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11 years 10 months ago
Inverse perturbation for optimal intervention in gene regulatory networks
Motivation: Analysis and intervention in the dynamics of gene regulatory networks is at the heart of emerging efforts in the development of modern treatment of numerous ailments i...
Nidhal Bouaynaya, Roman Shterenberg, Dan Schonfeld
132views more  NAR 2007»
12 years 2 months ago
TRED: a transcriptional regulatory element database, new entries and other development
Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require ...
C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang
101views more  PRL 2006»
12 years 3 months ago
Regulation probability method for gene selection
This paper proposes a novel method for gene selection. In the method, the gene regulation, an important mechanism of gene activities, is first introduced, and then the probabiliti...
Hong-Qiang Wang, De-Shuang Huang
90views more  JCB 2008»
12 years 3 months ago
A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast
Resolving the general organizational principles that govern the interactions during transcriptional gene regulation has great relevance for understanding disease progression, biof...
Vladimir Filkov, Nameeta Shah
87views more  BMCBI 2006»
12 years 3 months ago
Computational expression deconvolution in a complex mammalian organ
Background: Microarray expression profiling has been widely used to identify differentially expressed genes in complex cellular systems. However, while such methods can be used to...
Min Wang, Stephen R. Master, Lewis A. Chodosh
110views more  BMCBI 2006»
12 years 3 months ago
Design of a combinatorial DNA microarray for protein-DNA interaction studies
Background: Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Rec...
Julian Mintseris, Michael B. Eisen
126views more  BMCBI 2006»
12 years 3 months ago
A joint model of regulatory and metabolic networks
Background: Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is ...
Chen-Hsiang Yeang, Martin Vingron
90views more  BMCBI 2008»
12 years 3 months ago
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Background: The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent res...
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne,...
163views Bioinformatics» more  APBC 2004»
12 years 4 months ago
A Combined Model and a Varied Gibbs Sampling Algorithm Used for Motif Discovery
The conserved sequences in gene regulatory regions dominate gene regulation. Discovering these sequences and their functions is important in post genome era. A novel model is cons...
Xiaoming Wu, Bo Wang, Changxin Song, Jingzhi Cheng
116views Healthcare» more  MIE 2008»
12 years 4 months ago
Gene Regulation Ontology (GRO): Design Principles and Use Cases
The Gene Regulation Ontology (GRO) is designed as a novel approach to model complex events that are part of the gene regulatory processes. We introduce the design requirements for ...
Elena Beisswanger, Vivian Lee, Jung-jae Kim, Dietr...