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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/29785196/a-computational-approach-using-bioinformatics-to-screening-drug-targets-for-leishmania-infantum-species
#1
Miguel Angel Chávez-Fumagalli, Mônica Santos Schneider, Daniela Pagliara Lage, Grasiele de Sousa Vieira Tavares, Débora Vasconcelos Costa Mendonça, Thaís Teodoro de Oliveira Santos, Rodrigo Maia Pádua, Ricardo Andrez Machado-de-Ávila, João Paulo Viana Leite, Eduardo Antonio Ferraz Coelho
Background: The development of new therapeutic strategies to treat patients for leishmaniasis has become a priority. The antileishmanial activity of the strychnobiflavone flavonoid was recently demonstrated against Leishmania amazonensis and Leishmania infantum amastigotes and promastigotes. The biological effect of this molecule was identified due to its capacity to interfere in the parasite mitochondrial membrane; however, the underlying molecular mechanism remains unclear. Methods and Results: In this study, a computational approach using bioinformatics was performed to screen biological targets of strychnobiflavone in L...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#2
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29767357/a-guide-for-designing-and-analyzing-rna-seq-data
#3
Aniruddha Chatterjee, Antonio Ahn, Euan J Rodger, Peter A Stockwell, Michael R Eccles
The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29740493/bioinformatic-analysis-and-prediction-of-the-function-and-regulatory-network-of-long-non-coding-rnas-in-hepatocellular-carcinoma
#4
Ming-Rong Cao, Ze-Ping Han, Ji-Ming Liu, Yu-Guang Li, Yu-Bing Lv, Jia-Bin Zhou, Jin-Hua He
Computational analysis and bioinformatics have significantly advanced the ability of researchers to process and analyze biological data. Molecular data from human and model organisms may facilitate drug target validation and identification of biomarkers with increased predictive accuracy. The aim of the present study was to investigate the function of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) using online databases, and to predict their regulatory mechanism. HCC-associated lncRNAs, their downstream transcription factors and microRNAs (miRNAs/miRs), as well as the HCC-associated target genes, were identified using online databases...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29722865/predicting-rna-protein-binding-sites-and-motifs-through-combining-local-and-global-deep-convolutional-neural-networks
#5
Xiaoyong Pan, Hong-Bin Shen
Motivation: RNA-binding proteins (RBPs) take over 5∼10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using pattern learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs...
May 2, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29718113/prediction-of-lncrna-disease-associations-based-on-inductive-matrix-completion
#6
Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang
Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA-disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA-disease associations, especially for novel lncRNAs, remains challenging. Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA-disease associations based on inductive matrix completion...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29718104/exact-bayesian-inference-for-phylogenetic-birth-death-models
#7
K V Parag, O G Pybus
Motivation: Inferring the rates of change of a population from a reconstructed phylogeny of genetic sequences is a central problem in macro-evolutionary biology, epidemiology, and many other disciplines. A popular solution involves estimating the parameters of a birth-death process (BDP), which links the shape of the phylogeny to its birth and death rates. Modern BDP estimators rely on random Markov chain Monte Carlo (MCMC) sampling to infer these rates. Such methods, while powerful and scalable, cannot be guaranteed to converge, leading to results that may be hard to replicate or difficult to validate...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29718097/rbind-computational-network-method-to-predict-rna-binding-sites
#8
Kaili Wang, Yiren Jian, Huiwen Wang, Chen Zeng, Yunjie Zhao
Motivation: Non-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA-ligand and RNA-protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions. Results: Current RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29713460/sensing-the-cilium-digital-capture-of-ciliary-data-for-comparative-genomics-investigations
#9
Karen R Christie, Judith A Blake
Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work...
2018: Cilia
https://www.readbyqxmd.com/read/29707563/copd-time-to-improve-its-taxonomy
#10
Bartolomé R Celli, Alvar Agustí
Due to well-conducted epidemiological studies and advances in genetics, molecular biology, translational research, the advent of computed tomography of the lungs and bioinformatics, the diagnosis of chronic obstructive pulmonary disease (COPD) as a single entity caused by susceptibility to cigarette smoke is no longer tenable. Furthermore, the once-accepted concept that COPD results from a rapid and progressive loss of lung function over time is not true for a sizeable proportion of adults with the disease...
January 2018: ERJ Open Research
https://www.readbyqxmd.com/read/29704626/understanding-dengue-virus-evolution-to-support-epidemic-surveillance-and-counter-measure-development
#11
REVIEW
S Pollett, M C Melendrez, I Maljkovic Berry, S Duchêne, H Salje, Cummings Dat, R G Jarman
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods...
