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Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Related publications (35)

A point mutation in the two-component regulator PhoP-PhoR accounts for the absence of polyketide-derived acyltrehaloses but not that of phthiocerol dimycocerosates in Mycobacterium tuberculosis H37Ra

Similarities between Mycobacterium tuberculosis phoP-phoR mutants and the attenuated laboratory strain M. tuberculosis H37Ra in terms of morphological and cytochemical properties, lipid content, gene expression and virulence attenuation prompted us to anal ...

2007

An algorithmic framework for genome-wide modeling and analysis of translation networks

Vassily Hatzimanikatis

The sequencing of genomes of several organisms and advances in high throughput technologies for transcriptome and proteome anal. has allowed detailed mechanistic studies of transcription and translation using math. frameworks that allow integration of both ...

2006

Gene Expression Measurements by Quantitative Real-time PCR Depends on Short Amplicons and a Proper Normalization

Darlene Goldstein

Quantitative reverse transcriptase real-time PCR (QRT-PCR) is a robust method to quantitate RNA abundance. The procedure is highly sensitive and reproducible as long as the initial RNA is intact. However, breaks in the RNA due to chemical or enzymatic clea ...

2005

Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations

Vassily Hatzimanikatis

Translation is a central cellular process in every organism and understanding translation from the systems (genome-wide) perspective is very important for medical and biochem. engineering applications. Moreover, recent advances in cell-wide monitoring tool ...

2003

Regulation of gene expression by activation of the peroxisome proliferator-activated receptor gamma with rosiglitazone (BRL 49653) in human adipocytes

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To better define the mechanism of action of the thiazolidinediones, we incubated freshly isolated human adipocytes with rosiglitazone and investigated the changes in mRNA expression of genes encoding key proteins of adipose tissue functions. Rosiglitazone ...

1999

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