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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/28217262/the-effects-of-shared-information-on-semantic-calculations-in-the-gene%C3%A2-ontology
#1
Paul W Bible, Hong-Wei Sun, Maria I Morasso, Rasiah Loganantharaj, Lai Wei
The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179981/deep-assessment-of-genomic-diversity-in-cassava-for-herbicide-tolerance-and-starch-biosynthesis
#2
Jorge Duitama, Lina Kafuri, Daniel Tello, Ana María Leiva, Bernhard Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley Till, Hernán Ceballos
Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179980/increasing-european-support-for-neglected-infectious-disease-research
#3
REVIEW
Ole F Olesen, Marit Ackermann
Neglected infectious diseases (NIDs) are a persistent cause of death and disability in low-income countries. Currently available drugs and vaccines are often ineffective, costly or associated with severe side-effects. Although the scale of research on NIDs does not reflect their disease burden, there are encouraging signs that NIDs have begun to attract more political and public attention, which have translated into greater awareness and increased investments in NID research by both public and private donors...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179979/flexible-gastro-intestinal-endoscopy-clinical-challenges-and-technical-achievements
#4
REVIEW
Niehls Kurniawan, Martin Keuchel
Flexible gastro-intestinal (GI) endoscopy is an integral diagnostic and therapeutic tool in clinical gastroenterology. High quality standards for safety, patients' comfort, and efficiency have already been achieved. Clinical challenges and technical approaches are discussed in this short review. Image enhanced endoscopy for further characterization of mucosal and vascular patterns includes dye-spray or virtual chromoendoscopy. For confocal laser endoscopy, endocytoscopy, and autofluorescence clinical value has not yet been finally evaluated...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179978/mini-review-in-vitro-metabolic-engineering-for-biomanufacturing-of-high-value-products
#5
REVIEW
Weihua Guo, Jiayuan Sheng, Xueyang Feng
With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179977/programmable-genome-editing-tools-and-their-regulation-for-efficient-genome-engineering
#6
REVIEW
Tuhin Kumar Guha, Alvan Wai, Georg Hausner
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28179976/biobetters-from-an-integrated-computational-experimental-approach
#7
REVIEW
Serdar Kuyucak, Veysel Kayser
Biobetters are new drugs designed from existing peptide or protein-based therapeutics by improving their properties such as affinity and selectivity for the target epitope, and stability against degradation. Computational methods can play a key role in such design problems-by predicting the changes that are most likely to succeed, they can drastically reduce the number of experiments to be performed. Here we discuss the computational and experimental methods commonly used in drug design problems, focusing on the inverse relationship between the two, namely, the more accurate the computational predictions means the less experimental effort is needed for testing...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28149485/detection-of-side-chain-rearrangements-mediating-the-motions-of-transmembrane-helices-in-molecular-dynamics-simulations-of-g-protein-coupled-receptors
#8
Zied Gaieb, Dimitrios Morikis
Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28138368/investigating-structure-and-dynamics-of-proteins-in-amorphous-phases-using-neutron-scattering
#9
REVIEW
Maria Monica Castellanos, Arnold McAuley, Joseph E Curtis
In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28138367/machine-learning-and-data-mining-methods-in-diabetes-research
#10
REVIEW
Ioannis Kavakiotis, Olga Tsave, Athanasios Salifoglou, Nicos Maglaveras, Ioannis Vlahavas, Ioanna Chouvarda
The remarkable advances in biotechnology and health sciences have led to a significant production of data, such as high throughput genetic data and clinical information, generated from large Electronic Health Records (EHRs). To this end, application of machine learning and data mining methods in biosciences is presently, more than ever before, vital and indispensable in efforts to transform intelligently all available information into valuable knowledge. Diabetes mellitus (DM) is defined as a group of metabolic disorders exerting significant pressure on human health worldwide...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28066534/chagas-disease-research-and-development-is-there-light-at-the-end-of-the-tunnel
#11
REVIEW
Eric Chatelain
Chagas disease, or American trypanosomiasis, is the result of infection by the parasite Trypanosoma cruzi. It is endemic in Latin America, and spreading around the globe due to human migration. Although it was first identified more than a century ago, only two old drugs are available for treatment and a lot of questions related to the disease progression, its pathologies, and not to mention the assessment of treatment efficacy, are subject to debate and remain to be answered. Indeed, the current status of evidence and data available does not allow any absolute statement related to treatment needs and outcome for Chagas patients to be made...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28066533/molecular-mechanism-of-binding-between-17%C3%AE-estradiol-and-dna
#12
Tamsyn A Hilder, Justin M Hodgkiss
Although 17β-estradiol (E2) is a natural molecule involved in the endocrine system, its widespread use in various applications has resulted in its accumulation in the environment and its classification as an endocrine-disrupting molecule. These molecules can interfere with the hormonal system, and have been linked to various adverse effects such as the proliferation of breast cancer. It has been proposed that E2 could contribute to breast cancer by the induction of DNA damage. Mass spectrometry has demonstrated that E2 can bind to DNA but the mechanism by which E2 interacts with DNA has yet to be elucidated...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28066532/matched-molecular-pair-analysis-in-short-algorithms-applications-and-limitations
#13
REVIEW
Christian Tyrchan, Emma Evertsson
