scholarly journals OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis

RNA ◽  
2019 ◽  
Vol 25 (6) ◽  
pp. 657-668 ◽  
Author(s):  
Florian Thibord ◽  
Claire Perret ◽  
Maguelonne Roux ◽  
Pierre Suchon ◽  
Marine Germain ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Mirna Sequence ◽  
Genotype Data ◽  
Genome Wide ◽  
Alignment Analysis ◽  
Novel Algorithm

scholarly journals OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis

2018 ◽  
Author(s):  
Florian Thibord ◽  
Claire Perret ◽  
Maguelonne Roux ◽  
Pierre Suchon ◽  
Marine Germain ◽  
...  
Keyword(s):  
Mirna Sequence ◽  
Biological Knowledge ◽  
Genotype Data ◽  
Link Type ◽  
Genome Wide ◽  
Heterozygous Carriers ◽  
Alignment Analysis ◽  
Mirna Editing ◽  
Novel Algorithm ◽  
Alignment Step

AbstractNext-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs’ detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy.OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers.OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).

scholarly journals Genome-wide synteny through highly sensitive sequence alignment: Satsuma

2010 ◽  
Vol 26 (9) ◽  
pp. 1145-1151 ◽  
Author(s):  
M. G. Grabherr ◽  
P. Russell ◽  
M. Meyer ◽  
E. Mauceli ◽  
J. Alfoldi ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Genome Wide ◽  
Highly Sensitive

scholarly journals Recognition of another member of the malignant catarrhal fever virus group: an endemic gammaherpesvirus in domestic goats

2001 ◽  
Vol 82 (1) ◽  
pp. 227-232 ◽  
Author(s):  
Hong Li ◽  
Janice Keller ◽  
Donald P. Knowles ◽  
Timothy B. Crawford
Keyword(s):  
Dna Polymerase ◽  
Sequence Alignment ◽  
Gene Sequence ◽  
Homologous Sequence ◽  
Malignant Catarrhal Fever ◽  
Polymerase Gene ◽  
Virus Sequence ◽  
Herpesvirus 1 ◽  
Alignment Analysis ◽  
Recognition Of Another

A novel gammaherpesvirus in goats that is herein tentatively designated as caprine herpesvirus-2 was identified based on the sequence of a fragment from the herpesvirus DNA polymerase gene. Sequence alignment analysis revealed that the virus sequence isolated from goats was 67% identical to the homologous sequence from alcelaphine herpesvirus-1, 71% identical to ovine herpesvirus-2 and 73% identical to a recently recognized herpesvirus causing malignant catarrhal fever in white-tailed deer. Combined serological and PCR-survey data demonstrated that this virus is endemic in goats and its transmission pattern may be similar to that of ovine herpesvirus-2 in sheep.

G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation

2019 ◽  
Vol 35 (19) ◽  
pp. 3852-3854 ◽  
Author(s):  
You Tang ◽  
Xiaolei Liu
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Supplementary Information ◽  
Maximum Efficiency ◽  
Genotype Data ◽  
Simulation Tool ◽  
Genome Wide ◽  
Phenotype Data ◽  
Power Evaluation

Abstract Motivation Plenty of Genome-Wide-Association-Study (GWAS) methods have been developed for mapping genetic markers that associated with human diseases and agricultural economic traits. Computer simulation is a nice tool to test the performances of various GWAS methods under certain scenarios. Existing tools are either inefficient in terms of computation and memory efficiency or inconvenient to use to simulate big, realistic genotype data and phenotype data to evaluate available GWAS methods. Results Here, we present a GWAS simulation tool named G2P that can be used to simulate genotype data, phenotype data and perform power evaluation of GWAS methods. G2P is a user-friendly tool with all functions is provided in both graphical user interface and pipeline manners and it is available for Windows, Mac and Linux environments. Furthermore, G2P achieves maximum efficiency in terms of both memory usage and simulation speed; with G2P, the simulation of genotype data that includes 1 000 000 samples and 2 000 000 markers can be accomplished in 5 h. Availability and implementation The G2P software, user manual, and example datasets are freely available at GitHub: https://github.com/XiaoleiLiuBio/G2P. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Genome-Wide, Integrative Analysis Implicates Exosome-Derived MicroRNA Dysregulation in Schizophrenia

