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CANDC
2004
ACM
11 years 1 months ago
Identification of related gene/protein names based on an HMM of name variations
Gene and protein names follow few, if any, true naming conventions and are subject to great variation in different occurrences of the same name. This gives rise to two important p...
Lana Yeganova, Lawrence H. Smith, W. John Wilbur
CANDC
2004
ACM
11 years 1 months ago
The iProClass integrated database for protein functional analysis
Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological org...
Cathy H. Wu, Hongzhan Huang, Anastasia N. Nikolska...
CANDC
2004
ACM
11 years 1 months ago
Stochastic approaches for modelling in vivo reactions
In recent years, stochastic modelling has emerged as a physically more realistic alternative for modelling in vivo reactions. There are numerous stochastic approaches available in...
Thomas E. Turner, Santiago Schnell, Kevin Burrage
CANDC
2004
ACM
11 years 1 months ago
Retrieving definitional content for ontology development
Ontology construction requires an understanding of the meaning and usage of its encoded concepts. While definitions found in dictionaries or glossaries may be adequate for many co...
Lawrence H. Smith, W. John Wilbur
CANDC
2004
ACM
11 years 1 months ago
Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the p...
Ernesto Pérez-Rueda, Julio Collado-Vides, L...
CANDC
2004
ACM
11 years 1 months ago
The difficult interpretation of transcriptome data: the case of the GATC regulatory network
Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome an...
Alessandra Riva, Marie-Odile Delorme, Tony Chevali...
CANDC
2004
ACM
11 years 1 months ago
iProLINK: an integrated protein resource for literature mining
The exponential growth of large-scale molecular sequence data and of the PubMed scientific literature has prompted active research in biological literature mining and information ...
Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hon...
CANDC
2004
ACM
11 years 1 months ago
Cycling in ecological networks: Finn's index revisited
A chief cybernetic feature of natural living systems is the recycling of nutrients, which tends to enhance stability and is one of the principal causes of ecosystem complexity. In...
Stefano Allesina, Robert E. Ulanowicz
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