TY  - JOUR
A1  - Arhondakis, Stilianos
A1  - Frousios, Kimon
A1  - Iliopoulos, Costas S.
A1  - Pissis, Solon P.
A1  - Tischler, German
A1  - Kossida, Sophia
T1  - Transcriptome map of mouse isochores
JF  - BMC Genomics
N2  - Background: 

The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. 

Results: 

We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. 

Conclusions: 

This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
KW  - Biased gene conversion
KW  - Human genome
KW  - GC-Content
KW  - Mammalian genomes
KW  - Base composition
KW  - Expresses genes
KW  - Higher rates
KW  - RNA-SEQ
KW  - Evolution
KW  - Rodents
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-142773
VL  - 12
IS  - 511
ER  - 
TY  - THES
A1  - Tischler, German
T1  - Theory and Applications of Parametric Weighted Finite Automata
T1  - Theorie und Anwendungen parametrisch gewichteter endlicher Automaten
N2  - Parametric weighted finite automata (PWFA) are a multi-dimensional generalization of weighted finite automata. The expressiveness of PWFA contains the expressiveness of weighted finite automata as well as the expressiveness of affine iterated function system. The thesis discusses theory and applications of PWFA. The properties of PWFA definable sets are studied and it is shown that some fractal generator systems can be simulated using PWFA and that various real and complex functions can be represented by PWFA. Furthermore, the decoding of PWFA and the interpretation of PWFA definable sets is discussed.
N2  - Parametrisch gewichtete endliche Automaten (PWFA) sind eine multidimensionale Verallgemeinerung gewichteter endlicher Automaten, die sowohl die funktionale Mächtigkeit gewichteter endlicher Automaten als auch die affiner iterierter Funktionensystem umschließt. Die Arbeit diskutiert die Theorie und Anwendungen von PWFA. Es werden Eigenschaften der von PWFA definierbaren Mengen untersucht, gezeigt dass verschiedene fraktale Generatorsysteme mit PWFA simuliert werden können und dass viele praxisrelevante reelle und komplexe Funktionen und Relationen mit PWFA darstellbar sind. Ferner wird die Dekodierung von PWFA und die Interpretation PWFA-darstellbarer Mengen diskutiert.
KW  - Automat <Automatentheorie>
KW  - Automata Theory
Y1  - 2008
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-28145
ER  -