Articles

Designing minimal microbial strains of desired functionality using a genetic algorithm

The rational, in silico prediction of gene-knockouts to turn organisms into efficient cell factories is an essential and computationally challenging task in metabolic engineering. Elementary flux mode analys...

Authors: Govind Nair, Christian Jungreuthmayer, Michael Hanscho and Jürgen Zanghellini

A reconstruction problem for a class of phylogenetic networks with lateral gene transfers

Lateral, or Horizontal, Gene Transfers are a type of asymmetric evolutionary events where genetic material is transferred from one species to another. In this paper we consider LGT networks, a general model of p...

Authors: Gabriel Cardona, Joan Carles Pons and Francesc Rosselló

A polynomial time algorithm for computing the area under a GDT curve

Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the...

Authors: Aleksandar Poleksic

Instability in progressive multiple sequence alignment algorithms

Progressive alignment is the standard approach used to align large numbers of sequences. As with all heuristics, this involves a tradeoff between alignment accuracy and computation time.

Authors: Kieran Boyce, Fabian Sievers and Desmond G. Higgins

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data

Authors: Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Gary D Bader and Bahram Goliaei

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 ...

Authors: Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay and Ujjwal Maulik

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...

Authors: Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei and Gary D Bader

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....

Authors: Cédric Saule and Robert Giegerich

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...

Authors: Wei Peng, Jianxin Wang, Fangxiang Wu and Pan Yi

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 ...

Authors: Gustavo Sacomoto, Vincent Lacroix and Marie-France Sagot

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...

Authors: Joseph Crawford, Yihan Sun and Tijana Milenković

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...

Authors: Vladimír Boža, Broňa Brejová and Tomáš Vinař

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...

Authors: Dominik Kopczynski and Sven Rahmann

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...

Authors: Sharon Bruckner, Falk Hüffner and Christian Komusiewicz

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...

Authors: Wim Hordijk, Joshua I Smith and Mike Steel

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...

Authors: Duc-Hau Le

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...

Authors: Fábio V Martinez, Pedro Feijão, Marília DV Braga and Jens Stoye

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...

Authors: Gustavo Rodrigues Galvão, Orlando Lee and Zanoni Dias

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...

Authors: Luis C González, Hui Wang, Dennis R Livesay and Donald J Jacobs

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 ...

Authors: Steve Hoffmann, Peter F Stadler and Korbinian Strimmer

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...

Authors: Ludwig Krippahl and Pedro Barahona

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...

Authors: Junfeng Gu, Xu Yang, Ling Kang, Jinying Wu and Xicheng Wang

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 ...

Authors: Tristan T Aumentado-Armstrong, Bogdan Istrate and Robert A Murgita

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...

Authors: Sandeep S Amberkar and Lars Kaderali

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...

Authors: Burkhard Morgenstern, Bingyao Zhu, Sebastian Horwege and Chris André Leimeister

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...

Authors: Matteo Comin, Andrea Leoni and Michele Schimd

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...

Authors: Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi and Marie-France Sagot

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...

Authors: Le Van Vinh, Tran Van Lang, Le Thanh Binh and Tran Van Hoai

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...

Authors: Yaron AB Goldstein and Alexander Bockmayr

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 ...

Authors: Sagi Snir

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...

Authors: Rui Henriques and Sara C Madeira

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...

Authors: Mireille Régnier, Evgenia Furletova, Victor Yakovlev and Mikhail Roytberg

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....

Authors: Sylvain Soliman, François Fages and Ovidiu Radulescu

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...

Authors: Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler and Christoph Flamm

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...

Authors: Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska and Peter F Stadler

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...

Authors: Jing Qin, Markus Fricke, Manja Marz, Peter F Stadler and Rolf Backofen

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 ...

Authors: Carl Barton, Costas S Iliopoulos and Solon P Pissis

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...

Authors: Anwoy Kumar Mohanty, Aniruddha Datta and Vijayanagaram Venkatraj

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...

Authors: Andrew E Torda

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 ...

Authors: Soheila Montaseri, Fatemeh Zare-Mirakabad and Nasrollah Moghadam-Charkari

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...

Authors: Akshay Deepak and David Fernández-Baca

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

Authors: Constantinos Tsirogiannis and Brody Sandel

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...

Authors: Darya Filippova, Rob Patro, Geet Duggal and Carl Kingsford

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 ...

Authors: Sudheer Vakati and David Fernández-Baca

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.

Authors: Michał Modzelewski and Norbert Dojer

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...

Authors: Limor Leibovich and Zohar Yakhini

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...

Authors: Usha Kuppuswamy, Seshan Ananthasubramanian, Yanli Wang, Narayanaswamy Balakrishnan and Madhavi K Ganapathiraju

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...

Authors: Carl Barton, Costas S Iliopoulos and Solon P Pissis

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...

Authors: Ramanuja Simha and Hagit Shatkay

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...

Authors: Chun Fang, Tamotsu Noguchi and Hayato Yamana