Articles

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlyi...

Authors: Holger Wagner, Burkhard Morgenstern and Andreas Dress

Fast algorithms for computing sequence distances by exhaustive substring composition

The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are har...

Authors: Alberto Apostolico and Olgert Denas

"Hook"-calibration of GeneChip-microarrays: Theory and algorithm

The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationshi...

Authors: Hans Binder and Stephan Preibisch

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

Microarray experiments rely on several critical steps that may introduce biases and uncertainty in downstream analyses. These steps include mRNA sample extraction, amplification and labelling, hybridization, a...

Authors: Hans Binder, Knut Krohn and Stephan Preibisch

A stitch in time: Efficient computation of genomic DNA melting bubbles

It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through ...

Authors: Eivind Tøstesen

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps

One of the goals of global metabolomic analysis is to identify metabolic markers that are hidden within a large background of data originating from high-throughput analytical measurements. Metabolite-based clu...

Authors: Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Petr Karlovsky and Burkhard Morgenstern

A weighted average difference method for detecting differentially expressed genes from microarray data

Identification of differentially expressed genes (DEGs) under different experimental conditions is an important task in many microarray studies. However, choosing which method to use for a particular applicati...

Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu

Noisy: Identification of problematic columns in multiple sequence alignments

Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large num...

Authors: Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J Prohaska and Peter F Stadler

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets tha...

Authors: Amarendran R Subramanian, Michael Kaufmann and Burkhard Morgenstern

On the optimality of the neighbor-joining algorithm

The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "...

Authors: Kord Eickmeyer, Peter Huggins, Lior Pachter and Ruriko Yoshida

Protein sequence and structure alignments within one framework

Protein structure alignments are usually based on very different techniques to sequence alignments. We propose a method which treats sequence, structure and even combined sequence + structure in a single frame...

Authors: Gundolf Schenk, Thomas Margraf and Andrew E Torda

A scoring matrix approach to detecting miRNA target sites

Experimental identification of microRNA (miRNA) targets is a difficult and time consuming process. As a consequence several computational prediction methods have been devised in order to predict targets for fo...

Authors: Simon Moxon, Vincent Moulton and Jan T Kim

Learning from positive examples when the negative class is undetermined- microRNA gene identification

The application of machine learning to classification problems that depend only on positive examples is gaining attention in the computational biology community. We and others have described the use of two-cla...

Authors: Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe

Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is...

Authors: Gang Wu, Ming-Yang Kao, Guohui Lin and Jia-Huai You

Evaluating deterministic motif significance measures in protein databases

Assessing the outcome of motif mining algorithms is an essential task, as the number of reported motifs can be very large. Significance measures play a central role in automatically ranking those motifs, and t...

Authors: Pedro Gabriel Ferreira and Paulo J Azevedo

Efficient and accurate P-value computation for Position Weight Matrices

Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The usage of PWMs needs as a prereq...

Authors: Hélène Touzet and Jean-Stéphane Varré

Review of "Reconstructing Evolution: New mathematical and computational advances" edited by Olivier Gascuel and Mike Steel

Authors: Andreas Spillner

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

cis-Regulatory modules (CRMs) of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate ...

Authors: Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg and Vsevolod J Makeev

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation

Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Our goal is to find these coevolving residues.

Authors: Rodrigo Gouveia-Oliveira and Anders G Pedersen

Mapping sequences by parts

We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, t...

Authors: Gilles Didier and Carito Guziolowski

A basic analysis toolkit for biological sequences

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence ...

Authors: Raffaele Giancarlo, Alessandro Siragusa, Enrico Siragusa and Filippo Utro

Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail

The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For t...

Authors: Stefan Wolfsheimer, Bernd Burghardt and Alexander K Hartmann

Consistency of the Neighbor-Net Algorithm

Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, Neighbor-Net produces ...

Authors: David Bryant, Vincent Moulton and Andreas Spillner

Characteristics of predictor sets found using differential prioritization

Feature selection plays an undeniably important role in classification problems involving high dimensional datasets such as microarray datasets. For filter-based feature selection, two well-known criteria used...

