Articles

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by ...

Authors: Morten Muhlig Nielsen, Paula Tataru, Tobias Madsen, Asger Hobolth and Jakob Skou Pedersen

Superbubbles revisited

Superbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are c...

Authors: Fabian Gärtner, Lydia Müller and Peter F. Stadler

Coordinate systems for supergenomes

Genome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting compa...

Authors: Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller and Peter F. Stadler

Improved de novo peptide sequencing using LC retention time information

Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides tha...

Authors: Yves Frank, Tomas Hruz, Thomas Tschager and Valentin Venzin

Sorting signed circular permutations by super short operations

One way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. I...

Authors: Andre R. Oliveira, Guillaume Fertin, Ulisses Dias and Zanoni Dias

Split-inducing indels in phylogenomic analysis

Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps.

Authors: Alexander Donath and Peter F. Stadler

Locus-aware decomposition of gene trees with respect to polytomous species trees

Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most o...

Authors: Michał Aleksander Ciach, Anna Muszewska and Paweł Górecki

A fast and accurate enumeration-based algorithm for haplotyping a triploid individual

Haplotype assembly, reconstructing haplotypes from sequence data, is one of the major computational problems in bioinformatics. Most of the current methodologies for haplotype assembly are designed for diploid...

Authors: Jingli Wu and Qian Zhang

Finding local genome rearrangements

The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been...

Authors: Pijus Simonaitis and Krister M. Swenson

FSH: fast spaced seed hashing exploiting adjacent hashes

Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as the...

Authors: Samuele Girotto, Matteo Comin and Cinzia Pizzi

Outlier detection in BLAST hits

An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of kn...

Authors: Nidhi Shah, Stephen F. Altschul and Mihai Pop

OCTAL: Optimal Completion of gene trees in polynomial time

For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain a...

Authors: Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati and Tandy Warnow

Fast phylogenetic inference from typing data

Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of s...

Authors: João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves and Cátia Vaz

Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment

A profile-comparison method with position-specific scoring matrix (PSSM) is among the most accurate alignment methods. Currently, cosine similarity and correlation coefficients are used as scoring functions of...

Authors: Kazunori D. Yamada

A safe and complete algorithm for metagenomic assembly

Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bact...

Authors: Nidia Obscura Acosta, Veli Mäkinen and Alexandru I. Tomescu

Time-consistent reconciliation maps and forbidden time travel

In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge o...

Authors: Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke and Marc Hellmuth

Gene tree parsimony for incomplete gene trees: addressing true biological loss

Species tree estimation from gene trees can be complicated by gene duplication and loss, and “gene tree parsimony” (GTP) is one approach for estimating species trees from multiple gene trees. In its standard ...

Authors: Md Shamsuzzoha Bayzid and Tandy Warnow

Phylogeny reconstruction based on the length distribution of k-mismatch common substrings

Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between pairs of input sequences. Haubold et al. (J Comput Biol 16:1487–1500, 2009) showed how the...

Authors: Burkhard Morgenstern, Svenja Schöbel and Chris-André Leimeister

Generalized enhanced suffix array construction in external memory

Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a ...

Authors: Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann and Cristina D. A. Ciferri

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient...

Authors: Shixiang Wan and Quan Zou

Algorithms for matching partially labelled sequence graphs

In order to find correlated pairs of positions between proteins, which are useful in predicting interactions, it is necessary to concatenate two large multiple sequence alignments such that the sequences that ...

Authors: William R. Taylor

Biologically feasible gene trees, reconciliation maps and informative triples

The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous...

Authors: Marc Hellmuth

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

Genomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of whi...

Authors: Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout and Peter F. Stadler

A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification

Mixtures of beta distributions are a flexible tool for modeling data with values on the unit interval, such as methylation levels. However, maximum likelihood parameter estimation with beta distributions suffe...

Authors: Christopher Schröder and Sven Rahmann

ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks

This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks ...

