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- 1From: Algorithms for Molecular Biology. (Vol. 5) Peer-Reviewed
- 2From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network...
- 3From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Biclustering is an important analysis procedure to understand the biological mechanisms from microarray gene expression data. Several algorithms have been proposed to identify biclusters, but very little...
- 4From: Algorithms for Molecular Biology. (Vol. 5, Issue 39) Peer-ReviewedBackground Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic...
- 5From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for...
- 6From: Algorithms for Molecular Biology. (Vol. 5) Peer-Reviewed
- 7From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedA report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems...
- 8From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedPhylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard...
- 9From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of...
- 10From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve...
- 11From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools...
- 12From: Algorithms for Molecular Biology. (Vol. 5) Peer-Reviewed
- 13From: Algorithms for Molecular Biology. (Vol. 5) Peer-Reviewed
- 14From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedWe introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeography, and...
- 15From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all...
- 16From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic...
- 17From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial...
- 18From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin....
- 19From: Algorithms for Molecular Biology. (Vol. 5) Peer-Reviewed
- 20From: Algorithms for Molecular Biology. (Vol. 5) Peer-ReviewedBackground Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound....