Modeling and simulation of genetic regulatory systems: a literature review
H De Jong - Journal of computational biology, 2002 - liebertpub.com
In order to understand the functioning of organisms on the molecular level, we need to know
which genes are expressed, when and where in the organism, and to which extent. The …
which genes are expressed, when and where in the organism, and to which extent. The …
Cluster analysis for gene expression data: a survey
DNA microarray technology has now made it possible to simultaneously monitor the
expression levels of thousands of genes during important biological processes and across …
expression levels of thousands of genes during important biological processes and across …
Computational methods for the identification of differential and coordinated gene expression
JM Claverie - Human molecular genetics, 1999 - academic.oup.com
With the first complete 'draft'of the human genome sequence expected for Spring 2000, the
three basic challenges for today's bioinformatics are more than ever:(i) finding the genes;(ii) …
three basic challenges for today's bioinformatics are more than ever:(i) finding the genes;(ii) …
Genetic network inference: from co-expression clustering to reverse engineering
Abstract motivation: Advances in molecular biological, analytical and computational
technologies are enabling us to systematically investigate the complex molecular processes …
technologies are enabling us to systematically investigate the complex molecular processes …
Relating whole-genome expression data with protein-protein interactions
We investigate the relationship of protein-protein interactions with mRNA expression levels,
by integrating a variety of data sources for yeast. We focus on known protein complexes that …
by integrating a variety of data sources for yeast. We focus on known protein complexes that …
[BOOK][B] Algorithms and theory of computation handbook, volume 2: special topics and techniques
MJ Atallah, M Blanton - 2009 - books.google.com
This handbook provides an up-to-date compendium of fundamental computer science
topics, techniques, and applications. Along with updating and revising many of the existing …
topics, techniques, and applications. Along with updating and revising many of the existing …
'Gene shaving'as a method for identifying distinct sets of genes with similar expression patterns
Background Large gene expression studies, such as those conducted using DNA arrays,
often provide millions of different pieces of data. To address the problem of analyzing such …
often provide millions of different pieces of data. To address the problem of analyzing such …
Introduction to random Boolean networks
C Gershenson - arxiv preprint nlin/0408006, 2004 - arxiv.org
The goal of this tutorial is to promote interest in the study of random Boolean networks
(RBNs). These can be very interesting models, since one does not have to assume any …
(RBNs). These can be very interesting models, since one does not have to assume any …
Genetic network modeling
The inference of genetic interactions from measured expression data is one of the most
challenging tasks of modern functional genomics. When successful, the learned network of …
challenging tasks of modern functional genomics. When successful, the learned network of …
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions
The complexity of biological systems provides for a great diversity of relationships between
genes. The current analysis of whole-genome expression data focuses on relationships …
genes. The current analysis of whole-genome expression data focuses on relationships …