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- 1From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground The introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e.,...
- 2From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Biclustering algorithms for microarray data aim at discovering functionally related gene sets under different subsets of experimental conditions. Due to the problem complexity and the characteristics of...
- 3From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying...
- 4From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure...
- 5From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of...
- 6From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Kinship inference is the task of identifying genealogically relatedindividuals. Kinship information is important for determining matingstructures, notably in endangered populations. Although many solutions...
- 7From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set...
- 8From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Positional weight matrix (PWM) remains the most popular for quantification of transcription factor (TF) binding. PWM supplied with a score threshold defines a set of putative transcription factor binding...
- 9From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedWe study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function f(r) such that, for any set C of r-state characters, C is...
- 10From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these...
- 11From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected...
- 12From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Gene expression data could likely be a momentous help in the progress of proficient cancer diagnoses and classification platforms. Lately, many researchers analyze gene expression data using diverse...
- 13From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedWe generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignment...
- 14From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedAbstract We propose three algorithms for string edit distance with duplications and contractions. These include an efficient general algorithm and two improvements which apply under certain constraints on the cost...
- 15From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground The search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem...
- 16From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes. It is well-known...
- 17From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Estrogen is a chemical messenger that has an influence on many breast cancers as it helps cells to grow and divide. These cancers are often known as estrogen responsive cancers in which estrogen receptor...
- 18From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground RNA folding depends on the distribution of kinetic traps in the landscape of all secondary structures. Kinetic traps in the Nussinov energy model are precisely those secondary structures that are...
- 19From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields...
- 20From: Algorithms for Molecular Biology. (Vol. 8, Issue 1) Peer-ReviewedBackground Systematically perturbing a cellular system and monitoring the effects of the perturbations on gene expression provide a powerful approach to study signal transduction in gene expression systems. A...