From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

FJ Rang, WP Kloosterman, J de Ridder - Genome biology, 2018 - Springer
Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on
a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this …

Codon usage and tRNA content in unicellular and multicellular organisms.

T Ikemura - Molecular biology and evolution, 1985 - academic.oup.com
Choices of synonymous codons in unicellular organisms are here reviewed, and differences
in synonymous codon usages between Escherichia coli and the yeast Saccharomyces …

The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

PM Sharp, WH Li - Nucleic acids research, 1987 - academic.oup.com
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index,
is detailed. The index uses a reference set of highly expressed genes from a species to …

The 'effective number of codons' used in a gene

F Wright - Gene, 1990 - Elsevier
A simple measure is presented that quantifies how far the codon usage of a gene departs
from equal usage of synonymous codons. This measure of synonymous codon usage bias …

A protein kinase involved in the regulation of inflammatory cytokine biosynthesis

JC Lee, JT Laydon, PC McDonnell, TF Gallagher… - Nature, 1994 - nature.com
Production of interleukin-1 and tumour necrosis factor from stimulated human monocytes is
inhibited by a new series of pyridinyl-imidazole compounds. Using radiolabelled and radio …

A comprehensive set of sequence analysis programs for the VAX

J Devereux, P Haeberli, O Smithies - 1984 - academic.oup.com
Abstract The University of Wisconsin Genetics Computer Group (UWGCG) has been
organized to develop computational tools for the analysis and publication of biological …

An evolutionary perspective on synonymous codon usage in unicellular organisms

PM Sharp, WH Li - Journal of molecular evolution, 1986 - Springer
Observed patterns of synonymous codon usage are explained in terms of the joint effects of
mutation, selection, and random drift. Examination of the codon usage in 165 Escherichia …

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes

PM Sharp, TMF Tuohy, KR Mosurski - Nucleic acids research, 1986 - academic.oup.com
Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative
synonymous codon usage revealed two distinct groups of genes. One group corresponds to …

The selection-mutation-drift theory of synonymous codon usage.

M Bulmer - Genetics, 1991 - academic.oup.com
It is argued that the bias in synonymous codon usage observed in unicellular organisms is
due to a balance between the forces of selection and mutation in a finite population, with …

Human epidermal growth factor receptor cDNA sequence and aberrant expression of the amplified gene in A431 epidermoid carcinoma cells

A Ullrich, L Coussens, JS Hayflick, TJ Dull, A Gray… - Nature, 1984 - nature.com
Abstract The complete 1,210-amino acid sequence of the human epidermal growth factor
(EGF) receptor precursor, deduced from cDNA clones derived from placental and A431 …