi, Toshimichi Fujiwara
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28458783/flexible-analog-search-with-kernel-pca-embedded-molecule-vectors
#17
Stefano Rensi, Russ B Altman
Studying analog series to find structural transformations that enhance the activity and ADME properties of lead compounds is an important part of drug development. Matched molecular pair (MMP) search is a powerful tool for analog analysis that imitates researchers' ability to select pairs of compounds that differ only by small well-defined transformations. Abstraction is a challenge for existing MMP search algorithms, which can result in the omission of relevant, inexact MMPs, and inclusion of irrelevant, contextually dissimilar MMPs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28458782/protein-post-translational-modifications-in-silico-prediction-tools-and-molecular-modeling
#18
REVIEW
Martina Audagnotto, Matteo Dal Peraro
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28435614/time-resolved-biophysical-approaches-to-nucleocytoplasmic-transport
#19
REVIEW
Francesco Cardarelli
Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28392892/evaluation-of-multiple-approaches-to-identify-genome-wide-polymorphisms-in-closely-related-genotypes-of-sweet-cherry-prunus-avium-l
#20
Seanna Hewitt, Benjamin Kilian, Ramyya Hari, Tyson Koepke, Richard Sharpe, Amit Dhingra
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species...
2017: Computational and Structural Biotechnology Journal
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