Articles

FlexSnap: Flexible Non-sequential Protein Structure Alignment

Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if ...

Authors: Saeed Salem, Mohammed J Zaki and Chris Bystroff

A markov classification model for metabolic pathways

This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network paths...

Authors: Timothy Hancock and Hiroshi Mamitsuka

A simulation study comparing supertree and combined analysis methods using SMIDGen

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the enti...

Authors: M Shel Swenson, François Barbançon, Tandy Warnow and C Randal Linder

Linear-time protein 3-D structure searching with insertions and deletions

Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools...

Authors: Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane

Fast prediction of RNA-RNA interaction

Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for eff...

Authors: Raheleh Salari, Rolf Backofen and S Cenk Sahinalp

Phylogenetic comparative assembly

Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping ...

Authors: Peter Husemann and Jens Stoye

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the i...

Authors: Xiuwei Zhang and Bernard ME Moret

An asymmetric approach to preserve common intervals while sorting by reversals

The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios. However, the number of sequences is huge and some additional crit...

Authors: Marília DV Braga, Christian Gautier and Marie-France Sagot

Linear model for fast background subtraction in oligonucleotide microarrays

One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data...

Authors: K Myriam Kroll, Gerard T Barkema and Enrico Carlon

iTriplet, a rule-based nucleic acid sequence motif finder

With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete...

Authors: Eric S Ho, Christopher D Jakubowski and Samuel I Gunderson

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative models, such as Hidden Markov Mode...

Authors: Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli and Rita Casadio

Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods

Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optima...

Authors: László A Zahoránszky, Gyula Y Katona, Péter Hári, András Málnási-Csizmadia, Katharina A Zweig and Gergely Zahoránszky-Köhalmi

Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic arch...

Authors: Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M Chang, Roger B Fillingim, Margaret R Wallace, Roland Staud, Lee Kaplan and Rongling Wu

Tracking cells in Life Cell Imaging videos using topological alignments

With the increasing availability of live cell imaging technology, tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most...

Authors: Axel Mosig, Stefan Jäger, Chaofeng Wang, Sumit Nath, Ilker Ersoy, Kannap-pan Palaniappan and Su-Shing Chen

Review of “Bioinformatics: A Computing Perspective” edited by Shuba Gopal, Anne Haake, Rhys Price Jones and Paul Tymann

Authors: Dae-Won Kim and Hong-Seog Park

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is criti...

Authors: Sara C Madeira and Arlindo L Oliveira

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression-level measurements and a way o...

Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu

Evolving DNA motifs to predict GeneChip probe performance

Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 hu...

Authors: WB Langdon and AP Harrison

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networ...

Authors: Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R Chandra and I Saira Mian

An image processing approach to computing distances between RNA secondary structures dot plots

Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA stru...

Authors: Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro and Danny Barash

Lossless filter for multiple repeats with bounded edit distance

Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic...

Authors: Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti and Marie-France Sagot

CHSMiner: a GUI tool to identify chromosomal homologous segments

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degene...

Authors: Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu and Yixue Li

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces

In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. One of the simplest sampling methods is the...

Authors: Raazesh Sainudiin and Thomas York

HuMiTar: A sequence-based method for prediction of human microRNA targets

MicroRNAs (miRs) are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to ...

Authors: Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang and Peiyu Pu

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

Syntenator: Multiple gene order alignments with a gene-specific scoring function

Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case...

Authors: Christian Rödelsperger and Christoph Dieterich

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