Authors: Emna Ben Abdallah, Maxime Folschette, Olivier Roux and Morgan Magnin

Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming

Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject...

Authors: Louis Fippo Fitime, Olivier Roux, Carito Guziolowski and Loïc Paulevé

A graph extension of the positional Burrows–Wheeler transform and its applications

We present a generalization of the positional Burrows–Wheeler transform, or PBWT, to genome graphs, which we call the gPBWT. A genome graph is a collapsed representation of a set of genomes described as a grap...

Authors: Adam M. Novak, Erik Garrison and Benedict Paten

Isometric gene tree reconciliation revisited

Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the rec...

Authors: Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo and Tomáš Vinař

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accu...

Authors: Guillaume Fertin, Géraldine Jean and Eric Tannier

StreAM-\(T_g\): algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are w...

Authors: Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe and Kay Hamacher

The gene family-free median of three

The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We ...

Authors: Daniel Doerr, Metin Balaban, Pedro Feijão and Cedric Chauve

Complexity and algorithms for copy-number evolution problems

Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the n...

Authors: Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi and Ron Zeira

A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses

Given a peptide as a string of amino acids, the masses of all its prefixes and suffixes can be found by a trivial linear scan through the amino acid masses. The inverse problem is the ideal ...

Authors: Thomas Tschager, Simon Rösch, Ludovic Gillet and Peter Widmayer

Core column prediction for protein multiple sequence alignments

In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In ben...

Authors: Dan DeBlasio and John Kececioglu

Aligning coding sequences with frameshift extension penalties

Frameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene...

Authors: Safa Jammali, Esaie Kuitche, Ayoub Rachati, François Bélanger, Michelle Scott and Aïda Ouangraoua

Gerbil: a fast and memory-efficient k-mer counter with GPU-support

A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degra...

Authors: Marius Erbert, Steffen Rechner and Matthias Müller-Hannemann

The feasibility of genome-scale biological network inference using Graphics Processing Units

Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network int...

Authors: Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil and Daniel A. Beard

An efficient algorithm for testing the compatibility of phylogenies with nested taxa

Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection

Authors: Yun Deng and David Fernández-Baca

On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model

Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains t...

Authors: Daniel Bork, Ricson Cheng, Jincheng Wang, Jean Sung and Ran Libeskind-Hadas

On avoided words, absent words, and their application to biological sequence analysis

The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguisti...

Authors: Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis and Dimitris Polychronopoulos

Approximating the correction of weighted and unweighted orthology and paralogy relations

Given a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and “missing” edges represent paralogs. While a gene t...

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

Approximating the DCJ distance of balanced genomes in linear time

Rearrangements are large-scale mutations in genomes, responsible for complex changes and structural variations. Most rearrangements that modify the organization of a genome can be represented by the double cut...

Authors: Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye and Fábio Henrique Viduani Martinez

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this prob...

Authors: Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic a...

Authors: Laurent Noé

Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Authors: Timo Beller and Enno Ohlebusch

An efficient algorithm for protein structure comparison using elastic shape analysis

Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have ...

Authors: S. Srivastava, S. B. Lal, D. C. Mishra, U. B. Angadi, K. K. Chaturvedi, S. N. Rai and A. Rai

Analysis of gene copy number changes in tumor phylogenetics

Evolution of cancer cells is characterized by large scale and rapid changes in the chromosomal  landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of ...

Authors: Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng and Jijun Tang

Enumeration of minimal stoichiometric precursor sets in metabolic networks

What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal ...

Authors: Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu, Leen Stougie and Marie-France Sagot

Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis

Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a lo...

Authors: Jerome Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle and Jean-Luc Gala

BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge

Biclustering has been largely used in biological data analysis, enabling the discovery of putative functional modules from omic and network data. Despite the recognized importance of incorporating domain knowl...

Authors: Rui Henriques and Sara C. Madeira