Authors: Chia Huey Ooi, Madhu Chetty and Shyh Wei Teng

RNAstrand: reading direction of structured RNAs in multiple sequence alignments

Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional anno...

Authors: Kristin Reiche and Peter F Stadler

GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data

One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived fragments (TDFs). However, hig...

Authors: Koji Kadota, Ryoko Araki, Yuji Nakai and Masumi Abe

Data Mining in Bioinformatics (BIOKDD)

Authors: Mohammed J Zaki, George Karypis and Jiong Yang

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the fold...

Authors: Hui Yang, Srinivasan Parthasarathy and Duygu Ucar

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12

Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in th...

Authors: Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski and Peter Ortoleva

PhyloScan: identification of transcription factor binding sites using cross-species evidence

When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statisti...

Authors: C Steven Carmack, Lee Ann McCue, Lee A Newberg and Charles E Lawrence

Probability-based model of protein-protein interactions on biological timescales

Simulation methods can assist in describing and understanding complex networks of interacting proteins, providing fresh insights into the function and regulation of biological systems. Recent studies have inve...

Authors: Alexander L Tournier, Paul W Fitzjohn and Paul A Bates

A novel functional module detection algorithm for protein-protein interaction networks

The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clu...

Authors: Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan

Refining motifs by improving information content scores using neighborhood profile search

The main goal of the motif finding problem is to detect novel, over-represented unknown signals in a set of sequences (e.g. transcription factor binding sites in a genome). The most widely used algorithms for ...

Authors: Chandan K Reddy, Yao-Chung Weng and Hsiao-Dong Chiang

SMOTIF: efficient structured pattern and profile motif search

A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a p...

Authors: Yongqiang Zhang and Mohammed J Zaki

EXMOTIF: efficient structured motif extraction

Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient a...

Authors: Yongqiang Zhang and Mohammed J Zaki

Reconstructing protein structure from solvent exposure using tabu search

A new, promising solvent exposure measure, called half-sphere-exposure (HSE), has recently been proposed. Here, we study the reconstruction of a protein's C _α trace solely fr...

Authors: Martin Paluszewski, Thomas Hamelryck and Pawel Winter

An enhanced RNA alignment benchmark for sequence alignment programs

The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for t...

Authors: Andreas Wilm, Indra Mainz and Gerhard Steger

Computing distribution of scale independent motifs in biological sequences

The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structu...

Authors: Jonas S Almeida and Susana Vinga

Pattern statistics on Markov chains and sensitivity to parameter estimation

In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is ...

Authors: Grégory Nuel

Fast calculation of the quartet distance between trees of arbitrary degrees

A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by ...

Authors: Chris Christiansen, Thomas Mailund, Christian NS Pedersen, Martin Randers and Martin Stig Stissing

Automatic layout and visualization of biclusters

Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these...

Authors: Gregory A Grothaus, Adeel Mufti and TM Murali

A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons

An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing onl...

Authors: Jonathan E Allen and Steven L Salzberg

A combinatorial optimization approach for diverse motif finding applications

Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise ...

Authors: Elena Zaslavsky and Mona Singh

The approximability of the String Barcoding problem

The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings...

Authors: Giuseppe Lancia and Romeo Rizzi

Inverse bifurcation analysis: application to simple gene systems

Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from ...

Authors: James Lu, Heinz W Engl and Peter Schuster

P-value based visualization of codon usage data

Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by m...

Authors: Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke and Stephan Waack

On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences

Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree...

Authors: Katharina A Lehmann, Michael Kaufmann, Stephan Steigele and Kay Nieselt

Analysis of computational approaches for motif discovery

Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcri...

Authors: Nan Li and Martin Tompa

Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient as...

Authors: Elena Zotenko, Katia S Guimarães, Raja Jothi and Teresa M Przytycka

Multiple sequence alignment with user-defined anchor points

Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.

Authors: Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler and Peter F Stadler