The mutational profile of the yeast genome is shaped by replication

N Agier, G Fischer - Molecular biology and evolution, 2012 - academic.oup.com
Despite the scrutiny that has been directed for years at the yeast genome, relatively little is
known about the impact of replication on the substitution dynamics in Saccharomyces …

How does replication-associated mutational pressure influence amino acid composition of proteins?

P Mackiewicz, A Gierlik, M Kowalczuk… - Genome …, 1999 - genome.cshlp.org
We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding
sequences and, separately, on each position in codons of coding sequences. Our method …

Novel low abundance and transient rnas in yeast revealed by tiling microarrays and ultra high–throughput sequencing are not conserved across closely related yeast …

A Lee, KD Hansen, J Bullard, S Dudoit… - PLoS genetics, 2008 - journals.plos.org
A complete description of the transcriptome of an organism is crucial for a comprehensive
understanding of how it functions and how its transcriptional networks are controlled, and …

Comparative study of overlap** genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii

KR Sakharkar, MK Sakharkar… - … of systematic and …, 2005 - microbiologyresearch.org
Overlap** genes have been proposed as a means of achieving genome reduction by
compressing the maximum amount of information in limited sequence space. In this report …

Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome?

A Gierlik, M Kowalczuk, P Mackiewicz… - Journal of Theoretical …, 2000 - Elsevier
Compositional bias of yeast chromosomes was analysed using detrended DNA walks.
Unlike eubacterial chromosomes, the yeast chromosomes did not show the specific …

How many protein‐coding genes are there in the Saccharomyces cerevisiae genome?

P Mackiewicz, M Kowalczuk, D Mackiewicz, A Nowicka… - Yeast, 2002 - Wiley Online Library
We have compared the results of estimations of the total number of protein‐coding genes in
the Saccharomyces cerevisiae genome, which have been obtained by many laboratories …

The effect of DNA phase structure on DNA walks

S Cebrat, MR Dudek - The European Physical Journal B-Condensed …, 1998 - Springer
We have performed several kinds of DNA walks which often are the first steps for further
analysis of DNA structure and long range correlations. The DNA walks analysing frequency …

Origin and properties of non-coding ORFs in the yeast genome

P Mackiewicz, M Kowalczuk, A Gierlik… - Nucleic acids …, 1999 - academic.oup.com
In a recent paper we have estimated the total number of protein coding open reading frames
(ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800 …

Identification of protein‐coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides

J Wang, CT Zhang - European journal of biochemistry, 2001 - Wiley Online Library
The published sequence of the Vibrio cholerae genome indicates that, in addition to the
genes that encode proteins of known and unknown function, there are 1577 ORFs identified …

Mechanisms generating long-range correlation in nucleotide composition of the Borrelia burgdorferi genome

P Mackiewicz, A Gierlik, M Kowalczuk… - Physica A: Statistical …, 1999 - Elsevier
We have analysed protein coding and intergenic sequences in the Borrelia burgdorferi (the
Lyme disease bacterium) genome using different kinds of DNA walks. Genes occupying the …