2019 ◽  
Vol 45 (6) ◽  
pp. 1257-1266 ◽  
Author(s):  
Yang Du ◽  
Yun Yu ◽  
Yang Hu ◽  
Xiao-Wan Li ◽  
Ze-Xu Wei ◽  
...  
Keyword(s):  
Target Genes ◽  
Sequence Data ◽  
Protein Glycosylation ◽  
Mirna Sequence ◽  
First Episode ◽  
Data Set ◽  
Protein Levels ◽  
Genome Wide ◽  
Exosomal Mirnas ◽  
Mirna Expression Profiling

Abstract Genetic variants conferring risk for schizophrenia (SCZ) have been extensively studied, but the role of posttranscriptional mechanisms in SCZ is not well studied. Here we performed the first genome-wide microRNA (miRNA) expression profiling in serum-derived exosome from 49 first-episode, drug-free SCZ patients and 46 controls and identified miRNAs and co-regulated modules that were perturbed in SCZ. Putative targets of these SCZ-affected miRNAs were enriched strongly for genes that have been implicated in protein glycosylation and were also related to neurotransmitter receptor and dendrite (spine) development. We validated several differentially expressed blood exosomal miRNAs in 100 SCZ patients as compared with 100 controls by quantitative reverse transcription-polymerase chain reaction. The potential regulatory relationships between several SCZ-affected miRNAs and their putative target genes were also validated. These include hsa-miR-206, which is the most upregulated miRNA in the blood exosomes of SCZ patients and that previously reported to regulate brain-derived neurotrophic factor expression, which we showed reduced mRNA and protein levels in the blood of SCZ patients. In addition, we found 11 miRNAs in blood exosomes from the miRNA sequence data that can be used to classify samples from SCZ patients and control subjects with close to 90% accuracy in the training samples, and approximately 75% accuracy in the testing samples. Our findings support a role for exosomal miRNA dysregulation in SCZ pathophysiology and provide a rich data set and framework for future analyses of miRNAs in the disease, and our data also suggest that blood exosomal miRNAs are promising biomarkers for SCZ.

Titanium Acts on Osteoblast Translational Process

2008 ◽  
Vol 34 (4) ◽  
pp. 190-194 ◽  
Author(s):  
Annalisa Palmieri ◽  
Furio Pezzetti ◽  
Anna Avantaggiato ◽  
Lorenzo Lo Muzio ◽  
Antonio Scarano ◽  
...  
Keyword(s):  
Bone Formation ◽  
Translation Regulation ◽  
Mirna Sequence ◽  
Clinical Effects ◽  
Mirna Microarray ◽  
Osteoblast Activity ◽  
Genome Wide ◽  
Novel Method ◽  
Translational Process

Abstract Titanium is a highly biocompatible material and very osteogenic in vivo. However, how titanium regulates osteoblast activity to promote bone formation is incompletely characterized. We, therefore, attempted to get more information by using microRNA (miRNA) microarray techniques to investigate translation regulation in osteoblasts grown on titanium disks. The miRNA oligonucleotide microarray provides a novel method to carry out genome-wide miRNA profiling in human samples. By using miRNA microarrays containing 329 probes designed from the human miRNA sequence, several miRNA were identified in osteoblast-like cell line (MG 63) grown on titanium disks. There were 13 up-regulated miRNAs (ie, mir-23a, mir-222, mir-523, mir-22, mir-23b, mir-143, mir-377, mir-24, mir-422b, mir-26a, mir-29a, mir-17–5p, mir-182) and 2 down-regulated miRNAs (ie, mir-187, mir-339). The data reported are, to our knowledge, the first study on translation regulation in osteoblasts exposed to titanium. The data can be relevant to understand better the molecular mechanism of osteoblast activation and as a model for comparing other materials with similar clinical effects.

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