19 Result(s)
within
Mehdi Pirooznia
Life Sciences
-
Article
The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster
Mitochondrial DNA (mtDNA) replication and transcription are of paramount importance to cellular energy metabolism. Mitochondrial RNA polymerase is thought to be the primase for mtDNA replication. However, it i...
-
Article
Open AccessAssessing reproducibility of inherited variants detected with short-read whole genome sequencing
Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call qualit...
-
Article
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a...
-
Article
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk ...
-
Article
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics...
-
Article
Open AccessA verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference...
-
Article
Open AccessCross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and ...
-
Article
Fasting-induced FOXO4 blunts human CD4+ T helper cell responsiveness
Intermittent fasting blunts inflammation in asthma1 and rheumatoid arthritis2, suggesting that fasting may be exploited as an immune-modulatory intervention. However, the mechanisms underpinning the anti-inflamma...
-
Protocol
Bioinformatics Approaches for Functional Prediction of Long Noncoding RNAs
There is accumulating evidence that long noncoding RNAs (lncRNAs) play crucial roles in biological processes and diseases. In recent years, computational models have been widely used to predict potential lncRN...
-
Article
Open AccessSVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies
Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or ...
-
Article
Open AccessGenomic signatures and gene networking: challenges and promises
This is an editorial report of the supplement to BMC Genomics that includes 15 papers selected from the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology as well as other...
-
Article
Open AccessGeneration, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)
-
Article
Open AccessILOOP – a web application for two-channel microarray interwoven loop design
Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistic...
-
Article
Open AccessBatch Blast Extractor: an automated blastx parser application
BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time co...
-
Article
Open AccessA comparative study of different machine learning methods on microarray gene expression data
Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neur...
-
Article
Open AccessTranscriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida
Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological ...
-
Article
Open AccessCloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida
Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test o...
-
Article
Open AccessSVM Classifier – a comprehensive java interface for support vector machine classification of microarray data
Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpo...
-
Article
Open AccessRiboaptDB: A Comprehensive Database of Ribozymes and Aptamers
Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selec...
