IsoXpressor: a tool to assess transcriptional activity within isochores

LAK Ayad, AM Dourou, S Arhondakis… - Genome Biology and …, 2020 - academic.oup.com
Genomes are characterized by large regions of homogeneous base compositions known as
isochores. The latter are divided into GC-poor and GC-rich classes linked to distinct …

Transcriptome map of mouse isochores

S Arhondakis, K Frousios, CS Iliopoulos, SP Pissis… - BMC genomics, 2011 - Springer
Background The availability of fully sequenced genomes and the implementation of
transcriptome technologies have increased the studies investigating the expression profiles …

[HTML][HTML] Transcriptome map of mouse isochores in embryonic and neonatal cortex

K Frousios, CS Iliopoulos, G Tischler, S Kossida… - Genomics, 2013 - Elsevier
Several studies on adult tissues agree on the presence of a positive effect of the genomic
and genic base composition on mammalian gene expression. Recent literature supports the …

GC3 of genes can be used as a proxy for isochore base composition: a reply to Elhaik et al.

OK Clay, G Bernardi - Molecular Biology and Evolution, 2011 - academic.oup.com
In an article published in these pages, Elhaik et al.(Elhaik E, Landan G, Graur D. 2009. Can
GC content at third-codon positions be used as a proxy for isochore composition? Mol Biol …

Can GC content at third-codon positions be used as a proxy for isochore composition?

E Elhaik, G Landan, D Graur - Molecular Biology and Evolution, 2009 - academic.oup.com
The isochore theory depicts the genomes of warm-blooded vertebrates as a mosaic of long
genomic regions that are characterized by relatively homogeneous GC content. In the …

Segmenting the human genome into isochores

P Cozzi, L Milanesi, G Bernardi - Evolutionary Bioinformatics, 2015 - journals.sagepub.com
The human genome is a mosaic of isochores, which are long (> 200 kb) DNA sequences
that are fairly homogeneous in base composition and can be assigned to five families …

An isochore map of human chromosomes

M Costantini, O Clay, F Auletta, G Bernardi - Genome research, 2006 - genome.cshlp.org
Isochores are large DNA segments (≫ 300 kb on average) that are characterized by an
internal variation in GC well below the full variation seen in the mammalian genome …

Biological implications of isochore boundaries in the human genome

WX Zheng, CT Zhang - Journal of Biomolecular Structure and …, 2008 - Taylor & Francis
The human genome is composed of large sequence segments with fairly homogeneous GC
content, namely isochores, which have been linked to many important functions; biological …

How not to search for isochores: a reply to Cohen et al

O Clay, G Bernardi - Molecular biology and evolution, 2005 - academic.oup.com
In a recent paper in these pages, Cohen et al. search for isochores in the human genome,
based on a system of attributes that they assign to isochores. The putative isochores that …

The evolution of isochore patterns in vertebrate genomes

M Costantini, R Cammarano, G Bernardi - BMC genomics, 2009 - Springer
Background Previous work from our laboratory showed that (i) vertebrate genomes are
mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous …