Articles
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Citation: Algorithms for Molecular Biology 2015 10:25
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A multiobjective approach for identifying protein complexes and studying their association in multiple disorders
Detecting protein complexes within protein–protein interaction (PPI) networks is a major step toward the analysis of biological processes and pathways. Identification and characterization of protein complexes ...
Citation: Algorithms for Molecular Biology 2015 10:24 -
Inferring interaction type in gene regulatory networks using co-expression data
Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulator...
Citation: Algorithms for Molecular Biology 2015 10:23 -
Pareto optimization in algebraic dynamic programming
Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives....
Citation: Algorithms for Molecular Biology 2015 10:22 -
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison
The increase of protein–protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI networ...
Citation: Algorithms for Molecular Biology 2015 10:21 -
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs
The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced ...
Citation: Algorithms for Molecular Biology 2015 10:20 -
Fair evaluation of global network aligners
Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species. Then, function can be transferred from well- to poorly-annotated specie...
Citation: Algorithms for Molecular Biology 2015 10:19 -
GAML: genome assembly by maximum likelihood
Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for produci...
Citation: Algorithms for Molecular Biology 2015 10:18 -
An online peak extraction algorithm for ion mobility spectrometry data
Ion mobility (IM) spectrometry (IMS), coupled with multi-capillary columns (MCCs), has been gaining importance for biotechnological and medical applications because of its ability to detect and quantify volati...
Citation: Algorithms for Molecular Biology 2015 10:17 -
A graph modification approach for finding core–periphery structures in protein interaction networks
The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core...
Citation: Algorithms for Molecular Biology 2015 10:16 -
Algorithms for detecting and analysing autocatalytic sets
Autocatalytic sets are considered to be fundamental to the origin of life. Prior theoretical and computational work on the existence and properties of these sets has relied on a fast algorithm for detectingsel...
Citation: Algorithms for Molecular Biology 2015 10:15 -
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks
Protein complexes formed by non-covalent interaction among proteins play important roles in cellular functions. Computational and purification methods have been used to identify many protein complexes and thei...
Citation: Algorithms for Molecular Biology 2015 10:14 -
On the family-free DCJ distance and similarity
Structural variation in genomes can be revealed by many (dis)similarity measures. Rearrangement operations, such as the so called double-cut-and-join (DCJ), are large-scale mutations that can create complex ch...
Citation: Algorithms for Molecular Biology 2015 10:13 -
Sorting signed permutations by short operations
During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the...
Citation: Algorithms for Molecular Biology 2015 10:12 -
A virtual pebble game to ensemble average graph rigidity
The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensembl...
Citation: Algorithms for Molecular Biology 2015 10:11 -
A simple data-adaptive probabilistic variant calling model
Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing ...
Citation: Algorithms for Molecular Biology 2015 10:10 -
Protein docking with predicted constraints
This paper presents a constraint-based method for improving protein docking results. Efficient constraint propagation cuts over 95% of the search time for finding the configurations with the largest contact su...
Citation: Algorithms for Molecular Biology 2015 10:9 -
MoDock: A multi-objective strategy improves the accuracy for molecular docking
As a main method of structure-based virtual screening, molecular docking is the most widely used in practice. However, the non-ideal efficacy of scoring functions is thought as the biggest barrier which hinder...
Citation: Algorithms for Molecular Biology 2015 10:8 -
Algorithmic approaches to protein-protein interaction site prediction
Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction ...
Citation: Algorithms for Molecular Biology 2015 10:7 -
An integrative approach for a network based meta-analysis of viral RNAi screens
Big data is becoming ubiquitous in biology, and poses significant challenges in data analysis and interpretation. RNAi screening has become a workhorse of functional genomics, and has been applied, for example...
Citation: Algorithms for Molecular Biology 2015 10:6 -
Estimating evolutionary distances between genomic sequences from spaced-word matches
Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance...
Citation: Algorithms for Molecular Biology 2015 10:5 -
Clustering of reads with alignment-free measures and quality values
The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an...
Citation: Algorithms for Molecular Biology 2015 10:4 -
EUCALYPT: efficient tree reconciliation enumerator
Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tr...
Citation: Algorithms for Molecular Biology 2015 10:3 -
A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads
Metagenomics is the study of genetic materials derived directly from complex microbial samples, instead of from culture. One of the crucial steps in metagenomic analysis, referred to as “binning”, is to separa...
Citation: Algorithms for Molecular Biology 2015 10:2 -
Double and multiple knockout simulations for genome-scale metabolic network reconstructions
Constraint-based modeling of genome-scale metabolic network reconstructions has become a widely used approach in computational biology. Flux coupling analysis is a constraint-based method that analyses the imp...
Citation: Algorithms for Molecular Biology 2015 10:1 -
On the number of genomic pacemakers: a geometric approach
The universal pacemaker (UPM) model extends the classical molecular clock (MC) model, by allowing each gene, in addition to its individual intrinsic rate as in the MC, to accelerate or decelerate according to ...
Citation: Algorithms for Molecular Biology 2014 9:26 -
BicPAM: Pattern-based biclustering for biomedical data analysis
Biclustering, the discovery of sets of objects with a coherent pattern across a subset of conditions, is a critical task to study a wide-set of biomedical problems, where molecular units or patients are meanin...
Citation: Algorithms for Molecular Biology 2014 9:27 -
Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models
Finding new functional fragments in biological sequences is a challenging problem. Methods addressing this problem commonly search for clusters of pattern occurrences that are statistically significant. A meas...
Citation: Algorithms for Molecular Biology 2014 9:25 -
A constraint solving approach to model reduction by tropical equilibration
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance....
Citation: Algorithms for Molecular Biology 2014 9:24 -
Atom mapping with constraint programming
Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms...
Citation: Algorithms for Molecular Biology 2014 9:23 -
A priori assessment of data quality in molecular phylogenetics
Sets of sequence data used in phylogenetic analysis are often plagued by both random noise and systematic biases. Since the commonly used methods of phylogenetic reconstruction are designed to produce trees it...
Citation: Algorithms for Molecular Biology 2014 9:22 -
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splic...
Citation: Algorithms for Molecular Biology 2014 9:19 -
Optimal computation of all tandem repeats in a weighted sequence
Tandem duplication, in the context of molecular biology, occurs as a result of mutational events in which an original segment of DNA is converted into a sequence of individual copies. More formally, a repetition ...
Citation: Algorithms for Molecular Biology 2014 9:21 -
Using the message passing algorithm on discrete data to detect faults in boolean regulatory networks
An important problem in systems biology is to model gene regulatory networks which can then be utilized to develop novel therapeutic methods for cancer treatment. Knowledge about which proteins/genes are dysre...
Citation: Algorithms for Molecular Biology 2014 9:20 -
Not assessing the efficiency of multiple sequence alignment programs
One can search for messages in the digits of π or a Kazakhstan telephone book, but there may be hidden messages closer to home. A recent publication in this journal purportedly compared a set of multiple seque...
Citation: Algorithms for Molecular Biology 2014 9:18 -
RNA-RNA interaction prediction using genetic algorithm
RNA-RNA interaction plays an important role in the regulation of gene expression and cell development. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable ...
Citation: Algorithms for Molecular Biology 2014 9:17 -
Enumerating all maximal frequent subtrees in collections of phylogenetic trees
A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant s...
Citation: Algorithms for Molecular Biology 2014 9:16 -
Computing the skewness of the phylogenetic mean pairwise distance in linear time
The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree
Citation: Algorithms for Molecular Biology 2014 9:15 -
Identification of alternative topological domains in chromatin
Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are...
Citation: Algorithms for Molecular Biology 2014 9:14 -
Characterizing compatibility and agreement of unrooted trees via cuts in graphs
Deciding whether there is a single tree —a supertree— that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this ...
Citation: Algorithms for Molecular Biology 2014 9:13 -
MSARC: Multiple sequence alignment by residue clustering
Progressive methods offer efficient and reasonably good solutions to the multiple sequence alignment problem. However, resulting alignments are biased by guide-trees, especially for relatively distant sequences.
Citation: Algorithms for Molecular Biology 2014 9:12 -
Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs
Statistics in ranked lists is useful in analysing molecular biology measurement data, such as differential expression, resulting in ranked lists of genes, or ChIP-Seq, which yields ranked lists of genomic sequ...
Citation: Algorithms for Molecular Biology 2014 9:11 -
Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating...
Citation: Algorithms for Molecular Biology 2014 9:10 -
Fast algorithms for approximate circular string matching
Circular string matching is a problem which naturally arises in many biological contexts. It consists in finding all occurrences of the rotations of a pattern of length m in a text of length n. There exist optima...
Citation: Algorithms for Molecular Biology 2014 9:9 -
Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework
Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing comput...
Citation: Algorithms for Molecular Biology 2014 9:8 -
Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation
Identifying ligand-binding sites is a key step to annotate the protein functions and to find applications in drug design. Now, many sequence-based methods adopted various predicted results from other classifie...
Citation: Algorithms for Molecular Biology 2014 9:7 -
Segmentor3IsBack: an R package for the fast and exact segmentation of Seq-data
Change point problems arise in many genomic analyses such as the detection of copy number variations or the detection of transcribed regions. The expanding Next Generation Sequencing technologies now allow to ...
Citation: Algorithms for Molecular Biology 2014 9:6 -
Faster algorithms for RNA-folding using the Four-Russians method
The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n3) time using Nussinov’s dynamic programming algorithm....
Citation: Algorithms for Molecular Biology 2014 9:5 -
Assessing the efficiency of multiple sequence alignment programs
Multiple sequence alignment (MSA) is an extremely useful tool for molecular and evolutionary biology and there are several programs and algorithms available for this purpose. Although previous studies have com...
Citation: Algorithms for Molecular Biology 2014 9:4 -
Probabilistic approaches to alignment with tandem repeats
Short tandem repeats are ubiquitous in genomic sequences and due to their complex evolutionary history pose a challenge for sequence alignment tools.
Citation: Algorithms for Molecular Biology 2014 9:3
- ISSN: 1748-7188 (electronic)