April 25, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29703150/omgene-mutual-improvement-of-gene-models-through-optimisation-of-evolutionary-conservation
#12
Michael P Dunne, Steven Kelly
BACKGROUND: The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequently disagree on the model for a given predicted gene, with some or all of the variant gene models often failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29702223/an-integrative-approach-to-investigate-the-association-among-high-sensitive-c-reactive-protein-body-fat-mass-distribution-and-other-cardiometabolic-risk-factors-in-young-healthy-women
#13
Bin Wu, Jingshan Huang, Lihua Zhang, Mohan Vamsi Kasukurthi, Fangwan Huang, Jiang Bian, Keisuke Fukuo, Tsutomu Kazumi
Prior research has indicated that as an important biomarker of chronic low-grade inflammation, high-sensitivity C-reactive protein (hs-CRP) can play important roles on the onset of metabolic syndrome and cardiovascular diseases (CVD). We conducted an integrative approach, which combines biological wet-lab experiments, statistical analysis, and semantics-oriented bioinformatics & computational analysis, to investigate the association among hs-CRP, body fat mass (FM) distribution, and other cardiometabolic risk factors in young healthy women...
April 24, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29700068/advances-in-transcriptomics-investigating-cardiovascular-disease-at-unprecedented-resolution
#14
REVIEW
Robert C Wirka, Milos Pjanic, Thomas Quertermous
Whole-genome transcriptional profiling has become a standard genomic approach to investigate biological processes. RNA sequencing (RNAseq) in particular has witnessed myriad applications in genetics and various biomedical fields. RNAseq involves a relatively simple experimental protocol of RNA extraction and cDNA library preparation and, because of decreasing next-generation sequencing cost and lower computational burden for data processing, has obtained a central role in the modern biology. The recent application of RNAseq methodology to single-cell transcriptional profiling has enabled the more precise characterization of cell lineage and cell state genetic profiles...
April 27, 2018: Circulation Research
https://www.readbyqxmd.com/read/29688343/a-town-on-fire-integrating-16s-rrna-gene-amplicon-analyses-into-an-undergraduate-microbiology-lecture-class
#15
Tammy C Tobin, Ashley Shade
Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology (QIIME) to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences...
April 23, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29688313/automatic-selection-of-verification-tools-for-efficient-analysis-of-biochemical-models
#16
Mehmet Emin Bakir, Savas Konur, Marian Gheorghe, Natalio Krasnogor, Mike Stannett
Motivation: Formal verification is a computational approach that checks system correctness (in relation to a desired functionality). It has been widely used in engineering applications to verify that systems work correctly. Model checking, an algorithmic approach to verification, looks at whether a system model satisfies its requirements specification. This approach has been applied to a large number of models in systems and synthetic biology as well as in systems medicine. Model checking is, however, computationally very expensive, and is not scalable to large models and systems...
April 24, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29684914/serum-calcium-is-related-to-the-degree-of-artery-stenosis-in-acute-ischemic-stroke
#17
Jiayan Wu, Junchao Xie, Yanxin Zhao, Li Gong, Xueyuan Liu, Wangmi Liu
BACKGROUND/AIMS: Acute ischemic stroke is caused by stenosis of artery supplying to brain. We aimed to detect some metabolites in the serum that would be related to the degree of artery stenosis and to analyze potential mechanisms. METHODS: Patients diagnosed with acute ischemic stroke were divided into two groups according to their degree of artery stenosis (which was determined by computed tomographic angiography): a mild group (stenosis ≤ 30%) and a severe group (stenosis > 30%)...
2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29678128/spirpep-an-in-silico-digestion-based-platform-to-assist-bioactive-peptides-discovery-from-a-genome-wide-database
#18
Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak, Marasri Ruengjitchatchawalya
BACKGROUND: Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo...
April 20, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29669011/annotsv-an-integrated-tool-for-structural-variations-annotation
#19
Véronique Geoffroy, Yvan Herenger, Arnaud Kress, Corinne Stoetzel, Amélie Piton, Hélène Dollfus, Jean Muller
Summary: Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation. Therefore, we developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positive...
April 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29665774/prediction-of-microrna-disease-associations-based-on-distance-correlation-set
#20
Haochen Zhao, Linai Kuang, Lei Wang, Pengyao Ping, Zhanwei Xuan, Tingrui Pei, Zhelun Wu
BACKGROUND: Recently, numerous laboratory studies have indicated that many microRNAs (miRNAs) are involved in and associated with human diseases and can serve as potential biomarkers and drug targets. Therefore, developing effective computational models for the prediction of novel associations between diseases and miRNAs could be beneficial for achieving an understanding of disease mechanisms at the miRNA level and the interactions between diseases and miRNAs at the disease level. Thus far, only a few miRNA-disease association pairs are known, and models analyzing miRNA-disease associations based on lncRNA are limited...
April 17, 2018: BMC Bioinformatics
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