Articles

Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

Recent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogeneti...

Authors: Benjamin Drinkwater and Michael A. Charleston

BicNET: Flexible module discovery in large-scale biological networks using biclustering

Despite the recognized importance of module discovery in biological networks to enhance our understanding of complex biological systems, existing methods generally suffer from two major drawbacks. First, there...

Authors: Rui Henriques and Sara C. Madeira

Models and algorithms for genome rearrangement with positional constraints

Traditionally, the merit of a rearrangement scenario between two gene orders has been measured based on a parsimony criteria alone; two scenarios with the same number of rearrangements are considered equally g...

Authors: Krister M. Swenson, Pijus Simonaitis and Mathieu Blanchette

Circular sequence comparison: algorithms and applications

Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in seq...

Authors: Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis, Ahmad Retha and Fatima Vayani

An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem

The mutual exclusivity of somatic genome alterations (SGAs), such as somatic mutations and copy number alterations, is an important observation of tumors and is widely used to search for cancer signaling pathw...

Authors: Songjian Lu, Gunasheil Mandava, Gaibo Yan and Xinghua Lu

Jabba: hybrid error correction for long sequencing reads

Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, un...

Authors: Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert and Jan Fostier

Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays

Suffix arrays and their variants are used widely for representing genomes in search applications. Enhanced suffix arrays (ESAs) provide fast search speed, but require large auxiliary data structures for storin...

Authors: Thomas D. Wu

RNA folding with hard and soft constraints

A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evid...

Authors: Ronny Lorenz, Ivo L. Hofacker and Peter F. Stadler

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction

RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to i...

Authors: Sebastian Will and Hosna Jabbari

MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics

Measuring sequence similarity is central for many problems in bioinformatics. In several contexts alignment-free techniques based on exact occurrences of substrings are faster, but also less accurate, than ali...

Authors: Cinzia Pizzi

Bitpacking techniques for indexing genomes: I. Hash tables

Hash tables constitute a widely used data structure for indexing genomes that provides a list of genomic positions for each possible oligomer of a given size. The offset array in a hash table grows exponential...

Authors: Thomas D. Wu

The link between orthology relations and gene trees: a correction perspective

While tree-oriented methods for inferring orthology and paralogy relations between genes are based on reconciling a gene tree with a species tree, many tree-free methods are also available (usually based on se...

Authors: Manuel Lafond, Riccardo Dondi and Nadia El-Mabrouk

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high nu...

Authors: Guillaume Holley, Roland Wittler and Jens Stoye

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage

In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motiva...

Authors: Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini, Guilherme C. Oliveira, Luiz Mario R. Janini and Fernando Antoneli

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies

The accurate annotation of genes in newly sequenced genomes remains a challenge. Although sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect. Thi...

Authors: Henrike Indrischek, Nicolas Wieseke, Peter F. Stadler and Sonja J. Prohaska

Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics

Markov chains are a common framework for individual-based state and time discrete models in evolution. Though they played an important role in the development of basic population genetic theory, the analysis o...

Authors: Katja Reichel, Valentin Bahier, Cédric Midoux, Nicolas Parisey, Jean-Pierre Masson and Solenn Stoeckel

HIA: a genome mapper using hybrid index-based sequence alignment

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapid...

Authors: Jongpill Choi, Kiejung Park, Seong Beom Cho and Myungguen Chung

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