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Guest Editorial

Evgenii Vityaev, Nikolay Kolchanov, Evgenii Vityaev, Nikolay Kolchanov
2008 Intelligent Data Analysis  
"TRRD: technology for extraction, storage, and use of knowledge about the structural-functional organization of the transcriptional regulatory regions in the eukaryotic genes".  ...  In this paper the Transcription Regulatory Regions Database (TRRD,, designed for storage of data on the structural-functional organization of transcriptional regulatory  ... 
doi:10.3233/ida-2008-12501 fatcat:vzw6aljpxjdgzhq5sztm5jo57i

In Silico Identification of Regulatory Elements in Promoters [chapter]

Vikrant Nain, Shakti Sahi, Polumetla Ananda
2011 Computational Biology and Applied Bioinformatics  
TRRD The transcription regulatory region database (TRRD) is a database of transcription regulatory regions of the eukaryotic genome.  ...  In eukaryotes the most commonly used mechanism for maintaining cellular protein environment is transcriptional regulation of gene expression, by recruiting required transcription factors at promoter regions  ...  On the other hand, the growth of the computational power for processing and storage has also increased the necessity for deeper knowledge in the field.  ... 
doi:10.5772/22230 fatcat:wcruf4x7bvcsbaszaknsiejuxy

Semantic integration of data on transcriptional regulation

Michael Baitaluk, Julia Ponomarenko
2010 Computer applications in the biosciences : CABIOS  
However, there are no resources to integrate these data automatically or to provide a 'one-stop shop' experience for users seeking information essential for deciphering and modeling gene regulatory networks  ...  Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources.  ...  Sedova and A. Gupta for valuable discussions and assistance in creation of IntegromeDB and W. Bluhm for critical reading of the manuscript.  ... 
doi:10.1093/bioinformatics/btq231 pmid:20427517 pmcid:PMC2887046 fatcat:7g6zzhyjbzaplhqauhptunr47q

In Silico Approaches to Mechanistic and Predictive Toxicology: An Introduction to Bioinformatics for Toxicologists

Mark R. Fielden, Jason B. Matthews, Kirsten C. Fertuck, Robert G. Halgren, Tim R. Zacharewski
2002 Critical Reviews in Toxicology  
In addition, highly parallel gene expression profiling technologies will allow toxicologists to mine large databases of gene expression data to discover molecular biomarkers and other diagnostic and prognostic  ...  Novel genes can also be isolated in silico, while their function can be predicted and characterized by virtue of sequence homology to other known proteins.  ...  factors and their genomic binding sites, 102 and TRRD, a Transcription Regulatory Regions Database 103 (Table 1) .  ... 
doi:10.1080/20024091064183 pmid:11951993 fatcat:ictjulbjobbhpgdrlcgb2yhjoq

Preface Modeling and Simulation of Gene Regulation and Metabolic Pathways

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal, Julio Collado-Vides
1998 unpublished
In order to exploit molecular data, one must investigate the link between genes and proteins; the link between protein structure and protein function; and the concerted effects of many proteins acting  ...  During the last decade he has been analyzing the molecular mechanisms of eukaryotic gene regulation and has been collecting all transcriptional factors which can be found using his database system TRANSFAC  ...  Acknowledgement The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for its generous financial support.  ... 

Modelling and Simulation of Gene and Cell Regulation and Metabolic Pathways (Dagstuhl Seminar 98251)

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal
Kinetic models of biochemical pathways and gene expression systems are becoming very important (Mendes 1998, these proceedings) now that full genome  ...  Acknowledgement The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for its generous financial support.  ...  Extracted clusters are merged and represented into ortholog tables, which would be useful for function prediction of genes.  ... 
doi:10.4230/dagsemrep.215 fatcat:uc2tgmzmenanveonrv6p5wpopm


Sarah Mwangi, G Alan, Christoffels
Tsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative  ...  and transcription regulatory models were initially used as a prototype to describe transcription regulation in eukaryotes.  ...  Need for GmPromDB Data accrued from both the experimental and computational large-scale analyses of transcriptional control in various organisms have been compiled as databases for example: The eukaryotic  ...