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Here, we use ribosome-footprint profiing and mRNA-seq to determine the average ribosome density on each gene in S. cerevisiae. We then perform quantitative modeling to identify the molecular determinants of ribosome density. Analysis of S. cerevisiae
ORGANISM(S): Saccharomyces cerevisiae 
Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our result...
ORGANISM(S): Saccharomyces cerevisiae 
Mesenchymal Stem Cells are transformed by step-wise stable transfection with lentiviral vectors of TERT, E6, E7, SV40, and Ras.
ORGANISM(S): Homo sapiens 
The Ashkenazi Jewish population has long been considered a genetic isolate and presumed to have the genetic signatures of founder effects and isolation. We genotyped a large cohort of Ashkenazi Jews and analyzed their genetic structure compared to other worldwide populations. We genotyped 471 normal...
ORGANISM(S): Homo sapiens 
Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes wer...

Pulmonary fibrosis is a heterogenous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplific...

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