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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/29686800/interplay-between-virulence-and-variability-factors-as-a-potential-driver-of-invasive-meningococcal-disease
#1
REVIEW
Emilio Siena, Margherita Bodini, Duccio Medini
No abstract text is available yet for this article.
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29686799/differential-microbial-communities-of-omnivorous-and-herbivorous-cattle-in-southern-china
#2
Susanna K P Lau, Jade L L Teng, Tsz Ho Chiu, Elaine Chan, Alan K L Tsang, Gianni Panagiotou, Shao-Lun Zhai, Patrick C Y Woo
In Hong Kong, cattle were traditionally raised by farmers as draft animals to plough rice fields. Due to urbanization in the 20th century, they were gradually abandoned and became wild cattle straying in suburban Hong Kong. Recently, these cattle were observed to have become omnivorous by eating leftover barbeque food waste in country parks. Microbiome analysis was performed on fecal samples of the omnivorous cattle using deep sequencing and the resulting microbiome was compared with that of traditional herbivorous cattle in Southern China...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29686798/computational-methods-for-assessing-chromatin-hierarchy
#3
REVIEW
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29632657/ordering-protein-contact-matrices
#4
Chuan Xu, Guillaume Bouvier, Benjamin Bardiaux, Michael Nilges, Thérèse Malliavin, Abdel Lisser
Numerous biophysical approaches provide information about residues spatial proximity in proteins. However, correct assignment of the protein fold from this proximity information is not straightforward if the spatially close protein residues are not assigned to residues in the primary sequence. Here, we propose an algorithm to assign such residue numbers by ordering the columns and lines of the raw protein contact matrix directly obtained from proximity information between unassigned amino acids. The ordering problem is formatted as the search of a trail within a graph connecting protein residues through the nonzero contact values...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29552334/a-review-of-somatic-single-nucleotide-variant-calling-algorithms-for-next-generation-sequencing-data
#5
REVIEW
Chang Xu
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29552333/bioinformatic-analysis-reveals-conservation-of-intrinsic-disorder-in-the-linker-sequences-of-prokaryotic-dual-family-immunophilin-chaperones
#6
Sailen Barik
The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously reported a novel class of immunophilins that are natural chimera of these two, which we named dual-family immunophilin (DFI). The DFIs were found in either of two conformations: CYN-linker-FKBP (CFBP) or FKBP-3TPR-CYN (FCBP). While the 3TPR domain can serve as a flexible linker between the FKBP and CYN modules in the FCBP-type DFI, the linker sequences in the CFBP-type DFIs are relatively short, diverse in sequence, and contain no discernible motif or signature...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29321829/dna-methylation-in-stroke-update-of-latest-advances
#7
REVIEW
Jerzy Krupinski, Caty Carrera, Elena Muiño, Nuria Torres, Raid Al-Baradie, Natalia Cullell, Israel Fernandez-Cadenas
Epigenetic modifications are hereditable and modifiable factors that do not alter the DNA sequence. These epigenetic factors include DNA methylation, acetylation of histones and non-coding RNAs. Epigenetic factors have mainly been associated with cancer but also with other diseases and conditions such as diabetes or obesity. In addition, epigenetic modifications could play an important role in cardiovascular diseases, including stroke. We review the latest advances in stroke epigenetics, focusing on DNA methylation studies and the future perspectives in this field...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29276577/are-circulating-type-2-vaccine-derived-polioviruses-vdpvs-genetically-distinguishable-from-immunodeficiency-associated-vdpvs
#8
Kun Zhao, Jaume Jorba, Jing Shaw, Jane Iber, Qi Chen, Kelley Bullard, Olen M Kew, Cara C Burns
Public health response to vaccine-derived poliovirus (VDPV) that is transmitted from person to person (circulating VDPV [cVDPV]) differs significantly from response to virus that replicates in individuals with primary immunodeficiency (immunodeficiency-associated VDPV [iVDPV]). cVDPV outbreaks require a community immunization response, whereas iVDPV chronic infections require careful patient monitoring and appropriate individual treatment. To support poliovirus outbreak response, particularly for type 2 VDPV, we investigated the genetic distinctions between cVDPV2 and iVDPV2 sequences...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29213995/lrsim-a-linked-reads-simulator-generating-insights-for-better-genome-partitioning
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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