Molecular matched pair (MMP) analysis has been used for more than 40 years within molecular design and is still an important tool to analyse potency data and other compound properties. The methods used to find matched pairs range from manual inspection, through supervised methods to unsupervised methods, which are able to find previously unknown molecular pairs. Recent publications demonstrate the value of automatic MMP analysis of publicly available bioactivity databases. The MMP concept has its limitations, but because of its easy to use and intuitive nature, it will remain one of the most important tools in the toolbox of many drug designers...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28018557/a-hybrid-computer-aided-diagnosis-system-for-prediction-of-breast-cancer-recurrence-hpbcr-using-optimized-ensemble-learning
#14
Mohammad R Mohebian, Hamid R Marateb, Marjan Mansourian, Miguel Angel Mañanas, Fariborz Mokarian
Cancer is a collection of diseases that involves growing abnormal cells with the potential to invade or spread to the body. Breast cancer is the second leading cause of cancer death among women. A method for 5-year breast cancer recurrence prediction is presented in this manuscript. Clinicopathologic characteristics of 579 breast cancer patients (recurrence prevalence of 19.3%) were analyzed and discriminative features were selected using statistical feature selection methods. They were further refined by Particle Swarm Optimization (PSO) as the inputs of the classification system with ensemble learning (Bagged Decision Tree: BDT)...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27994799/worsening-of-verbal-fluency-after-deep-brain-stimulation-in-parkinson-s-disease-a-focused-review
#15
REVIEW
Andreas Højlund, Mikkel V Petersen, Kousik Sarathy Sridharan, Karen Østergaard
Worsening of verbal fluency after treatment with deep brain stimulation in Parkinson's disease patients is one of the most often reported cognitive adverse effect. The underlying mechanisms of this decline are not well understood. The present focused review assesses the evidence for the reliability of the often-reported decline of verbal fluency, as well as the evidence for the suggested mechanisms including disease progression, reduced medication levels, electrode positions, and stimulation effect vs. surgical effects...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27994798/mining-textural-knowledge-in-biological-images-applications-methods-and-trends
#16
REVIEW
Santa Di Cataldo, Elisa Ficarra
Texture analysis is a major task in many areas of computer vision and pattern recognition, including biological imaging. Indeed, visual textures can be exploited to distinguish specific tissues or cells in a biological sample, to highlight chemical reactions between molecules, as well as to detect subcellular patterns that can be evidence of certain pathologies. This makes automated texture analysis fundamental in many applications of biomedicine, such as the accurate detection and grading of multiple types of cancer, the differential diagnosis of autoimmune diseases, or the study of physiological processes...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27980708/bioinformatics-strategies-for-taxonomy-independent-binning-and-visualization-of-sequences-in-shotgun-metagenomics
#17
REVIEW
Karel Sedlar, Kristyna Kupkova, Ivo Provaznik
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27942354/heart-failure-diagnosis-severity-estimation-and-prediction-of-adverse-events-through-machine-learning-techniques
#18
REVIEW
Evanthia E Tripoliti, Theofilos G Papadopoulos, Georgia S Karanasiou, Katerina K Naka, Dimitrios I Fotiadis
Heart failure is a serious condition with high prevalence (about 2% in the adult population in developed countries, and more than 8% in patients older than 75 years). About 3-5% of hospital admissions are linked with heart failure incidents. Heart failure is the first cause of admission by healthcare professionals in their clinical practice. The costs are very high, reaching up to 2% of the total health costs in the developed countries. Building an effective disease management strategy requires analysis of large amount of data, early detection of the disease, assessment of the severity and early prediction of adverse events...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27872688/functional-roles-for-exosomal-micrornas-in-the-tumour-microenvironment
#19
REVIEW
Emma Bell, Molly A Taylor
Extracellular microRNAs are released from cells both passively and actively. The presence of these microRNAs in the tumour microenvironment (TME) can significantly impact on the plasticity of cancer cells leading to the promotion of metastatic and angiogenic processes. These extracellular microRNAs can act not only on other cancer cells, but also cells present in the TME, such as immune cells, endothelial cells, fibroblasts, and others acting to subvert the host immune system and drive tumour progression. In this review we highlight the current understanding of both the mechanisms by which microRNAs are released from tumour cells and the downstream functional effects that extracellular microRNAs have on recipient cells...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27872687/determining-the-molecular-pathways-underlying-the-protective-effect-of-non-steroidal-anti-inflammatory-drugs-for-alzheimer-s-disease-a-bioinformatics-approach
#20
Alejo J Nevado-Holgado, Simon Lovestone
Alzheimer's disease (AD) represents a substantial unmet need, due to increasing prevalence in an ageing society and the absence of a disease modifying therapy. Epidemiological evidence shows a protective effect of non steroidal anti inflammatory (NSAID) drugs, and genome wide association studies (GWAS) show consistent linkage to inflammatory pathways; both observations suggesting anti-inflammatory compounds might be effective in AD therapy although clinical trials to date have not been positive. In this study, we use pathway enrichment and fuzzy logic to identify pathways (KEGG database) simultaneously affected in both AD and by NSAIDs (Sulindac, Piroxicam, Paracetamol, Naproxen, Nabumetone, Ketoprofen, Diclofenac and Aspirin)...
2017: Computational and Structural Biotechnology Journal
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